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Biophysics of Artificially Expanded Genetic Information Systems. Thermodynamics of DNA Duplexes Containing Matches and Mismatches Involving 2-Amino-3-nitropyridin-6-one (Z) and Imidazo[1,2?a]-1,3,5-triazin-4(8H)one (P)
Xiaoyu Wang, Shuichi Hoshika, Raymond J. Peterson, Myong-Jung Kim, Steven A. Benner, and Jason D. Kahn
ACS Synthetic Biology , American Chemical Society (2017) DOI: 10.1021/acssynbio.6b00224
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Isothermal titration calorimetry uncovers substrate promiscuity of bicupin oxalate oxidase from Ceriporiopsis subvermispora
Rana H, Moussatche P, Rocha LS, Abdellaoui S, Minteer SD, Moomaw EW
Biochem. Biophys. Rep. , Elsevier (2016) 5:396-400 doi:10.1016/j.bbrep.2016.01.016
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Assays To Detect the Formation of Triphosphates of Unnatural Nucleotides: Application to Escherichia coli Nucleoside Diphosphate Kinase
Mariko F. Matsuura, Ryan W. Shaw, Jennifer D. Moses, Hyo-Joong Kim, Myong-Jung Kim, Myong-Sang Kim, Shuichi Hoshika, Nilesh Karalkar, and Steven A. Benner
ACS Synthetic Biology , American Chemical Society (2016) 5 (3), pp 234-240 DOI: 10.1021/acssynbio.5b00172
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Synthesis and Enzymology of 2'-Deoxy-7-deazaisoguanosine Triphosphate and Its Complement: A Second Generation Pair in an Artificially Expanded Genetic Information System
Karalkar NB, Leal NA, Kim MS, Bradley KM, Benner SA
ACS Synthetic Biology , American Chemical Society (2016) doi: 10.1021/acssynbio.5b00276
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Allosteric inhibitors of Coxsackie virus A24 RNA polymerase
CH Schein, D Rowold, KH Choi
Bioorg. Med. Chem. (2016) Volume 24, Issue 4, 15 February 2016, Pages 570-577

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Cross-Reactivity Among Peanut and Tree Nut Allergens
SJ Maleki, H Cheng, JC Wolf, SS Teuber, C Schein, CC Grimm
J Allergy Clin Immunol , American Academy of Allergy, Asthma & Immunology (2016) 137 (2), AB237

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Alternative Watson-Crick Synthetic Genetic Systems
Steven A. Benner, Nilesh B. Karalkar, Shuichi Hoshika, Roberto Laos, Ryan W. Shaw, Mariko Matsuura, Diego Fajardo, and Patricia Moussatche
Cold Spring Harb Perspect Biol , Cold Spring Harbor Laboratory Press (2016) doi: 10.1101/cshperspect.a023770
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Aptamers against Cells Overexpressing Glypican 3 from Expanded Genetic Systems Combined with Cell Engineering and Laboratory Evolution
Zhang, L, Yang, Z, Trinh, TL, Teng, I-T, Wang, S, Bradley, KM, Hoshika, S, Wu, Q, Cansiz, S, Rowold, DJ, McLendon, C, Kim, M-S, Wu, Y, Cui, C, Liu, Y, Hou, W, Stewart, K, Wan, S, Liu, C, Benner, SA, Tan, W
Angew. Chem. Int. Ed. 55 (2016) doi: 10.1002/anie.201605058
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Standard and AEGIS nicking molecular beacons detect amplicons from the Middle East respiratory syndrome coronavirus
Ozlem Yaren, Lyudmyla G. Glushakova, Kevin M. Bradley, Shuichi Hoshika,Steven A. Benner
J Virol Methods (236) , Elsevier 54-61 (2016) doi:10.1016/j.jviromet.2016.07.008
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A norovirus detection architecture based on isothermal amplification and expanded genetic systems
Ozlem Yaren, Kevin M. Bradley, Patricia Moussatche, Shuichi Hoshika, Zunyi Yang,Shu Zhu, Stephanie M. Karst, Steven A. Benner
J Virol Methods (237) , Elsevier 64-71 (2016) doi: 10.1016/j.jviromet.2016.08.012
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Polymerase Interactions with Wobble Mismatches in Synthetic Genetic Systems and Their Evolutionary Implications
Christian B. Winiger, Myong-Jung Kim, Shuichi Hoshika, Ryan W. Shaw, Jennifer D. Moses, Mariko F. Matsuura, Dietlind L. Gerloff, and Steven A. Benner
Biochemistry 55 (28) 3847-3850 (2016) DOI: 10.1021/acs.biochem.6b00533
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Laboratory evolution of artificially expanded DNA gives redesignable aptamers that target the toxic form of anthrax protective antigen
Biondi E, Lane JD, Das D, Dasgupta S, Piccirilli JA, Hoshika S, Bradley KM, Krantz BA, Benner SA
Nucl. Acids Res. (2016) Oct 3. pii: gkw890. PubMed PMID: 27701076
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Crystal structures of deprotonated nucleobases from an expanded DNA alphabet
Mariko F. Matsuura, Hyo-Joong Kim, Daisuke Takahashi, Khalil A. Abboud and Steven A. Benner
Structural Chemistry , Acta Crystallographica (2016) C72, 952-959. doi: 10.1107/S2053229616017071
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Opal Absorbs and Stabilizes RNA - A Hierarchy of Prebiotic Silica Minerals
Biondi, E.; Howell, L.; Benner, S.A.
SynLett (2016) 27, A-E
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Evolution of functional six-nucleotide DNA
Zhang, L., Yang, Z., Sefah, K., Bradley, K. M., Hoshika, S., Kim, M-J,. Kim, H-J., Zhu., Jimenez, E., Cansiz, S., Teng, I-T., Champanhac, C, McLendon, C., Liu, C., Zhang, W., Gerloff, D. L., Huang, Z., Tan, W., Benner, S. A.
J. Am. Chem. Soc. (2015) DOI: 10.1021/jacs.5b02251
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Transcription, Reverse Transcription, and Analysis of RNA Containing Artificial Genetic Components
Nicole A. Leal, Hyo-Joong Kim, Shuichi Hoshika, Myong-Jung Kim, Matthew A. Carrigan, and Steven A. Benner
ACS Synthetic Biology , American Chemical Society (2015) Apr 17;4(4):407-13. doi: 10.1021/sb500268n
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Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism
Jonathan D. Magasin and Dietlind L. Gerloff
Bioinformatics (2015) 31:311-317
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3D topology of the SMC2/SMC4 sub-complex from chicken condensin I revealed by cross-linking and molecular modeling
Barysz H, Kim JH, Chen ZA, Hudson DF, Rappsilber J, Gerloff DL, Earnshaw WC
Open Biology , The Royal Society Publishing (2015) 5:150005
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Formation of Two Homo-chromophoric H-Aggregates in DNA-Assembled Alternating Dye Stacks
C.B. Winiger; Dr. S.M. Langenegger; Prof. Dr. G. Calzaferri; Prof. Dr. R. Haner
Angew. Chem. Int. Ed. (54) 3643-3647 (2015) DOI:10.1002/anie.201410041

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Structural basis for a six nucleotide genetic alphabet
Georgiadis, M. M., Singh, I., Kellett, W. F., Hoshika, S., Benner, S. A. Richards, N. G. J.
J. Am. Chem. Soc. (2015) DOI: 10.1021/jacs.5b3482
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Sequence specificity for uridylylation of the viral peptide linked to the genome (VPg) of enteroviruses
Catherine H Schein, Mengyi Ye, Aniko V Paul, M Steven Oberste, Nora Chapman, Dmitri V Filippov, Kyung Choi
Virology , Elsevier (2015) 484:80-85

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Inositol hexakisphosphate analogs and uses thereof
TC Savidge, P Urvil, D Nauduri, N Oezguen, C Schein, W Braun
US Patent , United States Patent Office (2015) Patent No. 9,200,015

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Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA
Lyudmyla G. Glushakova, Nidhi Sharma, Shuichi Hoshika, Andrea C. Bradley, Kevin M. Bradley, Zunyi Yang, Steven A. Benner
Anal Biochem , Elsevier (2015) Nov 15;489:62-72. doi: 10.1016/j.ab.2015.08.015
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High-throughput multiplexed xMAP Luminex array panel for detection of twenty two medically important mosquito-borne arboviruses based on innovations in synthetic biology
Lyudmyla G. Glushakova, Andrea Bradley, Kevin M. Bradley, Barry W. Alto, Shuichi Hoshika, Daniel Hutter, Nidhi Sharma, Zunyi Yang, Myong-Jung Kim, Steven A. Benner
J Virol Methods 214 , Elsevier 60-74 (2015) doi: 10.1016/j.jviromet.2015.01.003
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A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair
Armando R. Hernandez, Yaming Shao, Shuichi Hoshika, Zunyi Yang, Sandip A. Shelke, Julien Herrou, Hyo-Joong Kim, Myong-Jung Kim, Joseph A. Piccirilli, and Steven A. Benner
Angew. Chem. Int. Ed. 54 9853-9856 (2015) doi: 10.1002/anie.201504731
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Restriction enzymes cleave DNA immobilized on micron-sized diamond crystallites
Yaren O, Benner SA
Diamond Relat. Mater. , Elsevier (2015) 52, 18-24
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Helicase Dependent Isothermal Amplification of DNA and RNA using Self-Avoiding Molecular Recognition Systems
Zunyi Yang, Chris McLendon, Daniel Hutter, Kevin M. Bradley, Shuichi Hoshika, Carole Frye, and Steven A. Benner
ChemBioChem (2015) June 15; 16(9): 1365-1370. doi:10.1002/cbic.201500135.
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RNA structural analysis by enzymatic digestion
Biondi E., Burke D.H.
Methods Mol Biol , Springer (2014) 1086:41-52

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Protein Domains of Unknown Function Are Essential in Bacteria
Norman F. Goodacre, Dietlind L. Gerloff, Peter Uetz
mBio , American Society for Microbiology (2014) 5(1):e00744-13
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Applications of the Complementarity Plot in error detection and structure validation of proteins
Sankar Basu, Dhananjay Bhattacharyya and Rahul Banerjee
Indian J. Biochem. Biophys. , NISCAIR (2014) 51 (June) (Accepted, In press)

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Membrane Interaction and Functional Plasticity of Inositol Polyphosphate 5-Phosphatases
Werner Braun and Catherine H. Schein
Structure (2014) http://dx.doi.org/10.1016/j.str.2014.04.008

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Ribonucleosides for an Artificially Expanded Genetic Information System
Hyo-Joong Kim, Nicole A. Leal, Shuichi Hoshika, Steven A. Benner
J. Org. Chem. (2014) 79 (7), pp 3194-3199
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OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS) to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands
Kevin M. Bradley and Steven A. Benner
Beilstein J. Org. Chem. , Beilstein Institute (2014) 10, 1826-1833, doi:10.3762/bjoc.10.192
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Recombinase-Based Isothermal Amplification of Nucleic Acids with Self-Avoiding Molecular Recognition Systems (SAMRS)
Nidhi Sharma, Shuichi Hoshika, Daniel Hutter, Kevin M. Bradley, and Steven A. Benner
ChemBioChem (2014) DOI: 10.1002/cbic.201402250
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Influence of perylenediimide-pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity
C.B. Winiger; Dr. S.M. Langenegger; Dr. O. Khorev; Prof. Dr. R. Haner
Beilstein J. Org. Chem. (10) , Beilstein Institute 1589-1595 (2014) DOI:10.1002/anie.201407968

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Long Distance EET in Light-Harvesting Supramolecular Polymers
C.B. Winiger; Dr. S. Li; Dr. G.R. Kumar; Dr. S.M. Langenegger; Prof. Dr. R. Haner
Angew. Chem. Int. Ed. (53) 13609-13613 (2014) DOI:10.1002/anie.201407968

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DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides. Frontiers in Microbiology
Laos, R., Thomson, J. M., & Benner, S. A.
Frontiers in Microbiology (2014) 5, 565. http://doi.org/10.3389/fmicb.2014.00565
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Hominids adapted to metabolize ethanol long before human-directed fermentation
Matthew A. Carrigan, Oleg Uryasev, Carole B. Frye, Blair L. Eckman, Candace R. Myers, Thomas D. Hurley, and Steven A. Benner
Proc. Natl. Acad. Sci. USA 112 (2) 458-463 (2014) doi: 10.1073/pnas.1404167111
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MaGnET: Malaria Genome Exploration Tool
Sharman JL and Gerloff DL
Bioinformatics (2013) 2350-2352
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Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, "UCAA-motif" RNA Aptamers
Whatley A.S., Ditzler M.A., Lange M.J., Biondi E., Sawyer A.W., Chang J.L., Franken J.D., Burke D.H.
Mol Ther Nucleic Acids , Nature (2013) 2:e71

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Kinetic and Spectroscopic Studies of Bicupin Oxalate Oxidase and Putative Active Site Mutants
Moomaw EW, Hoffer E, Moussatche P, Salerno JC, Grant M, et al.
PLOS One , Public Library of Science (2013) 8(3): e57933
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Directed Evolution of Polymerases To Accept Nucleotides with Nonstandard Hydrogen Bond Patterns
Laos R, Shaw R, Leal NA, Gaucher E, Benner S.
Biochemistry (2013) 52, 5288-5294
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Conversion strategy using an expanded genetic alphabet to assay nucleic acids
Yang, Z., Durante, M., Glushakova, L., Sharma, N., Leal, N., Bradley, K., Chen, F., Benner, S. A.
Anal. Chem. (2013) 85(9):4705-12
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The "strong" RNA world hypothesis. Fifty years old.
Neveu, Mark; Kim, Hyo-Joong; Benner, Steven A
Astrobiology 13 (4) (2013) DOI: 10.1089/ast.2012.0868
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Models and Standards of Proof in Cross-Disciplinary Science: The Case of Arsenic DNA
Steven A. Benner, William Bains, and Sara Seager
Astrobiology 13 (5) (2013) DOI: 10.1089/ast.2012.0954

