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Steven Benner's Publications

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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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Adsorption of RNA on mineral surfaces and mineral precipitates
Elisa Biondi, Yoshihiro Furukawa, Jun Kawai, and Steven A. Benner
Beilstein J. Org. Chem. , Beilstein Institute (2017) 13, 393-404
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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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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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A Single Deoxynucleoside Kinase Variant from Drosophila melanogaster Synthesizes Monophosphates of Nucleosides That Are Components of an Expanded Genetic System
Mariko F. Matsuura, Christian B. Winiger, Ryan W. Shaw, Myong-Jung Kim, Myong-Sang Kim, Ashley B. Daugherty, Fei Chen, Patricia Moussatche, Jennifer D. Moses, Stefan Lutz, and Steven A. Benner
ACS Synthetic Biology , American Chemical Society (2016) DOI: 10.1021/acssynbio.6b00228
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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)
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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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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)
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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)
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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)
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Synthetic biology
Sismour, AM; Benner, SA
Expert Opin. Biol. Ther. 5 (11) 1409-1414 (2005)
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Planetary systems biology
Benner, SA; Ricardo, A
Mol. Cell 17 (4) 471-472 (2005)
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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)
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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)
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Synthetic Biology
Sismour, AM; Benner, SA
Nat. Rev. Genet. 6 533-543 (2005)
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Understanding nucleic acids using synthetic chemistry
Benner, SA
Acc. Chem. Res. 37 (10) 784-797 (2004)
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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Catalysis: The omnipresent phenomenon.
Benner, SA
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)
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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)
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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)
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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)
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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)
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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)
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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)
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Reconstructing ancient forms of life
Benner, SA
J. Cell. Biol. (19) 200-200 (1995)

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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)
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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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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)
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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)
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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)
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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)
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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)
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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)
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The phospho-&#946;-galactosidase and synaptotagmin predictions
Benner, SA; Gerloff, D; Chelvanayagam, G
Proteins 23 (3) 446-453 (1995)
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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)
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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)
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Evaluating predictions of secondary structure in proteins
Jenny, TF; Benner, SA
Biochem. Biophys. Res. Comm. 200 (1) 149-155 (1994)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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Predicting the conformation of proteins - man versus machine
Benner, SA; Gerloff, DL
FEBS Lett. 325 29-33 (1993)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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Evolutionary guidance in biological chemistry
Benner, SA
Biochemistry 31 (7) 2188-2188 (1992)

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