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Nucleic Acid Polymerases. Chapter 7: Engineered DNA Polymerases
Roberto Laos, Ryan W. Shaw, Steven A. Benner
Nucl. Acids & Mol. Bio. , ed. Katsuhiko S. Murakami, Michael A. Trakselis , Springer (2013)
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Lewis acid catalysis of phosphoryl transfer from a copper(II)-NTP complex in a kinase ribozyme
Biondi E., Poudyal R.R., Forgy J.C., Sawyer A.W., Maxwell A.W., Burke D.H
Nucl. Acids Res. (2013) 41(5):3327-38

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Assessment of 3D models for allergen research
Power, T.D, Ivanciuc, O., Schein, C.H. and Braun, W.
Proteins: Struct., Funct., Bioinf. , Wiley (2013) 81 (4):545-554

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A general synthetic method toward uridylylated picornavirus VPg proteins
Heden van Noort, G.J., Schein, C.H., Overkleeft, H.S., Marel, G.A., Filippov, D.V.
J. Pept. Sci. , Wiley (2013) 19 (6):333-336

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SARAMA: A Standalone Suite of Programs for the Complementarity Plot-A Graphical Structure Validation Tool for Proteins
Sankar Basu, Dhananjay Bhattacharyya and Rahul Banerjee
J. Bioinf. Intell. Control , American Scientific Publishers (2013) 2 (4): 321-323

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polDNAmelt: Local Melting Within Polymeric DNA-An Improved Method and Its Applications
Sankar Basu and Dhananjay Bhattacharyya
J. Bioinf. Intell. Control , American Scientific Publishers (2013) 2 (4): 316-320

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DOTA Conjugate with an Albumin-Binding Entity Enables the First Folic Acid-Targeted Lu-177-Radionuclide Tumor Therapy in Mice
Dr. C. Mueller; Dr. H. Struthers; C. Winiger; Dr. K. Zhernosekov; Prof. Dr. R. Schibli
J. Nucl. Med. (54) , Society of Nuclear Medicine and Molecular Imaging 124-131 (2013) DOI: 10.2967/jnumed.112.107235

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Engineered DNA Polymerases
K. Murakami and M.A. Trakselis (eds.)
Nucleic Acid Polymerases, Nucleic Acids and Molecular Biology , Springer-Verlag Berlin Heidelberg (2013)

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Use of codon models in molecular dating and functional analysis
Steven A. Benner
Codon Evolution , ed. Gina M Cannarozzi, Adrian Scheider , Oxford University Press 133-144 (2012)

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Synthesis and Properties of 5-Cyano-Substituted Nucleoside Analog with a Donor-Donor-Acceptor Hydrogen-Bonding Pattern
Hyo-Joong Kim, Fei Chen, and Steven A. Benner
J. Org. Chem. (2012)
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The Natural History of Class I Primate Alcohol Dehydrogenases Includes Gene Duplication, Gene Loss, and Gene Conversion
Matthew A. Carrigan, Oleg Uryasev, Ross P. Davis, LanMin Zhai, Thomas D. Hurley, Steven A. Benner
PLOS One 7 (7) , Public Library of Science (2012)

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Non-genomic progesterone signalling and its non-canonical receptor
Moussatche P, Lyons TJ
Biochem Soc Trans (2012) Feb;40(1):200-4
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A small ribozyme with dual-site kinase activity
Biondi E., Maxwell A.W.R., and Burke D.H.
Nucl. Acids Res. (2012) 40(15):7528-40

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Separating and analyzing sulfur-containing RNAs with organomercury gels
Biondi E, Burke DH.
Methods Mol Biol , Springer (2012) 2012;883:111-20
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Structure-Based Redesign of an Edema Toxin Inhibitor
Chen, D, Ma, L., Kanalas, J.J., Gao, J, Pawlik J, Estrella-Jimenez, JE, Walter M.A., Peterson, JW, Gilbertson S.R. and Schein C.H.
Bioorg. Med. Chem. (2012) 20, 368-376 PMCID: PMC3251925

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Simplifying complex sequence information: a PCP-consensus protein binds antibodies against all four Dengue serotypes
Bowen, D.M., Lewis, J.A., Lu, W. and Schein, C.H.
Vaccine , Elsevier (2012) 30(42), 6081-6087

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Physicochemical property consensus sequences for functional analysis, design of multivalent antigens and targeted antivirals
Schein, C.H., Bowen, D.M., Lewis, J.A., Choi, K., Paul, A., van der Heden van Noort, G.J., Lu, W. and Filippov, D.V.
BMC Bioinformatics (2012) 13(Suppl 13):S9.

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Ara h 1 structure is retained after roasting and is important for enhanced binding to IgE
Nesbit, J.B., Hurlburt, B.K., Schein, C.H., Cheng, H. and Maleki, S.J.
Mol. Nutr. Food Res. , Wiley (2012) 56, 1-9

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Pharmacophore Selection and Redesign of Non-nucleotide Inhibitors of Anthrax Edema Factor
Schein C.H., Chen D, Ma L, Kanalas JJ, Gao J, Jimenez ME, Sower LE, Walter MA, Gilbertson SR, Peterson JW
Toxins , MDPI (2012) 4(11):1288-1300

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Self Complementarity within proteins: bridging the gap between binding and folding
Sankar Basu, Dhananjay Bhattacharyya and Rahul Banerjee
Biophys. J. , AP Cell Press (2012) 102 (11): 2605-2614

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Synthesis and incorporation into oligodeoxynucleotides of carbocyclic exo-amino nucleosides
Yaren O, Rothlisberger P, Leumann CJ
Synthesis , Thieme (2012) 7, 1011-1025
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Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.
Chen, F; Yang, ZY; Yan, M; Alvarado, JB; Wang, G; Benner, SA
Nucl. Acids Res. 39 (9) 3949-3961 (2011)
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Characterization of Ceriporiopsis subvermispora bicupin oxalate oxidase expressed in Pichia pastoris
Moussatche, P; Angerhofer, A; Imaram, W; Hoffer, E; Uberto, K; Brooks, C; Bruce, C; Sledge, D; Richards, NGJ; Moomaw, EW
Arch. Biochem. Biophys. (2011) May 1;509(1):100-7. Epub 2011 Mar 2
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Synthetic Biology, Tinkering Biology, and Artificial Biology: A Perspective from Chemistry
Benner, SA; Chen, F; Yang, ZY
Chemical Synthetic Biology , ed. Pier Luigi Luisi and Cristiano Chiarabelli , Wiley 69-106 (2011)

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Setting the Stage: The History, Chemistry, and Geobiology behind RNA
Benner, SA; Kim, HJ; Yang, ZY
RNA Worlds: From Life's Origins to Diversity in Gene Regulation , ed. John F. Atkins, Raymond F. Gesteland, Thomas R. Cech , Cold Spring Harbor Laboratory Press 7-19 (2011)

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Amplification, Mutation, and Sequencing of a Six-Letter Synthetic Genetic System
Yang, Z; Chen, F; Alvarado, JB; Benner, SA
J. Am. Chem. Soc. 133 (38) 15105-15112 (2011) dx.doi.org/10.1021/ja204910n
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Phylogenetic and preliminary phenotypic analysis of yeast PAQR receptors: potential antifungal targets
Villa NY, Moussatche P, Chamberlin SG, Kumar A, Lyons TJ
J Mol Evol (2011) Oct;73(3-4):134-52. Epub 2011 Oct 19.
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Computationally Predicted IgE Epitopes of Walnut Allergens Contribute to Cross-Reactivity with peanuts
Maleki, S.J., Teuber, S.S, Cheng H, Chen D, Comstock, S.S., Ruan, S., and Schein, C.H.
Allergy , Wiley (2011) 66(12), 1522-1529. PMCID: PMC3203311

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Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs
Sankar Basu, Dhananjay Bhattacharyya and Rahul Banerjee
BMC Bioinformatics (2011) 12:195

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An SNP-Based Linkage Map for Zebrafish Reveals Sex Determination Loci
Bradley KM, Breyer JP, Melville DB, Broman KW, Knapik EW, Smith JR
G3 , Genetics Society of America (2011) Jun 1;1(1):3-9
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A Parallel Screen for the Discovery of Novel DNA Base Pairs
Yaren O, Mosimann M, Leumann CJ
Angew. Chem. Int. Ed. (2011) 50, 1935-1938. PMID: 21328674
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Labeled nucleoside triphosphates with reversibly terminating aminoalkoxyl groups
Hutter, D; Kim, MJ; Karalkar, N; Leal, NA; Chen, F; Guggenheim, E; Visalakshi, V; Olejnik, J; Gordon, S; Benner, SA
Nuc. Nuc. Nuc. acids 29 (11) 879-895 (2010)
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Expanded Genetic Alphabets in the Polymerase Chain Reaction
Yang, ZY; Chen, F; Chamberlin, SG; Benner, SA
Angew. Chem. Int. Ed. 49 (1) 177-180 (2010)

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Artificial Genetic Systems: Self-Avoiding DNA in PCR and Multiplexed PCR
Hoshika, S; Chen, F; Leal, NA; Benner, SA
Angew. Chem. Int. Ed. 49 (32) 5554-5557 (2010)

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Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection
Chen, F; Gaucher, EA; Leal, NA; Hutter, D; Havemann, SA; Govindarajan, S; Ortlund, EA; Benner, SA
Proc. Natl. Acad. Sci. USA 107 (5) 1948-1953 (2010)

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Chemistry, Life, and the Search for Aliens
Benner, SA
Proc. SPIE 7819 (10) 1-12 (2010)
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Improving efficiencies of locus-specific DNA methylation assessment for bovine in vitro produced embryos
Wroclawska, E; Brant, JO; Yang, TP; Moore, K
Syst. Biol. Reprod. Med. 56 96-105 (2010)

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Interview with Steven Benner
Impey, C; Benner, SA
Talking about Life: Conversations on Astrobiology , ed. Chris Impey , Cambridge University Press 58-68 (2010)

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Q&A: Life, synthetic biology and risk
Benner, SA
BMC Biology 8 (77) (2010) doi:10.1186/1741-7007-8-77

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Synthetic biology, tinkering biology, and artificial biology. What are we learning?
Steven A. Benner, Zunyi Yang, and Fei Chen
Comptes Rendus Chimie , French Academy of Sciences (2010)
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Convergent donor and acceptor substrate utilization among kinase ribozymes
Biondi E., Nickens D.G., Warren S., Saran D., and Burke D.H.
Nucl. Acids Res. (2010) 38(19):6785-95

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2'-Deoxy-1-methylpseudocytidine, a stable analog of 2'-deoxy-5-methylisocytidine
Kim, HJ; Leal, NA; Benner, SA
Bioorg. Med. Chem. 17 (10) 3728-3732 (2009)
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A Convenient Synthesis of N,N'-dibenzyl-2,4-diaminopyrimidine-2'-deoxyribonucleoside and 1-Methyl-2'-Deoxypseudoisocytidine
Wellington, KW; Ooi, HC; Benner, SA
Nuc. Nuc. Nuc. acids 28 (4) 275-291 (2009)
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Directed evolution of a filamentous fungus for thermotolerance
de Crecy, E; Jaronski, S; Lyons, B; Lyons, TJ; Keyhani, NO
BMC Biotechnology 9 74 (2009)
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Signatures of a Shadow Biosphere
Davies, PCW; Benner, SA; Cleland, CE; Lineweaver, CH; McKay, CP; Wolfe-Simon, F
Astrobiology 9 (2) 241-249 (2009)
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Antagonism of Human Adiponectin Receptors and Their Membrane Progesterone Receptor Paralogs by TNF alpha and a Ceramidase Inhibitor
Kupchak, BR; Garitaonandia, I; Villa, NY; Smith, JL; Lyons, TJ
Biochemistry 48 (24) 5504-5506 (2009)
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Metal dependence of oxalate decarboxylase activity
Moomaw, EW; Angerhofer, A; Moussatche, P; Ozarowski, A; García-Rubio, I; Richards, NG
Biochemistry 48 (26) 6116-6125 (2009)
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Adiponectin identified as an agonist for PAQR3/RKTG using a yeast-based assay system
Garitaonandia, I; Smith, JL; Kupchak, BR; Lyons, TJ
J. Recept. Signal Transduction 29 (1) 67-73 (2009)
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Sphingolipids Function as Downstream Effectors of a Fungal PAQR
Villa, NY; Kupchak, BR; Garitaonandia, I; Smith, JL; Alonso, E; Alford, C; Cowart, LA; Hannun, YA; Lyons, TJ
Mol. Pharmacol. 75 (4) 866-875 (2009)
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The challenges of sequencing by synthesis
Fuller, CW; Middendorf, LR; Benner, SA; Church, GM; Harris, T; Huang, XH; Jovanovich, SB; Nelson, JR; Schloss, JA; Schwartz, DC; Vezenov, DV
Nat. Biotechnol. 27 (11) 1013-1023 (2009)
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Dissecting the regulation of yeast genes by the osmotin receptor
Kupchak, BR; Villa, NY; Kulemina, LV; Lyons, TJ
Biochem. Biophys. Res. Comm. 374 (2) 210-213 (2008)
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Design of a novel molecular beacon: modification of the stem with artificially genetic alphabet
Sheng, PP; Yang, ZY; Kim, YM; Wu, YR; Tan, WH; Benner, SA
Chem. Comm. (41) 5128-5130 (2008)
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The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular disease
Johnson, RJ; Gaucher, EA; Sautin, YY; Henderson, GN; Angerhofer, AJ; Benner, SA
Medical Hypotheses 71 (1) 22-31 (2008)
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Self-Avoiding Molecular Recognition Systems (SAMRS)
Hoshika, S; Chen, F; Leal, NA; Benner, SA
Nucleic Acids Symp. Ser. 52 (1) 129-130 (2008)

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Incorporation of Multiple Sequential Pseudothymidines by DNA Polymerases and Their Impact on DNA Duplex Structure
Havemann, SA; Hoshika, S; Hutter, D; Benner, SA
Nuc. Nuc. Nuc. acids 27 (3) 261-278 (2008)
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Synthesis of pyrophosphates for in vitro selection of catalytic RNA molecules
Kim, HJ; Kim, MJ; Karalkar, N; Hutter, D; Benner, SA
Nuc. Nuc. Nuc. acids 27 43-56 (2008)

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Heterologous expression of human mPR alpha, mPR beta and mPR gamma in yeast confirms their ability to function as membrane progesterone receptors
Smith, JL; Kupchak, BR; Garitaonandia, I; Hoang, LK; Maina, AS; Regalla, LM; Lyons, TJ
Steroids 73 (11) 1160-1173 (2008)
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Synthetic Biology for Improved Personalized Medicine
Benner, SA; Hoshika, S; Sukeda, M; Hutter, D; Leal, NA; Yang, ZY; Chen, F
Nucleic Acids Symp. Ser. 52 (1) 243-244 (2008) doi: 10.1093/nass/nrn123
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Paleotemperature trend for Precambrian life inferred from resurrected proteins
Gaucher, EA; Ganesh, O; Govindarajan, S
Nature (2007) In press

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Study of modification pattern-RNAi activity relationships by using siRNAs modified with 4'-thioribonucleosides
Hoshika, S; Minakawa, N; Shionoya, A; Imada, K; Ogawa, N; Matsuda, A
ChemBioChem 8 (17) 2133-2138 (2007)
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Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters
Danchin, EGJ; Gaucher, EA; Pontarotti, P
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 139-150 (2007)

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Experimental resurrection of ancient biomolecules: gene synthesis, heterologous protein expression, and functional assays
Gaucher, EA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 153-163 (2007)

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Ancestral sequence reconstruction as a tool to understand natural history and guide synthetic biology: realizing and extending the vision of Zuckerkandl and Pauling
Gaucher, EA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 20-33 (2007)

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A thermophilic last universal ancestor inferred from its estimated amino acid composition
Brooks, DJ; Gaucher, EA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 200-207 (2007)

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The resurrection of ribonucleases from mammals: from ecology to medicine
Sassi, SO; Benner, SA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 208-224 (2007)

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The early days of paleogenetics: connecting molecules to the planet
Benner, SA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 3-19 (2007)

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Investigating the roles of putative active site residues in the oxalate decarboxylase from Bacillus subtilis
Svedruzic, D; Liu, Y; Reinhardt, LA; Wroclawska, E; Cleland, WW; Richards, NGJ
Arch. Biochem. Biophys. 464 (1) 36-47 (2007)
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Synthesis of a novel bicyclic nucleoside with a 3,7-anhydrooctofuranosyl skeleton
Kim, MJ; Chun, MW
Aust. J. Chem. 60 (4) 291-295 (2007)
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Probing the mechanism of FET3 repression by Izh2p overexpression
Kupchak, BR; Garitaonandia, I; Villa, NY; Mullen, MB; Weaver, MG; Regalla, LA; Kendall, EA; Lyons, TJ
Biochim. Biophys. Acta 1773 (7) 1124-1132 (2007)
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Transport and Storage of Metal Ions in Biology
Lyons, TJ; Eide, DJ
Biological Inorganic Chemistry: Structure and Reactivity , ed. I. Bertini, H. Gray, E. Stiefel, and J.S. Valentine , University Science Books 57-77 (2007)

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Sequence-indexed mutations in maize using the UniformMu transposon-tagging population
Settles, AM; Holding, DR; Tan, BC; Latshaw, SP; Liu, J; Suzuki, M; Li, L; O'Brien, BA; Fajardo, DS; Wroclawska, E; Tseung, CW; Lai, JS; Hunter, CT; Avigne, WT; Baier, J; Messing, J; Hannah, LC; Koch, KE; Becraft, PW; Larkins, BA; McCarty, DR
BMC Genomics 8 (1) 116-144 (2007)
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Leishmania promastigotes activate PI3K/Akt signalling to confer host cell resistance to apoptosis
Ruhland, A; Leal, N; Kima, PE
Cell Microbiol. 9 (1) 84-96 (2007)
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PduL is an evolutionarily distinct phosphotransacylase involved in B-12-dependent 1,2-propanediol degradation by Salmonella enterica serovar typhimurium LT2
Liu, Y; Leal, NA; Sampson, EM; Johnson, CLV; Havemann, GD; Bobik, TA
J. Bacteriol. 189 (5) 1589-1596 (2007)
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In vivo expression of human ATP : cob(I)atamin adenosyltransferase (ATR) using recombinant adeno-associated virus (rAAV) serotypes 2 and 8
Erger, KE; Conlon, TJ; Leal, NA; Zori, R; Bobik, TA; Flotte, TR
J. Gene Med. 9 (6) 462-469 (2007)
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The evolution of seminal ribonuclease: Pseudogene reactivation or multiple gene inactivation events?
Sassi, SO; Braun, EL; Benner, SA
Mol. Biol. Evol. 24 (4) 1012-1024 (2007)
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Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages
Yang, ZY; Sismour, AM; Benner, SA
Nucl. Acids Res. 35 (9) 3118-3127 (2007)
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Enzymatic incorporation of a third nucleobase pair
Yang, ZY; Sismour, AM; Sheng, PP; Puskar, NL; Benner, SA
Nucl. Acids Res. 35 (13) 4238-4249 (2007)
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The origin of proteins and nucleic acids
Ricardo, A; Benner, SA
Planets and Life: The Emerging Science of Astrobiology , ed. Woodruff T. Sullivan and John A. Baross , Cambridge University Press 154-173 (2007)

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Alien biochemistries
Ward, PD; Benner, SA
Planets and Life: The Emerging Science of Astrobiology , ed. Woodruff T. Sullivan and John A. Baross , Cambridge University Press 537-544 (2007)

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Inferred thermophily of the Last Universal Ancestor based on estimated amino acid composition
Brooks, DJ; Gaucher, EA
Ancestral Sequence Reconstruction , ed. David A. Liberles , Oxford University Press 200-207 (2007)
<Abstract>

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Crystallographic snapshots of oxalyl-CoA decarboxylase give insights into catalysis by nonoxidative ThDP-dependent decarboxylases
Berthold, CL; Toyota, CG; Moussatche, P; Wood, MD; Leeper, F; Richards, NGJ; Lindqvist, Y
Structure 15 (7) 853-861 (2007)
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In vitro production of bovine embryos in medium supplemented with a serum replacer: Effects on blastocyst development, cryotolerance and survival to term
Moore, K; Rodriguez-Sallaberry, CJ; Kramer, JM; Johnson, S; Wroclawska, E; Goicoa, S; Niasari-Nasalaji, A
Theriogenology 68 (9) 1316-1325 (2007)
<Abstract>

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Molecular evolutionary models to guide experiments in protein engineering and directed evolution
Gaucher, EA
TBD (2007) In review

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Montmorillonite protection of an UV-irradiated hairpin ribozyme. Evolution of the RNA world in a mineral environment
Biondi E., Branciamore S., Maurel M.-C., and Gallori E.
BMC Evol. Biol. (2007) 7(Suppl 2):S2

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Catalytic activity of hammerhead ribozymes in a clay mineral environment: implications for the RNA World
Biondi E., Branciamore S., Fusi L., Gago, and Gallori E.
Gene (2007) 389:10-18

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A major zebrafish polymorphism resource for genetic mapping
Bradley KM, Elmore JB, Breyer JP, Yaspan BL, Jessen JR, Knapik EW, Smith JR
Genome Biol , BioMed Central (2007) 8(4):R55
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Molecular Paleoscience: Systems Biology from the Past
Benner, SA; Sassi, SO; Gaucher, EA
Adv. Enzymol. Relat. Areas Mol. Biol. 75 (2006)

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Synthesis and antiviral activity of 7-deazaneplanocin A against orthopoxviruses (vaccinia and cowpox virus)
Arumugham, B; Kim, HJ; Prichard, MN; Kern, ER; Chu, CK
Bioorg. Med. Chem. Lett. 16 (2) 285-287 (2006)
<Abstract>

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Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins
Bradley, ME; Benner, SA
BMC Bioinformatics 7 89 (2006)
<Abstract>

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Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics
Li, T; Chamberlin, SG; Caraco, MD; Liberles, DA; Gaucher, EA; Benner, SA
BMC Evol. Biol. 6 25 (2006)
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Application of DETECTER, an Evolutionary Genomic Tool to Analyze Genetic Variation, to the Cystic Fibrosis Gene Family
Gaucher, EA; DeKee, DW; Benner, SA
BMC Genomics 7 44 (2006)
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The diverse biological functions of phosphatidylinositol transfer proteins in eukaryotes
Phillips, SE; Vincent, P; Rizzieri, KE; Schaaf, G; Bankaitis, VA; Gaucher, EA
Crit. Rev. Biochem. Mol. Biol. 41 (1) 21-49 (2006)
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Reaction of tetramethylimidazol-2-ylidene with (Tp(tBu,Me))YbE(thf) (E=I, CH2SMe3): simple adduct and a hydrocarbyl tethered carbene ligand
Ferrence, GM; Arduengo, AJ; Jockisch, A; Kim, HJ; McDonald, R; Takats, J
J. Alloys Compd. 418 184-188 (2006)
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Orthogonal activation of the reengineered A(3) adenosine receptor (neoceptor) using tailored nucleoside agonists
Gao, ZG; Duong, HT; Sonina, T; Kim, SK; Van Rompaey, P; Van Calenbergh, S; Mamedova, L; Kim, HO; Kim, MJ; Kim, AY; Liang, BT; Jeong, LS; Jacobson, KA
J. Med. Chem. 49 (9) 2689-2702 (2006)
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2-Hydroxymethylboronate as a Reagent To Detect Carbohydrates: Application to the Analysis of the Formose Reaction
Ricardo, A; Frye, F; Carrigan, MA; Tipton, JD; Powell, DH; Benner, SA
J. Org. Chem. 71 (25) 9503-9505 (2006)
<Abstract>

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Zinc in yeast: mechanisms involved in homeostasis
Regalla, LM; Lyons, TJ
Molecular Biology of Metal Homeostasis and Detoxification: From Microbes to Man , ed. Springer , Markus J. Tamás and Enrico Martinoia 37-58 (2006)

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Dynamic assembly of primers on nucleic acid templates
Leal, NA; Sukeda, M; Benner, SA
Nucl. Acids Res. 34 4702-4710 (2006)
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Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern
Yang, ZY; Hutter, D; Sheng, PP; Sismour, AM; Benner, SA
Nucl. Acids Res. 34 (21) 6095-6101 (2006)
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A review: Synthesis of aryl C-glycosides via the heck coupling reaction
Wellington, KW; Benner, SA
Nuc. Nuc. Nuc. acids 25 (12) 1309-1333 (2006)
<Abstract>

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Looking for the primordial genetic honeycomb
Gallori E., Biondi E., and Branciamore S.
Orig. Life Evol. Biosph. , Springer (2006) 36:493-499

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Desorption/ionization on porous silicon mass spectrometry studies on pentose-borate complexes
Li, Q; Ricardo, A; Benner, SA; Winefordner, JD; Powell, DH
Anal. Chem. 77 (14) 4503-4508 (2005)
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Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: The sulfotransferase IA gene family example
Bradley, ME; Benner, SA
BMC Evol. Biol. 5 22 (2005)
<Abstract>

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One-pot glycosylation (OPG) for the chemical synthesis of oligosaccharides
Yu, B; Yang, ZY; Cao, HZ
Curr. Org. Chem. 9 (2) 179-194 (2005)
<Abstract>

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Synthetic biology
Sismour, AM; Benner, SA
Expert Opin. Biol. Ther. 5 (11) 1409-1414 (2005)
<Abstract>

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RNA interference induced by siRNAs modified with 4 '-thioribonucleosides in cultured mammalian cells
Hoshika, S; Minakawa, N; Kamiya, H; Harashima, H; Matsuda, A
FEBS Lett. 579 (14) 3115-3118 (2005)
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Solution H-1 NMR confirmation of folding in short o-phenylene ethynylene oligomers
Jones, TV; Slutsky, MM; Laos, R; de Greef, TFA; Tew, GN
J. Am. Chem. Soc. 127 (49) 17235-17240 (2005)
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Structural basis for activation of the thiamin diphosphate-dependent enzyme oxalyl-CoA decarboxylase by adenosine diphosphate
Berthold, CL; Moussatche, P; Richards, NGJ; Lindqvist, Y
J. Biol. Chem. 280 (50) 41645-41654 (2005)
<Abstract>

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Planetary systems biology
Benner, SA; Ricardo, A
Mol. Cell 17 (4) 471-472 (2005)
<Abstract>

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A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous
Gaucher, EA; Miyamoto, MM
Mol. Phylogenet. Evol. 37 (3) 928-931 (2005)
<Abstract>

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The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system
Sismour, AM; Benner, SA
Nucl. Acids Res. 33 5640-5646 (2005)
<Abstract>

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Synthesis of 3'-ureidoadenosines and their high binding affinity at the mutant A3 adenosine receptor
Kim, AY; Chung, HO; Kim, MJ; Chun, MW; Lee, KM; Jacobson, KA; Jeong, LS
Nucleic Acids Res. Suppl. 49 105-106 (2005)

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Resurrecting ancestral alcohol dehydrogenases from yeast
Thomson, JM; Gaucher, EA; Burgan, MF; De Kee, DW; Li, T; Aris, JP; Benner, SA
Nature Genet. 37 (6) 630-635 (2005)
<Abstract>

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Synthetic Biology
Sismour, AM; Benner, SA
Nat. Rev. Genet. 6 533-543 (2005)
<Abstract>

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Synthesis of 3 '-ureidoadenosine analogues and their binding affinity to the A(3) adenosine receptor
Chun, MW; Lee, HW; Kim, AY; Kim, MJ; Kim, HO; Gao, ZG; Jacobson, KA; Jeong, LS
Nuc. Nuc. Nuc. acids 24 1119-1121 (2005)
<Abstract>

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Synthesis of 3 '-deoxy-3 '-C-hydroxym ethyl analogues of tiazofurin and ribavirin
Chun, MW; Kim, MJ; Shin, JH; Jeong, LS
Nuc. Nuc. Nuc. acids 24 975-977 (2005)

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Synthesis of homo-N-nucleoside with 1,2,4-triazole-3-carboxamide
Chun, MW; Kim, JH; Kim, MJ; Kim, BR; Jeong, LS
Nuc. Nuc. Nuc. acids 24 979-981 (2005)
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Synthesis and biological evaluation of novel isonucleosides with 1,2,4-triazole-3-carboxamide
Kim, MJ; Chung, SY; Chun, MW
Synth. Commun. 35 (20) 2653-2663 (2005)
<Abstract>

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Understanding nucleic acids using synthetic chemistry
Benner, SA
Acc. Chem. Res. 37 (10) 784-797 (2004)
<Abstract>

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Cytoplasmic glycosylation of protein-hydroxyproline and its relationship to other glycosylation pathways
West, CM; van der Wel, H; Sassi, S; Gaucher, EA
Biochim. Biophys. Acta 1673 29-44 (2004)
<Abstract>

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Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection
Carrigan, MA; Ricardo, A; Ang, DN; Benner, SA
Biochemistry 43 (36) 11446-11459 (2004)
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Oligodeoxynucleotides having a loop consisting of 3 '-deoxy-4 '-C-(2-hydroxyethyl)thymidines form stable hairpins
Yamamoto, Y; Shuto, S; Tamura, Y; Kodama, T; Hoshika, S; Ichikawa, S; Ueno, Y; Ohtsuka, E; Komatsu, Y; Matsuda, A
Biochemistry 43 (27) 8690-8699 (2004)
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A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor.
Brooks, DJ; Fresco, JR; Singh, M
Bioinformatics 20 2251-2257 (2004)
<Abstract>

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Nucleosides and nucleotides. Part 226: Alternate-strand triple-helix formation by 3 '-3 '-linked oligodeoxynucleotides composed of asymmetrical sequences
Hoshika, S; Ueno, Y; Kamiya, H; Matsuda, A
Bioorg. Med. Chem. Lett. 14 (12) 3333-3336 (2004)
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Design and synthesis of 3 '-ureidoadenosine-5 '-uronamides: effects of the 3 '-ureido group on binding to the A(3) adenosine receptor
Jeong, LS; Kim, MJ; Kim, HO; Gao, ZG; Kim, SK; Jacobson, KA; Chun, MW
Bioorg. Med. Chem. Lett. 14 (19) 4851-4854 (2004)
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The planetary biology of cytochrome P450 aromatases
Gaucher, EA; Graddy, LG; Li, T; Simmen, RC; Simmen, FA; Schreiber, DR; Liberles, DA; Janis, CM; Benner, SA
BMC Biology 2 (1) 19 (2004)
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Multiplexed genetic analysis using an expanded genetic alphabet
Johnson, SC; Marshall, DJ; Harms, G; Miller, CM; Sherrill, CB; Beaty, EL; Lederer, SA; Roesch, EB; Madsen, G; Hoffman, GL; Laessig, RH; Kopish, GJ; Baker, MW; Benner, SA; Farrell, PM; Prudent, JR
Clin. Chem. 50 (11) 2019-2027 (2004)
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Is there a common chemical model for life in the universe?
Benner, SA; Ricardo, A; Carrigan, MA
Curr. Op. Chem Biol. 8 (6) 672-689 (2004)
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Contribution of a conserved phenylalanine residue to the activity of Escherichia coli uracil DNA glycosylase
Shaw, RW; Feller, JA; Bloom, LB
DNA Repair 3 (10) 1273-1283 (2004)
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Significance of cytoplasmic prolyl hydroxylation and complex glycosylation in the cellular slime mold Dictyostelium
West, CM; van der Wel, H; Sassi, S; Gaucher, E; Ercan, A
Glycobiology 14 (11) 1063-1063 (2004)

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Expanding the genetic alphabet: Pyrazine nucleosides that support a donor-donor-acceptor hydrogen-bonding pattern
von Krosigk, U; Benner, SA
Helv. Chim. Acta 87 (6) 1299-1324 (2004)
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Human ATP:Cob(I)alamin adenosyltransferase and its interaction with methionine synthase reductase
Leal, NA; Olteanu, H; Banerjee, R; Bobik, TA
J. Biol. Chem. 279 (46) 47536-47542 (2004)
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Autophosphorylation activity of the Arabidopsis ethylene receptor multigene family
Moussatche, P; Klee, HJ
J. Biol. Chem. 279 (47) 48734-48741 (2004)
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Zinc and the Msc2 zinc transporter protein are required for endoplasmic reticulum function
Ellis, CD; Wang, FD; MacDiarmid, CW; Clark, S; Lyons, T; Eide, DJ
J. Cell. Biol. 166 (3) 325-335 (2004)
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Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments
Chang, MSS; Benner, SA
J. Mol. Biol. 341 (2) 617-631 (2004)
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Artificial genetic systems: Exploiting the "aromaticity" formalism to improve the tautomeric ratio for isoguanosine derivatives
Martinot, TA; Benner, SA
J. Org. Chem. 69 (11) 3972-3975 (2004)
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The Sup35 domains required for maintenance of weak, strong or undifferentiated yeast [PSI+] prions
Bradley, ME; Liebman, SW
Mol. Microbiol. 51 (6) 1649-1659 (2004)
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Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2 '-deoxyadenosine
Hendrickson, CL; Devine, KG; Benner, SA
Nucl. Acids Res. 32 (7) 2241-2250 (2004)
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A novel replicating circular DNAzyme
Chen, F; Wang, RJ; Li, Z; Liu, B; Wang, XP; Sun, YH; Hao, DY; Zhang, J
Nucl. Acids Res. 32 (8) 2336-2341 (2004)
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Synthesis and physical and physiological properties of 4 '-thioRNA: application to post-modification of RNA aptamer toward NF-kappa B
Hoshika, S; Minakawa, N; Matsuda, A
Nucl. Acids Res. 32 (13) 3815-3825 (2004)
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PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1
Sismour, AM; Lutz, S; Park, JH; Lutz, MJ; Boyer, PL; Hughes, SH; Benner, SA
Nucl. Acids Res. 32 728-735 (2004)
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Synthesis and biological evaluation of novel apio nucleosides with thiazole-4-carboxamide and 1,2,4-triazole-3-carboxamide
Kim, MJ; Jeong, LS; Kim, JH; Shin, JH; Chung, SY; Lee, SK; Chun, MW
Nuc. Nuc. Nuc. acids 23 (4) 715-724 (2004)
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Inhibition of ampicillin-resistant bacteria by novel mono-DNAzymes and di-DNAzyme targeted to beta-lactamase mRNA
Chen, F; Li, Z; Wang, RJ; Liu, B; Zeng, Z; Zhang, HY; Zhang, J
Oligonucleotides 14 (2) 80-89 (2004)
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2 '-deoxycytidines carrying amino and thiol functionality: Synthesis and incorporation by vent (exo(-)) polymerase
Roychowdhury, A; Illangkoon, H; Hendrickson, CL; Benner, SA
Org. Lett. 6 (4) 489-492 (2004)
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Metalloregulation of yeast membrane steroid receptor homologs
Lyons, TJ; Villa, NY; Regalla, LM; Kupchak, BR; Vagstad, A; Eide, DJ
Proc. Natl. Acad. Sci. USA 101 (15) 5506-5511 (2004)
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Borate minerals stabilize ribose
Ricardo, A; Carrigan, MA; Olcott, AN; Benner, SA
Science 303 (5655) 196-196 (2004)

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Redesigning genetics
Benner, SA
Science 306 (5296) 625-626 (2004)

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Mineral Surfaces as a Cradle of Primordial Genetic Material
Gallori E, Biondi E, Franchi M
Life in the Universe , ed. Seckbach J, Chela-Flores J, Owen T, Raulin F , Netherlands: Springer 145-148 (2004)
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PduP is a Coenzyme-A-Acylating Propionaldehyde Dehydrogenase Associated with the Polyhedral Bodies Involved in B<sub>12</sub>-dependent 1,2-propanediol Degradation by <i>Salmonella enterica</i> serovar Typhimurium LT2
Leal, NA; Havemann, GD; Bobik, TA
Arch. Microbiol. 180 (5) 353-361 (2003)
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The NASA astrobiology roadmap
Marais, DJD; Allamandola, LJ; Benner, SA; Boss, AP; Deamer, D; Falkowski, PG; Farmer, JD; Hedges, SB; Jakosky, BM; Knoll, AH; Liskowsky, DR; Meadows, VS; Meyer, MA; Pilcher, CB; Nealson, KH; Spormann, AM; Trent, JD; Turner, WW; Woolf, NJ; Yorke, HW
Astrobiology 3 (2) 219-235 (2003)
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First PCR amplification of DNA containing a nonstandard base pair A.
Lutz, S; Park, JH; Benner, SA
Biochemistry 42 (28) 8598-8598 (2003)

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Nucleosides and nucleotides. 218. Alternate-strand triple-helix formation by the 3 '-3 '-linked oligodeoxynucleotides using a purine motif
Hoshika, S; Ueno, Y; Matsuda, A
Bioconjugate Chem. 14 (3) 607-613 (2003)
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Synthesis and biological evaluation of thymine nucleosides fused with 3 ',4 '-tetrahydrofuran ring
Kim, MJ; Kim, HO; Kim, HD; Kim, JH; Jeong, LS; Chun, MW
Bioorg. Med. Chem. Lett. 13 (20) 3499-3501 (2003)
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Greater GNN pattern bias in sequence elements encoding conserved residues of ancient proteins may be an indicator of amino acid composition of early proteins.
Brooks, DJ; Fresco, JR
Gene 303 177-185 (2003)
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Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein
Gaucher, EA; Miyamoto, MM; Benner, SA
Genetics 163 (4) 1549-1553 (2003)
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Destabilizing interactions among [PSI+] and [PIN+] yeast prion variants
Bradley, ME; Liebman, SW
Genetics 165 (4) 1675-1685 (2003)
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Initiation of mucin-type O-glycosylation in lower eukaryotes (O-alpha-GlcNAc-type) and higher eukaryotes (O-alpha-GalNAc-type) is homologous
West, CM; Wang, F; van der Wel, H; Gaucher, E; Sassi, S; Metcalf, T; Heise, N; Mendonca-Previato, L; Previato, JO
Glycobiology 13 (11) 875-876 (2003)

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A direct synthesis of nucleoside analogs homologated at the 3 '- and 5 '-positions
Schmidt, J; Eschgfaller, B; Benner, SA
Helv. Chim. Acta 86 (9) 2937-2958 (2003)
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Synthesis and properties of oligodeoxynucleotide analogs with bis(methylene) sulfone bridges
Eschgfaller, B; Schmidt, JG; Konig, M; Benner, SA
Helv. Chim. Acta 86 (9) 2959-2997 (2003)
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Identification of the Human and Bovine ATP:cob(I)alamin Adenosyltransferase cDNAs Based on Complementation of a Bacterial Mutant
Leal, NA; Park, SD; Kima, PE; Bobik, TA
J. Biol. Chem. 278 (11) 9227-9234 (2003)
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Expanding the genetic alphabet: Non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern
Hutter, D; Benner, SA
J. Org. Chem. 68 (25) 9839-9842 (2003)
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Synthetic biology with artificially expanded genetic information systems. From personalized medicine to extraterrestrial life
Benner, SA; Hutter, D; Sismour, AM
Nucleic Acids Res. Suppl. 3 125-126 (2003)
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Act natural
Benner, SA
Nature 421 (6919) 118-118 (2003)

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Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
Gaucher, EA; Thomson, JM; Burgan, MF; Benner, SA
Nature 425 (6955) 285-288 (2003)
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Synthesis of 2-(3 '-azido- and 3 '-amino-3 '-deoxy-beta-D-ribofuranosyl)thiazole-4-carboxamide
Liang, CW; Kim, MJ; Jeong, LS; Chun, MW
Nuc. Nuc. Nuc. acids 22 (11) 2039-2048 (2003)
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C-5 modified nucleosides: Direct insertion of alkynyl-thio functionality in pyrimidines
Held, HA; Roychowdhury, A; Benner, SA
Nuc. Nuc. Nuc. acids 22 (4) 391-404 (2003)
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Synthesis and biological evaluation of pyrimidine nucleosides fused with 3 ',4 '-tetrahydrofuran ring
Chun, MW; Kim, MJ; Kim, HO; Moon, HR; Kim, HD; Kim, JH; Jeong, LS
Nuc. Nuc. Nuc. acids 22 719-721 (2003)
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Synthesis of 5-azacytidine nucleosides with rigid sugar moiety as potential antitumor agents
Chun, MW; Kim, MJ; Kim, HO; Kim, HD; Kim, JH; Moon, HR; Jeong, LS
Nuc. Nuc. Nuc. acids 22 915-917 (2003)
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Susceptible to intolerance - a range of hormonal actions in a susceptible Arabidopsis pathogen response
O'Donnell, PJ; Schmelz, EA; Moussatche, P; Lund, ST; Jones, JB; Klee, HJ
Plant J. 33 (2) 245-257 (2003)
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Nucleobase pairing in Watson-Crick-like genetic expanded information systems
Geyer, CR; Battersby, TR; Benner, SA
Structure 11 (12) 1485-1498 (2003)
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1 -&gt; 2 Migration and concurrent glycosidation of phenyl 1-thio-alpha-mannopyranosides via 2,3-O-cyclic dioxonium intermediates
Yang, ZY; Cao, HZ; Hu, J; Shan, RL; Yu, B
Tetrahedron 59 (2) 249-254 (2003)
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Guanidine reduces stop codon read-through caused by missense mutations in SUP35 or SUP45
Bradley, ME; Bagriantsev, S; Vishveshwara, N; Liebman, SW
Yeast 20 (7) 625-632 (2003)
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Phosphates, DNA, and the search for nonterrean life: A second generation model for genetic molecules
Benner, SA; Hutter, D
Bioorg. Chem. 30 (1) 62-80 (2002)
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Complex glycosylation of Skp1 in Dictyostelium: implications for the modification of other eukaryotic cytoplasmic and nuclear proteins
West, CM; van der Wel, H; Gaucher, EA
Glycobiology 12 (2) (2002)
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Identification of a Golgi-associated UDP-GlcNAc : polypeptide mucin-type alpha-N-acetylglucosaminyltransferase that modifies cell surface proteins in Dictyostelium
West, CM; van der Wel, H; Metcalf, T; Kaplan, L; Gaucher, EA
Glycobiology 12 (10) 697-697 (2002)

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From phosphate to bis(methylene) sulfone: Non-ionic backbone linkers in DNA
Hutter, D; Blaettler, MO; Benner, SA
Helv. Chim. Acta 85 (9) 2777-2806 (2002)
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Fourier transform-ion cyclotron resonance mass spectrometric resolution, identification, and screening of non-covalent complexes of Hck Src homology 2 domain receptor and ligands from a 324-member peptide combinatorial library
Wigger, M; Eyler, JR; Benner, SA; Li, WQ; Marshall, AG
J. Am. Soc. Mass Spec. 13 (10) 1162-1169 (2002)
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Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences
Fukami-Kobayashi, K; Schreiber, DR; Benner, SA
J. Mol. Biol. 319 (3) 729-743 (2002)
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Oligodeoxyribonucleotide analogues with bridging dimethylene sulfide, sulfoxide, and sulfone groups. Toward a second-generation model of nucleic acid structure
Huang, Z; Benner, SA
J. Org. Chem. 67 (12) 3996-4013 (2002)
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Evolution of amino acid frequencies in proteins over deep time: Inferred order of introduction of amino acids into the genetic code.
Brooks, DJ; Fresco, JR; Lesk, AM; Singh, M
Mol. Biol. Evol. 19 1645-1655 (2002)
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Increased frequency of cysteine, tyrosine and phenylalanine residues since the Last Universal Ancestor.
Brooks, DJ; Fresco, JR
Mol. Cell. Proteomics 1 125-131 (2002)
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Challenging artificial genetic systems: thymidine analogs with 5-position sulfur functionality
Held, HA; Benner, SA
Nucl. Acids Res. 30 (17) 3857-3869 (2002)
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Interactions among prions and prion "strains" in yeast
Bradley, ME; Edskes, HK; Hong, JY; Wickner, RB; Liebman, SW
Proc. Natl. Acad. Sci. USA 99 (7) 16392-16399 (2002)
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The past as the key to the present: Resurrection of ancient proteins from eosinophils
Benner, SA
Proc. Natl. Acad. Sci. USA 99 (8) 4760-4761 (2002)

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Evolution - Planetary biology - Paleontological, geological, and molecular histories of life
Benner, SA; Caraco, MD; Thomson, JM; Gaucher, EA
Science 296 (5569) 864-868 (2002)
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Ribonucleases in ruminants - Response
Benner, SA
Science 297 (5584) 1122-1122 (2002)

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Predicting functional divergence in protein evolution by site-specific rate shifts
Gaucher, EA; Gu, X; Miyamoto, MM; Benner, SA
Trends Biochem. Sci. 27 (6) 315-321 (2002)
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Nucleosides and nucleotides. 208. alternate-strand triple-helix formation by the 3 '-3 '-linked oligodeoxynucleotides with the anthraquinonyl group at the junction point
Ueno, Y; Mikawa, M; Hoshika, S; Matsuda, A
Bioconjugate Chem. 12 (4) 635-642 (2001)
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Stereoselective synthesis of 2-S-ethyl(phenyl)-2-thio-beta-glucopyranosides via 1,2-migration and concurrent glycosidation of ethyl(phenyl) 2,3-orthoester-1-thio-alpha-mannopyranosides
Yang, ZY; Yu, B
Carbohydr. Res. 333 (2) 105-114 (2001)
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Prions affect the appearance of other prions: The story of [PIN+]
Derkatch, IL; Bradley, ME; Hong, JY; Liebman, SW
Cell 106 (2) 171-182 (2001)
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Solution structure of the mEGF/TGF alpha(44-50) chimeric growth factor
Chamberlin, SG; Brennan, L; Puddicombe, SM; Davies, DE; Turner, DL
Euro. J. Biochem. 268 (23) 6247-6255 (2001)
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A bifunctional diglycosyltransferase forms the Fuca1,2Galb,3-disaccharide on Skp1 in the cytoplasm of Dictyostelium
van der Wel, H; Fisher, SZ; Gaucher, EA; West, CM
Glycobiology 11 (10) 884-884 (2001)

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A stable dirhodium tetracarboxylate carbenoid: Crystal structure, bonding analysis, and catalysis
Snyder, JP; Padwa, A; Stengel, T; Arduengo, AJ; Jockisch, A; Kim, HJ
J. Am. Chem. Soc. 123 (45) 11318-11319 (2001)

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Functional genomic, biochemical and genetic characterization of the <i>Salmonella pduO</i> gene, an ATP:cob(I)alamin adenosyltransferase gene
Johnson, CLV; Pechonick, EM; Park, SD; Havemann, GD; Leal, NA; Bobik, TA
J. Bacteriol. 183 1577-1584 (2001)
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PTC effect of carbon black filled polypropylene
He, XJ; Chen, F; Chen, XF
J. Mater. Sci. Lett. 20 (7) 589-590 (2001)

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Fluorescent charge-neutral analogue of xanthosine: Synthesis of a 2 '-deoxyribonucleoside bearing a 5-aza-7-deazaxanthine base
Rao, P; Benner, SA
J. Org. Chem. 66 (15) 5012-5015 (2001)
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Natural progression
Benner, SA
Nature 409 (6819) 459-459 (2001)

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Nonenzymatic autoligation in direct three-color detection of RNA and DNA point mutations
Xu, YZ; Karalkar, NB; Kool, ET
Nat. Biotechnol. 19 (2) 148-152 (2001)
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Synthesis of novel 3 '-deoxy-3 '-C-hydroxymethyl nucleosides with conformationally rigid sugar moiety as potential antiviral agents
Chun, MW; Kim, MJ; Jo, UH; Kim, JH; Kim, HD; Jeong, LS
Nuc. Nuc. Nuc. acids 20 699-702 (2001)
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Synthesis of novel D- and L-3 '-deoxy-3 '-C-hydroxymethyl nucleoside with exocyclic methylene as potential ribonucleotide reductase inhibitor
Chun, MW; Kim, MJ; Jo, UH; Kim, JH; Kim, HD; Jeong, LS
Nuc. Nuc. Nuc. acids 20 703-706 (2001)
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Stereoselective synthesis of 2-S-phenyl-2-deoxy-beta-glycosides using phenyl 2,3-O-thionocarbonyl-1-thioglycoside donors via 1,2-migration and concurrent glycosidation
Yu, B; Yang, ZY
Org. Lett. 3 (3) 377-379 (2001)
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Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors
Gaucher, EA; Miyamoto, MM; Benner, SA
Proc. Natl. Acad. Sci. USA 98 (2) 548-552 (2001)
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Evolution, language and analogy in functional genomics
Benner, SA; Gaucher, EA
Trends in Genetics 17 (7) 414-418 (2001)
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Beyond BLAST: Paleogenomics tools to infer function to genetic sequences.
Benner, S; Chamberlin, S
Am. J. Hum. Genet. 67 (4) 260-260 (2000)

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X-ray crystallographic and analytical ultracentrifugation analyses of truncated and full-length yeast copper chaperones for SOD (LYS7): A dimer-dimer model of LYS7-SOD association and copper delivery
Hall, LT; Sanchez, RJ; Holloway, SP; Zhu, HN; Stine, JE; Lyons, TJ; Demeler, B; Schirf, V; Hansen, JC; Nersissian, AM; Valentine, JS; Hart, PJ
Biochemistry 39 (13) 3611-3623 (2000)
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Rearrangement of sugar 1,2-orthoesters to glycosidic products: a mechanistic implication
Yang, ZY; Lin, WB; Yu, B
Carbohydr. Res. 329 (4) 879-884 (2000)
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Dependence and independence of [PSI+] and [PIN+]: A two-prion system in yeast?
Derkatch, IL; Bradley, ME; Masse, SVL; Zadorsky, SP; Polozkov, GV; Inge-Vechtomov, SG; Liebman, SW
EMBO J. 19 (9) 1942-1952 (2000)
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Synthesis and characterization of oligonucleotides containing 2 '-deoxyxanthosine using phosphoramidite chemistry
Jurczyk, SC; Horlacher, J; Devined, KG; Benner, SA; Battersby, TR
Helv. Chim. Acta 83 (7) 1517-1524 (2000)
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The copper transport protein Atox1 promotes neuronal survival
Kelner, GS; Lee, MH; Clark, ME; Maciejewski, D; McGrath, D; Rabizadeh, S; Lyons, T; Bredesen, D; Jenner, P; Maki, RA
J. Biol. Chem. 275 (1) 580-584 (2000)
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The metal binding properties of the zinc site of yeast copper-zinc superoxide dismutase: implications for amyotrophic lateral sclerosis
Lyons, TJ; Nersissian, A; Huang, HJ; Yeom, H; Nishida, CR; Graden, JA; Gralla, EB; Valentine, JS
J. Biol. Inorg. Chem. 5 (2) 189-203 (2000)
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Evaluation measures of multiple sequence alignments
Gonnet, GH; Korostensky, C; Benner, S
J. Comp. Bio. 7 261-276 (2000)
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Evolutionary history of the uterine serpins
Peltier, MR; Raley, LC; Liberles, DA; Benner, SA; Hansen, PJ
J. Exp. Zoo. 288 (2) 165-174 (2000)
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A statistical view of FMRFamide neuropeptide diversity
Espinoza, E; Carrigan, M; Thomas, SG; Shaw, G; Edison, AS
Mol. Neurobiol. 21 35-56 (2000)
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The missing organic molecules on Mars
Benner, SA; Devine, KG; Matveeva, LN; Powell, DH
Proc. Natl. Acad. Sci. USA 97 (6) 2425-2430 (2000)
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Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast
Lyons, TJ; Gasch, AP; Gaither, LA; Botstein, D; Brown, PO; Eide, DJ
Proc. Natl. Acad. Sci. USA 97 (14) 7957-7962 (2000)
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Functional inferences from reconstructed evolutionary biology involving rectified databases. An evolutionarily-grounded approach to functional genomics.
Benner, SA; Chamberlin, SG; Liberles, DA; Govindarajan, S; Knecht, L
Res. MicroBiol. 151 (2) 97-106 (2000)
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Unite efforts and conquer mysteries of artificial genetics
Benner, SA
Science 290 (5496) 1506-1506 (2000)

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A novel and expeditious approach to the stereoselective synthesis of 2-S-ethyl(phenyl)-2-deoxy-beta-glycosides, ready precursors to 2-deoxy-beta-glycosides
Yu, B; Yang, ZY
Tet. Lett. 41 (16) 2961-2964 (2000)
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Evolutionary, mechanistic, and predictive analyses of the hydroxymethyldihydropterin pyrophosphokinase family of proteins
Gerloff, DL; Cannarozzi, GM; Joachimiak, M; Cohen, FE; Schreiber, D; Benner, SA
Biochem. Biophys. Res. Comm. 254 (1) 70-76 (1999)
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Simple one-pot synthesis of a 2 '-tritium labeled C-deoxynucleoside
Lutz, S; Benner, SA
Bioorg. Med. Chem. Lett. 9 (5) 723-726 (1999)
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Sequence analysis of FMRFamide-like peptides and precursors
Carrigan, M; Espinoza, E; Thomas, S; Benner, SA; Edison, AS
Brain Res. 848 (1999)

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Structural changes to ribonuclease A and their effects on biological activity
Soucek, J; Raines, RT; Haugg, M; Raillard-Yoon, SA; Benner, SA
Comp. Biochem. Phys. C 123 (2) 103-111 (1999)
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The PNM2 mutation in the prion protein domain of SUP35 has distinct effects on different variants of the [PSI+] prion in yeast
Derkatch, IL; Bradley, ME; Zhou, P; Liebman, SW
Curr. Genet. 35 (2) 59-67 (1999)
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Crystal structure of a hybrid between ribonuclease A and bovine seminal ribonuclease - the basic surface, at 2.0 angstrom resolution
Vatzaki, EH; Allen, SC; Leonidas, DD; Trautwein-Fritz, K; Stackhouse, J; Benner, SA; Acharya, KR
Euro. J. Biochem. 260 (1) 176-182 (1999)
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An alternative to the origins of life theories: Amino acid-like DNA molecules with catalytic activity
Ang, DN; Suh, B; Westermann-Clark, E; Battersby, T; Benner, SA
FASEB J. 13 (7) (1999)

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Synthesis of 2 '-deoxyisoguanosine 5 '-triphosphate and 2 '-deoxy-5-methylisocytidine 5 '-triphosphate
Jurczyk, SC; Kodra, JT; Park, JH; Benner, SA; Battersby, TR
Helv. Chim. Acta 82 (7) 1005-1015 (1999)
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A mild and efficient method for the preparation of 5 '-dimethoxytrityl-2 '-deoxynucleoside using poly(4-vinylpyridine)-costyrene
Karalkar, NB; Akerkar, VG; Salunkhe, MM
Indian J. Chem., Sect B 38 (3) 370-371 (1999)
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Quantitative analysis of receptors for adenosine nucleotides obtained via in vitro selection from a library incorporating a cationic nucleotide analog
Battersby, TR; Ang, DN; Burgstaller, P; Jurczyk, SC; Bowser, MT; Buchanan, DD; Kennedy, RT; Benner, SA
J. Am. Chem. Soc. 121 (42) 9781-9789 (1999)
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Catalysts, anticatalysts, and receptors for unactivated phosphate diesters in water
Zepik, HH; Benner, SA
J. Org. Chem. 64 (22) 8080-8083 (1999)
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Biological chemistry of copper-zinc superoxide dismutase and its link to amyotrophic lateral sclerosis
Lyons, TJ; Gralla, EB; Valentine, JS
Met. Ions Biol. Syst. 36 (1) 125-177 (1999)

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An in vitro screening technique for DNA polymerases that can incorporate modified nucleotides. Pseudothymidine as a substrate for thermostable polymerases
Lutz, S; Burgstaller, P; Benner, SA
Nucl. Acids Res. 27 (13) 2792-2798 (1999)
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Synthesis of a monocharged peptide nucleic acid (PNA) analog and its recognition as substrate by DNA polymerases
Lutz, MJ; Will, DW; Breipohl, G; Benner, SA; Uhlmann, E
Nucl. Nucl. 18 (3) 393-401 (1999)
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Synthesis and antiviral activities of 1,3-oxathiolanyl nucleosides with 5-hydroxymethyl substituent
Chun, MW; Choi, SP; Kim, MJ; Bae, CJ
Nucl. Nucl. 18 615-616 (1999)
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The molecular origins of life - Assembling pieces of the puzzle
Benner, SA
Science 283 (5410) 2026-2026 (1999)

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Chance and Necessity in Biomolecular Chemistry - Is Life as We Know It Universal?
Benner, SA; Switzer, CY
Simplicity and Complexity in Proteins and Nucleic Acids , ed. H. Frauenfelder, J. Deisenhofer, P.G. Wolynes , Dahlem University Press 339-363 (1999)

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How small can a microorganism be?
Benner, SA
Size Limits of Very Small Microorganisms: Proceedings of a Workshop, Steering Group on Astrobiology of the Space Studies Board , National Research Council 126-135 (1999)

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Post-genomic science: Converting primary structure into physiological function
Benner, SA; Trabesinger, N; Schreiber, D
Adv. Enz. Reg. 38 (1) 155-180 (1998)

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A unified model of c-erbB receptor homo- and heterodimerisation
Chamberlin, SG; Davies, DE
Biochim. Biophys. Acta 1384 (2) 223-232 (1998)
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Structure prediction in a post-genomic environment: A secondary and tertiary structural model for the initiation factor 5A family
Gerloff, DL; Joachimiak, M; Cohen, FE; Cannarozzi, GM; Chamberlin, SG; Benner, SA
Biochem. Biophys. Res. Comm. 251 (1) 173-181 (1998)
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Origin of dimeric structure in the ribonuclease superfamily
Ciglic, MI; Jackson, PJ; Raillard, SA; Haugg, M; Jermann, TM; Opitz, JG; Trabesinger-Ruf, N; Benner, SA
Biochemistry 37 (12) 4008-4022 (1998)
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Origin of the catalytic activity of bovine seminal ribonuclease against double-stranded RNA
Opitz, JG; Ciglic, MI; Haugg, M; Trautwein-Fritz, K; Raillard, SA; Jermann, TM; Benner, SA
Biochemistry 37 (12) 4023-4033 (1998)
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Structure-function studies of ligand-induced epidermal growth factor receptor dimerization
Neelam, B; Richter, A; Chamberlin, SG; Puddicombe, SM; Wood, L; Murray, MB; Nandagopal, K; Niyogi, SK; Davies, DE
Biochemistry 37 (14) 4884-4891 (1998)
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Recognition of a non-standard base pair by thermostable DNA polymerases
Lutz, MJ; Horlacher, J; Benner, SA
Bioorg. Med. Chem. Lett. 8 (10) 1149-1152 (1998)
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Recognition of 2 '-deoxyisoguanosine triphosphate by HIV-1 reverse transcriptase and mammalian cellular DNA polymerases
Lutz, MJ; Horlacher, J; Benner, SA
Bioorg. Med. Chem. Lett. 8 (5) 499-504 (1998)
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The dark side of dioxygen biochemistry
Valentine, JS; Wertz, DL; Lyons, TJ; Liou, LL; Goto, JJ; Gralla, EB
Curr. Op. Chem Biol. 2 (2) 253-262 (1998)
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Determination of solution structures of paramagnetic proteins by NMR
Turner, DL; Brennan, L; Chamberlin, SG; Louro, RO; Xavier, AV
Euro. Biophys. J. Biophys. Lett. 27 (4) 367-375 (1998)
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A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure
Chelvanayagam, G; Knecht, L; Jenny, T; Benner, SA; Gonnet, GH
Folding Des. 3 (3) 149-160 (1998)
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Synthesis of oligonucleotides containing 2 '-deoxyisoguanosine and 2 '-deoxy-5-methylisocytidine using phosphoramidite chemistry
Jurczyk, SC; Kodra, JT; Rozzell, JD; Benner, SA; Battersby, TR
Helv. Chim. Acta 81 (5) 793-811 (1998)
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Synthesis of sulfoxides by the oxidation of sulfides with polymer supported periodate ion
Karalkar, NB; Salunkhe, MM; Talekar, KP; Maldar, NN
Indian J. Chem., Sect B 37 (11) 1184-1185 (1998)
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Distorting duplex DNA by dimethylenesulfone substitution: A new class of "transition state analog" inhibitors for restriction enzymes
Blattler, MO; Wenz, C; Pingoud, A; Benner, SA
J. Am. Chem. Soc. 120 (11) 2674-2675 (1998)

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Metal ion reconstitution studies of yeast copper-zinc superoxide dismutase: the "phantom" subunit and the possible role of Lys7p
Lyons, TJ; Nersissian, A; Goto, JJ; Zhu, H; Gralla, EB; Valentine, JS
J. Biol. Inorg. Chem. 3 (6) 650-662 (1998)
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Synthesis and biodistribution of a short nonionic oligonucleotide analogue in mouse with a potential to mimic peptides
Eschgfaller, B; Konig, M; Boess, F; Boelsterli, UA; Benner, SA
J. Med. Chem. 41 (3) 276-283 (1998)
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Functionalization of nucleoside analogs: Regiospecific conversion of 4 ''-hydroxyl groups to thioesters and deoxygenation of 3 '-hydroxyl groups
Huang, Z; Benner, SA
Nuc. Nuc. Nuc. acids 17 (5) 895-899 (1998)
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Overexpression of the SUP45 gene encoding a Sup35p-binding protein inhibits the induction of the de novo appearance of the [PSI+] prion
Derkatch, IL; Bradley, ME; Liebman, SW
Proc. Natl. Acad. Sci. USA 95 (5) 2400-2405 (1998)
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Redesigning nucleic acids
Benner, SA; Battersby, TR; Eschgfaller, B; Hutter, D; Kodra, JT; Lutz, S; Arslan, T; Baschlin, DK; Blattler, M; Egli, M; Hammer, C; Held, HA; Horlacher, J; Huang, Z; Hyrup, B; Jenny, TF; Jurczyk, SC; Konig, M; von Krosigk, U; Lutz, MJ; MacPherson, LJ; Moro
Pure Appl. Chem. 70 (2) 263-266 (1998)
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Libraries for receptor-assisted combinatorial synthesis (RACS). The olefin metathesis reaction
Giger, T; Wigger, M; Audetat, S; Benner, SA
SynLett (6) 688 (1998)
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Synthesis and properties of new chelating resin with a spacer containing alpha-nitroso-beta-naphthol as the functional group
Akerkar, VG; Karalkar, NB; Sharma, RK; Salunkhe, MM
Talanta 46 (6) 1461-1467 (1998)
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Bona fide predictions of protein secondary structure using transparent analyses of multiple sequence alignments
Benner, SA; Cannarozzi, G; Gerloff, D; Turcotte, M; Chelvanayagam, G
Chem. Rev. 97 (8) 2725-2843 (1997)

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Redesigning nucleic acids
Benner, SA
FASEB J. 11 (9) (1997)

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Genetic and environmental factors affecting the de novo appearance of the [PSI+] prion in Saccharomyces cerevisiae
Derkatch, IL; Bradley, ME; Zhou, P; Chernoff, YO; Liebman, SW
Genetics 147 (2) 507-519 (1997)
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Recognition of uncharged polyamide-linked nucleic acid analogs by DNA polymerases and reverse transcriptases
Lutz, MJ; Benner, SA; Hein, S; Breipohl, G; Uhlmann, E
J. Am. Chem. Soc. 119 (13) 3177-3178 (1997)

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Targeting determinants and proposed evolutionary basis for the sec and the delta pH protein transport systems in chloroplast thylakoid membranes
Henry, R; Carrigan, M; McCaffery, M; Ma, XY; Cline, K
J. Cell. Biol. 136 (4) 823-832 (1997)
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The B-12-dependent ribonucleotide reductase from the archaebacterium Thermoplasma acidophila: An evolutionary solution to the ribonucleotide reductase conundrum
Tauer, A; Benner, SA
Proc. Natl. Acad. Sci. USA 94 (1) 53-58 (1997)
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A predicted consensus structure for the C-terminus of the beta and gamma chains of fibrinogen
Gerloff, DL; Cohen, FE; Benner, SA
Proteins 27 (2) 279-289 (1997)
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A predicted consensus structure for the N-terminal fragment of the heat shock protein HSP90 family
Gerloff, DL; Cohen, FE; Korostensky, C; Turcotte, M; Gonnet, GH; Benner, SA
Proteins 27 (3) 450-458 (1997)
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An analysis of simultaneous variation in protein structures
Chelvanayagam, G; Eggenschwiler, A; Knecht, L; Gonnet, GH; Benner, SA
Prot. Eng. 10 (4) 307-316 (1997)
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Assessing enzyme substrate specificity using combinatorial libraries and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry
Wigger, M; Nawrocki, JP; Watson, CH; Eyler, JR; Benner, SA
Rapid Comm. Mass Spec. 11 (16) 1749-1752 (1997)
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Synthesis of an N-alkyl derivative of 2'-deoxyisoguanosine
Kodra, JT; Benner, SA
SynLett (8) 939-2843 (1997)
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Developing new synthetic catalysts. How nature does it
Benner, SA; Jermann, TM; Opitz, JG; Raillard, SA; Zankel, TR; Trautwein-Fritz, K; Stackhouse, J; Ciglic, MI; Haugg, M; Trabesinger-Ruf, N; Weinhold, EG
Acta Chem. Scand. 50 (3) 243-248 (1996)
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Targeting the epidermal growth factor receptor for therapy of carcinomas
Davies, DE; Chamberlin, SG
Biochem. Pharmacol. 51 (9) 1101-1110 (1996)
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The interaction of a chimeric EGF containing the C-tail of TGF alpha with the EGF receptor reveals hidden ligand complexities.
Puddicombe, S; Wood, L; Chamberlin, S; Davies, D
FASEB J. 10 (6) 2171-2171 (1996)

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The mitogenic effect of low affinity ligands is enhanced by overexpression of EGF receptors
Davies, D; Adam, R; Murray, M; Niyogi, S; Chamberlin, S
FASEB J. 10 (6) 2172-2172 (1996)

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Amphiregulin is a poor effector of ligand-induced EGF receptor dimerisation.
Richter, A; Neelam, B; Chamberlin, S; Davies, D
FASEB J. 10 (6) 2173-2173 (1996)

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Catalysis: The omnipresent phenomenon.
Benner, SA
FASEB J. 10 (6) (1996)

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A high intensity signal is required for EGF receptor mediated morphogenesis and migration.
Solic, N; Murray, M; Chamberlin, S; Niyogi, S; Davies, D
FASEB J. 10 (6) (1996)

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A mathematical model of c-erbB receptor dimerisation.
Chamberlin, S; Davies, D
FASEB J. 10 (6) (1996)

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Pseudogenes in ribonuclease evolution: A source of new biomacromolecular function?
TrabesingerRuef, N; Jermann, T; Zankel, T; Durrant, B; Frank, G; Benner, SA
FEBS Lett. 382 (3) 319-322 (1996)
<Abstract>

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Induction of anchorage-independent growth by amphiregulin
Adam, RM; Chamberlin, SG; Davies, DE
Growth Factors 13 193-203 (1996)
<Abstract>

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Synthesis and characterization of non-standard nucleosides and nucleotides bearing the acceptor-donor-donor pyrimidine analog 6-amino-3-methylpyrazin-2(1H)-one
Voegel, JJ; Benner, SA
Helv. Chim. Acta 79 (7) 1863-1880 (1996)
<Abstract>

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Synthesis, molecular recognition, and enzymology of oligonucleotides containing the non-standard base pair between 5-aza-7-deazaisoguanine and 6-amino-3-methylpyrazin-2(1H)-one, a donor-acceptor-acceptor purine analog and an acceptor-donor-donor pyrimidine analog
Voegel, JJ; Benner, SA
Helv. Chim. Acta 79 (7) 1881-1898 (1996)
<Abstract>

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Nonionic analogs of RNA with dimethylene sulfone bridges
Richert, C; Roughton, AL; Benner, SA
J. Am. Chem. Soc. 118 (19) 4518-4531 (1996)
<Abstract>

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The significance of valine 33 as a ligand-specific epitope of transforming growth factor alpha
Puddicombe, SM; Chamberlin, SG; MacGarvie, J; Richter, A; Drummond, DR; Collins, J; Wood, L; Davies, DE
J. Biol. Chem. 271 (26) 15367-15372 (1996)
<Abstract>

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The interaction of an epidermal growth factor transforming growth factor alpha tail chimera with the human epidermal growth factor receptor reveals unexpected complexities
Puddicombe, SM; Wood, L; Chamberlin, SG; Davies, DE
J. Biol. Chem. 271 (48) 30392-30397 (1996)
<Abstract>

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Chimera of dimethylene sulfone-, methyl sulfide-, and methyl sulfoxide-linked ribonucleotides and DNA
Baeschlin, DK; Hyrup, B; Benner, SA; Richert, C
J. Org. Chem. 61 (21) 7620-7626 (1996)

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Differential discrimination of DNA polymerases for variants of the non-standard nucleobase pair between xanthosine and 2,4-diaminopyrimidine, two components of an expanded genetic alphabet
Lutz, MJ; Held, HA; Hottiger, M; Hubscher, U; Benner, SA
Nucl. Acids Res. 24 (7) 1308-1313 (1996)
<Abstract>

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Mutations in copper-zinc superoxide dismutase that cause amyotrophic lateral sclerosis alter the zinc binding site and the redox behavior of the protein
Lyons, TJ; Liu, HB; Goto, JJ; Nersissian, A; Roe, JA; Graden, JA; Cafe, C; Ellerby, LM; Bredesen, DE; Gralla, EB; Valentine, JS
Proc. Natl. Acad. Sci. USA 93 (22) 12240-12244 (1996)
<Abstract>

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Analysis of combinatorial libraries using electrospray Fourier transform ion cyclotron resonance mass spectrometry
Nawrocki, JP; Wigger, M; Watson, CH; Hayes, TW; Senko, MW; Benner, SA; Eyler, JR
Rapid Comm. Mass Spec. 10 (14) 1860-1864 (1996)
<Abstract>

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Protein structure prediction
Benner, SA; Geroff, DL; Rozzell, JD
Science 274 (5292) 1448-1449 (1996)

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Four step synthesis of a 5'-deoxy-5'-iodomethylthymidine
Baeschlin, DK; Daube, M; Blattler, MO; Benner, SA; Richert, C
Tet. Lett. 37 (10) 1591-1592 (1996)
<Abstract>

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Reconstructing ancient forms of life
Benner, SA
J. Cell. Biol. (19) 200-200 (1995)

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MODULATION OF THE RECEPTOR-BINDING AFFINITY OF AMPHIREGULIN BY MODIFICATION OF ITS CARBOXYL-TERMINAL TAIL
Adam, R; Drummond, DR; Solic, N; Holt, SJ; Sharma, RP; Chamberlin, SG; Davies, DE
Biochim. Biophys. Acta 1266 (1) 83-90 (1995)
<Abstract>

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Immunosuppressive activity of angiogenin in comparison with bovine seminal ribonuclease and pancreatic ribonuclease
Matousek, J; Soucek, J; Riha, J; Zankel, TR; Benner, SA
Comp. Biochem. Phys. B 112 (2) 235-241 (1995)
<Abstract>

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pH-independent triple helix formation by an oligonucleotide containing a pyrazine donor-donor-acceptor base
Vonkrosigk, U; Benner, SA
J. Am. Chem. Soc. 117 (19) 5361-5362 (1995)

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Crystal structure of a dimethylene sulfone-linked ribodinucleotide analog
Roughton, AL; Portmann, S; Benner, SA; Egli, M
J. Am. Chem. Soc. 117 (27) 7249-7250 (1995)

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CONTRIBUTION OF THE TRANSFORMING GROWTH-FACTOR-ALPHA B-LOOP BETA-SHEET TO BINDING AND ACTIVATION OF THE EPIDERMAL GROWTH-FACTOR RECEPTOR
Richter, A; Drummond, DR; Macgarvie, J; Puddicombe, SM; Chamberlin, SG; Davies, DE
J. Biol. Chem. 270 (4) 1612-1616 (1995)
<Abstract>

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CONSTRAINED PEPTIDE ANALOGS OF TRANSFORMING GROWTH-FACTOR-ALPHA RESIDUES CYSTEINE-21-32 ARE MITOGENICALLY ACTIVE - USE OF PROLINE MIMETICS TO ENHANCE BIOLOGICAL POTENCY
Chamberlin, SG; Sargood, KJ; Richter, A; Mellor, JM; Anderson, DW; Richards, NGJ; Turner, DL; Sharma, RP; Alexander, P; Davies, DE
J. Biol. Chem. 270 (36) 21062-21067 (1995)
<Abstract>

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X-ray crystal-structure of a dimethylene sulfone-bridged ribonucleotide dimer in a single-stranded state
Hyrup, B; Richert, C; Schulteherbruggen, T; Benner, SA; Egli, M
Nucl. Acids Res. 23 (13) 2427-2433 (1995)
<Abstract>

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Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily
Jermann, TM; Opitz, JG; Stackhouse, J; Benner, SA
Nature 374 (6517) 57-59 (1995)
<Abstract>

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Uncertainty in ancient phylogenies - reply
Benner, SA; Jermann, TM; Opitz, JG; Stackhouse, J; Knecht, LJ; Gonnet, GH
Nature 377 (6545) 109-110 (1995)

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Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns
Horlacher, J; Hottiger, M; Podust, VN; Hubscher, U; Benner, SA
Proc. Natl. Acad. Sci. USA 92 (14) 6329-6333 (1995)
<Abstract>

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Predicted secondary and supersecondary structure for the serine-threonine-specific protein phosphatase family
Jenny, TF; Gerloff, DL; Cohen, MA; Benner, SA
Proteins 21 (1) 1-10 (1995)
<Abstract>

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A consensus prediction of the secondary structure for the 6-phospho-&#946;-D-galactosidase superfamily
Gerloff, DL; Benner, SA
Proteins 21 (4) 273-281 (1995)
<Abstract>

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A predicted consensus structure for the protein-kinase C2 homology (C2H) domain, the repeating unit of synaptotagmin
Gerloff, DL; Chelvanayagam, G; Benner, SA
Proteins 22 (4) 299-310 (1995)
<Abstract>

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The phospho-&#946;-galactosidase and synaptotagmin predictions
Benner, SA; Gerloff, D; Chelvanayagam, G
Proteins 23 (3) 446-453 (1995)
<Abstract>

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Engineering yeast alcohol dehydrogenase. Replacing Trp54 by Leu broadens substrate specificity
Weinhold, EG; Benner, SA
Prot. Eng. 8 (5) 457-461 (1995)
<Abstract>

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SYNTHESIS OF FRAGMENTS OF TRANSFORMING GROWTH-FACTOR-ALPHA INCORPORATING EXO-2-AZABICYCLO[2,2,1]HEPTANE-3-CARBOXYLIC ACIDS AS PROLINE SUBSTITUTES
Mellor, JM; Richards, NGJ; Sargood, KJ; Anderson, DW; Chamberlin, SG; Davies, DE
Tet. Lett. 36 (37) 6765-6768 (1995)
<Abstract>

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Predicting the conformation of proteins from sequences - progress and future progress
Benner, SA; Jenny, TF; Cohen, MA; Gonnet, GH
Adv. Enz. Reg. 34 (5179) 269-353 (1994)

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Analysis of amino-acid substitution during divergent evolution - the 400 by 400 dipeptide substitution matrix
Gonnet, GH; Cohen, MA; Benner, SA
Biochem. Biophys. Res. Comm. 199 (2) 489-496 (1994)
<Abstract>

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Evaluating predictions of secondary structure in proteins
Jenny, TF; Benner, SA
Biochem. Biophys. Res. Comm. 200 (1) 149-155 (1994)
<Abstract>

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Reverse transphosphorylation by ribonuclease A needs an intact p(2)-binding site - point mutations at lys-7 and arg-10 alter the catalytic properties of the enzyme
Boix, E; Nogues, MV; Schein, CH; Benner, SA; Cuchillo, CM
J. Biol. Chem. 269 (4) 2529-2534 (1994)
<Abstract>

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Orthocyclophanes .3. Ketonands, Novel ketonic crowns of polyoxo[1(N)]orthocyclophane constitution
Lee, WY; Park, CH; Kim, HJ; Kim, SS
J. Org. Chem. 59 (4) 878-884 (1994)
<Abstract>

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A prediction of the secondary structure of the pleckstrin homology domain
Jenny, TF; Benner, SA
Proteins 20 (1) 1-3 (1994)
<Abstract>

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Amino acid substitution during functionally constrained divergent evolution of protein sequences
Benner, SA; Cohen, MA; Gonnet, GH
Prot. Eng. 7 (11) 1323-1332 (1994)
<Abstract>

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Predicting protein crystal-structures
Benner, SA; Gerloff, DL; Jenny, TF
Science 265 (5179) 1642-1644 (1994)

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Guanosine derivatives bearing an N2-3-imidazolepropionic acid
Heeb, NV; Benner, SA
Tet. Lett. 35 (19) 3045-3048 (1994)
<Abstract>

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Expanding the genetic lexicon: incorporating non-standard amino acids into proteins by ribosome-based synthesis
Benner, SA
Trends Biotech. 12 (5) 158-163 (1994)
<Abstract>

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A secondary structure prediction of the hemorrhagic metalloprotease family
Gerloff, DL; Jenny, TF; Knecht, LJ; Benner, SA
Biochem. Biophys. Res. Comm. 194 (1) 560-565 (1993)

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Enzymatic recognition of the base pair between isocytidine and isoguanosine
Switzer, CY; Moroney, SE; Benner, SA
Biochemistry 32 (39) 10489-10496 (1993)
<Abstract>

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A word in your protein (reprinted from nature, vol 361, pg 12, 1993)
Gonnet, GH; Benner, SA
Chem. Tech. 23 (3) 66-66 (1993)

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The nitrogenase MoFe protein - a secondary structure prediction
Gerloff, DL; Jenny, TF; Knecht, LJ; Gonnet, GH; Benner, SA
FEBS Lett. 318 (2) 118-124 (1993)
<Abstract>

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Predicting the conformation of proteins - man versus machine
Benner, SA; Gerloff, DL
FEBS Lett. 325 29-33 (1993)
<Abstract>

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The donor-acceptor-acceptor purine analog: Transformation of 5-aza-7-deaza-1H-isoguanine (= 4-aminoimidazo-[1,2-a]-1,3,5-triazin-2(1H)-one) to 2'-deoxy-5-aza-7-deaza-isoguanosine using purine nucleoside phosphorylase
Voegel, JJ; Altorfer, MM; Benner, SA
Helv. Chim. Acta 76 (5) 2061-2069 (1993)
<Abstract>

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Determination of the absolute-configuration of dimethyl (2S,3S)-2-allyl-3-hydroxyglutarate - a chiral building-block for preparing branched-chain nucleoside analogs
Arslan, T; Herradon, B; Schweizer, BW; Benner, SA
Helv. Chim. Acta 76 (8) 2969-2975 (1993)
<Abstract>

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Carbocyclic analogs of nucleosides .4. preparation of enantiomerically pure analogs of purine nucleosides for the synthesis of sulfone-linked oligonucleotide analogs
Jenny, TF; Benner, SA
Helv. Chim. Acta 76 (2) 826-841 (1993)
<Abstract>

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Biscyclophanes .2. Regioselectivity in the acid-catalyzed cycloalkylation of benzylbenzylic alcohol (BBA)
Lee, WY; Sim, WB; Kim, HJ; Yoon, SH
J. Chem. Soc., Perkin Trans. 1 (6) 719-729 (1993)
<Abstract>

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Empirical and structural models for insertions and deletions in the divergent evolution of proteins
Benner, SA; Cohen, MA; Gonnet, GH
J. Mol. Biol. 229 (4) 1065-1082 (1993)

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Predicted secondary structure for the src homology 3 domain
Benner, SA; Cohen, MA; Gerloff, D
J. Mol. Biol. 229 (2) 295-305 (1993)

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Reduction of 2-substituted 3-oxoglutarates mediated by baker's yeast. Variation in enantioselectivity without corresponding variation in diastereoselectivity
Arslan, T; Benner, SA
J. Org. Chem. 58 (8) 2260-2264 (1993)
<Abstract>

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Synthesis and tautomeric equilibrium of 6-amino-5-benzyl-3-methylpyrazin-2-one - an acceptor-donor-donor nucleoside base analog
Voegel, JJ; Vonkrosigk, U; Benner, SA
J. Org. Chem. 58 (26) 7542-7547 (1993)
<Abstract>

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A word in your protein
Gonnet, GH; Benner, SA
Nature 361 (6408) 121-121 (1993)

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Synthesis, structure and activity of artificial, rationally designed catalytic polypeptides
Johnsson, K; Allemann, RK; Widmer, H; Benner, SA
Nature 365 (6446) 530-532 (1993)
<Abstract>

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Reading the palimpsest: Contemporary biochemical data and the RNA world
Benner, SA; Cohen, MA; Gonnet, GH; Berkowitz, DB; Johnsson, KP
The RNA World , ed. Raymond F. Gesteland, Thomas R. Cech, and John F. Atkins , Cold Spring Harbor Laboratory Press 27-70 (1993)

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Catalysis: design versus selection
Benner, SA
Science 261 (5127) 1402-1403 (1993)

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Selective protection and deprotection procedures for thiol and hydroxyl groups
Huang, Z; Benner, SA
SynLett (1) 83-84 (1993)
<Abstract>

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Evolutionary guidance in biological chemistry
Benner, SA
Biochemistry 31 (7) 2188-2188 (1992)

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MULTIDOMAIN BINDING OF TRANSFORMING GROWTH FACTOR-ALPHA TO THE EPIDERMAL GROWTH-FACTOR RECEPTOR
Richter, A; Conlan, JW; Ward, ME; Chamberlin, SG; Alexander, P; Richards, NGJ; Davies, DE
Biochemistry 31 (40) 9546-9554 (1992)
<Abstract>

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Carbocyclic analogs of nucleosides .2. synthesis of 2',3'-dideoxy-5'-homonucleoside analogs
Jenny, TF; Horlacher, J; Previsani, N; Benner, SA
Helv. Chim. Acta 75 (6) 1944-1954 (1992)
<Abstract>

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OXYGENATION OF COBALT(II)-SUBSTITUTED LIMULUS-POLYPHEMUS HEMOCYANIN - KINETICS, CD, AND MCD STUDIES
Larrabee, JA; Baumann, TF; Chisdes, SJ; Lyons, TJ
Inorg. Chem. 31 (17) 3630-3635 (1992)
<Abstract>

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A biomimetic biotechnological process for converting starch to fructose - thermodynamic and evolutionary considerations in applied enzymology
Moradian, A; Benner, SA
J. Am. Chem. Soc. 114 (18) 6980-6987 (1992)
<Abstract>

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Ribosome-mediated incorporation of a nonstandard amino-acid into a peptide through expansion of the genetic-code
Bain, JD; Switzer, C; Chamberlin, AR; Benner, SA
Nature 356 (6369) 537-539 (1992)
<Abstract>

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Correct structure prediction
Benner, SA; Cohen, MA; Gerloff, D
Nature 359 (6398) 781-781 (1992)

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N2-isobutyrl-O6-[2-(para-nitrophenyl)ethyl]guanine: A new building block for the efficient synthesis of carbocyclic guanosine analogs
Jenny, TF; Schneider, KC; Benner, SA
Nucl. Nucl. 11 (6) 1257-1261 (1992)
<Abstract>

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Exhaustive matching of the entire protein sequence database
Gonnet, GH; Cohen, MA; Benner, SA
Science 256 (5062) 1443-1445 (1992)
<Abstract>

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Computer-speed and sequence comparison - response
Benner, SA; Cohen, MA; Gonnet, GH
Science 257 (5077) 1609-1610 (1992)

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Efficient regioselective synthesis of guanosine analogs
Jenny, TF; Benner, SA
Tet. Lett. 33 (44) 6619-6620 (1992)
<Abstract>

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A C-nucleotide base pair - methylpseudouridine-directed incorporation of formycin triphosphate into RNA catalyzed by T7 RNA-polymerase
Piccirilli, JA; Moroney, SE; Benner, SA
Biochemistry 30 (42) 10350-10356 (1991)
<Abstract>

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Site-directed mutagenesis of bovine pancreatic ribonuclease: lysine-41 and aspartate-121
Trautwein, K; Holliger, P; Stackhouse, J; Benner, SA
FEBS Lett. 281 275-277 (1991)
<Abstract>

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A direct route to 3-(D-ribofuranosyl)pyridine nucleosides
Piccirilli, JA; Krauch, T; Macpherson, LJ; Benner, SA
Helv. Chim. Acta 74 (2) 397-406 (1991)
<Abstract>

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Building blocks for oligonucleotide analogs with dimethylene-sulfide, -sulfoxide, and -sulfone groups replacing phosphodiester linkages
Huang, Z; Schneider, KC; Benner, SA
J. Org. Chem. 56 (12) 3869-3882 (1991)
<Abstract>

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Synthesis of RNA containing inosine - analysis of the sequence requirements for the 5' splice site of the tetrahymena group-I intron
Green, R; Szostak, JW; Benner, SA; Rich, A; Usman, N
Nucl. Acids Res. 19 (15) 4161-4166 (1991)
<Abstract>

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Structural determinants of stereospecificity in yeast alcohol dehydrogenase
Weinhold, EG; Glasfeld, A; Ellington, AD; Benner, SA
Proc. Natl. Acad. Sci. USA 88 (19) 8420-8424 (1991)
<Abstract>

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A hybrid of bovine pancreatic ribonuclease and human angiogenin: an external loop as a module controlling substrate-specificity?
Allemann, RK; Presnell, SR; Benner, SA
Prot. Eng. 4 (7) 831-835 (1991)
<Abstract>

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RNA world
Benner, SA; Ellington, AD
Science 252 (5010) 1232-1232 (1991)

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Carbocyclic analogs of nucleosides via modified Mitsunobu reactions
Jenny, TF; Previsani, N; Benner, SA
Tet. Lett. 32 (48) 7029-7032 (1991)
<Abstract>

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The ribonuclease from an extinct bovid ruminant
Stackhouse, J; Presnell, SR; Mcgeehan, GM; Nambiar, KP; Benner, SA
FEBS Lett. 262 (1) 104-106 (1990)

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Interferon-&#947; activates the cleavage of double-stranded RNA by bovine seminal ribonuclease
Schein, CH; Haugg, M; Benner, SA
FEBS Lett. 270 229-232 (1990)

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Oligonucleotides containing flexible nucleoside analogs
Schneider, KC; Benner, SA
J. Am. Chem. Soc. 112 (1) 453-455 (1990)

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Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet
Piccirilli, JA; Krauch, T; Moroney, SE; Benner, SA
Nature 343 (6253) 33-37 (1990)

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Progenote or protogenote
Benner, SA; Ellington, AD
Science 248 (4958) 943-944 (1990)

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Building-blocks for oligonucleotide analogs with dimethylene-sulfide, dimethylene-sulfoxide, and dimethylene-sulfone groups replacing phosphodiester linkages
Schneider, KC; Benner, SA
Tet. Lett. 31 (3) 335-338 (1990)

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Enzyme kinetics and molecular evolution
Benner, SA
Chem. Rev. 89 (4) 789-806 (1989)

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The stereospecificity of the ferrous-ion-dependent alcohol-dehydrogenase from zymomonas-mobilis
Glasfeld, A; Benner, SA
Euro. J. Biochem. 180 (2) 373-375 (1989)

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An improved system for expressing pancreatic ribonuclease in <i>Escherichia coli</i>
Mcgeehan, GM; Benner, SA
FEBS Lett. 247 (1) 55-56 (1989)

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Enzymatic incorporation of a new base pair into DNA and RNA
Switzer, C; Moroney, SE; Benner, SA
J. Am. Chem. Soc. 111 (21) 8322-8323 (1989)

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Modern metabolism as a palimpsest of the RNA world
Benner, SA; Ellington, AD; Tauer, A
Proc. Natl. Acad. Sci. USA 86 (18) 7054-7058 (1989)

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The return of pancreatic ribonucleases
Benner, SA; Allemann, RK
Trends Biochem. Sci. 14 (10) 396-397 (1989)

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Stereospecificity in enzymology - its place in evolution
Benner, SA; Glasfeld, A; Piccirilli, JA
Topics Stereochem. 19 (3) 127-207 (1989)

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Extracellular 'communicator RNA'
Benner, SA
FEBS Lett. 233 (2) 225-228 (1988)

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Crystal-structures of 2 simple n-substituted dihydronicotinamides - possible implications for stereoelectronic arguments in enzymology
Glasfeld, A; Zbinden, P; Dobler, M; Benner, SA; Dunitz, JD
J. Am. Chem. Soc. 110 (15) 5152-5157 (1988)

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Stereochemical profile of the dehydrogenases of <i>Drosophila melanogaster</i>
Allemann, RK; Hung, R; Benner, SA
J. Am. Chem. Soc. 110 (16) 5555-5560 (1988)

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The design of synthetic genes
Presnell, SR; Benner, SA
Nucl. Acids Res. 16 (5) 1693-1702 (1988)

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Return of the 'last ribo-organism'
Benner, SA; Ellington, AD
Nature 332 (6166) 688-689 (1988)

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Interpreting the behavior of enzymes. Purpose or pedigree?
Benner, S. A., Ellington, A. D
Crit. Rev. Biochem. Mol. Biol. (1988) 23, 369-426

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Redesigning life - organic-chemistry and the evolving protein
Benner, SA
Chimia 41 (5) 142-148 (1987)

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Natural selection, protein engineering, and the last riboorganism: Rational model building in biochemistry
Benner, SA; Allemann, RK; Ellington, AD; Ge, L; Glasfeld, A; Leanz, GF; Krauch, T; Macpherson, LJ; Moroney, S; Piccirilli, JA; Weinhold, E
Cold Spring Harb. Symp. Quant. Biol. 52 (2) 53-63 (1987)

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Expression of bovine pancreatic ribonuclease A in <i>Escherichia-coli</i>
Nambiar, KP; Stackhouse, J; Presnell, SR; Benner, SA
Euro. J. Biochem. 163 (1) 67-71 (1987)

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The stereospecificity of oxaloacetate decarboxylase - a stereochemical imperative
Piccirilli, JA; Rozzell, JD; Benner, SA
J. Am. Chem. Soc. 109 (26) 8084-8085 (1987)

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Free energy differences between enzyme bound states
Ellington, AD; Benner, SA
J. Theoret. Biol. 127 (4) 491-506 (1987)

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The last ribo-organism
Benner, SA; Ellington, AD
Nature 329 (6137) 295-296 (1987)

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Evolution guidance - engineering alcohol-dehydrogenase and ribonuclease
Weinhold, EG; Ellington, A; Presnell, SR; Mcgeehan, GM; Benner, SA
Prot. Eng. 1 (3) 236-237 (1987)

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Benner's model - a successful prediction
Benner, SA
Chem. Eng. News 64 (4) 3-3 (1986)

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Body-temperature and the specific-heat of water
Dunitz, JD; Benner, SA
Nature 324 (6096) 418-418 (1986)

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Dynamic transduction of energy and internal equilibria in enzymes: A reexamination of pyruvate kinase
Stackhouse, J; Nambiar, KP; Burbaum, JJ; Stauffer, DM; Benner, SA
J. Am. Chem. Soc. 107 (9) 2757-2763 (1985)

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Total synthesis and cloning of a gene coding for the ribonuclease-s protein
Nambiar, KP; Stackhouse, J; Stauffer, DM; Kennedy, WP; Eldredge, JK; Benner, SA
Science 223 (4642) 1299-1301 (1984)

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A mechanistic basis for the stereoselectivity of enzymatic transfer of hydrogen from nicotinamide cofactors
Nambiar, KP; Stauffer, DM; Kolodziej, PA; Benner, SA
J. Am. Chem. Soc. 105 (18) 5886-5890 (1983)

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Analogs for acetoacetate as an enzyme substrate - stereochemical preferences
Benner, SA; Morton, TH
J. Am. Chem. Soc. 103 (4) 991-993 (1981)

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Stereospecificity and stereochemical infidelity of acetoacetate decarboxylase (AAD)
Benner, SA; Rozzell, JD; Morton, TH
J. Am. Chem. Soc. 103 (4) 993-994 (1981)

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Mechanism of the reaction of diphenylphosphinodithioic acid with nitriles
Benner, SA
Tet. Lett. 22 (20) 1855-1858 (1981)

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Preparation of an ecdysone immunogen for radioimmunoassay work
Hung, DT; Benner, SA; Williams, CM
J. Biol. Chem. 255 (13) 6047-6048 (1980)

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The Tricarboxylic Acid Cycle
Steven Benner
Yale Scientific (1976) 50 (7), 4-10, 34-36

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Asymmetry in organic chemistry. A left-handed molecule looks at the world.
Steven Benner
Yale Scientific (1976) 50 (February), 16-20

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Sailing from Genoa.
Steven Benner
Yale Scientific (1976) 50 (7), 2-3

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Enzyme mechanism
Steven Benner
Yale Scientific (1975) 49 (October), 4-8

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The Sahel famine. A crisis of technology misuse.
Steven Benner
Yale Scientific (1975) 49, 2-20

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Energy crisis
Steven Benner
Yale Scientific (1974) 48 (4), 10-15

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