Steven A. Benner - Publications

Affiliations: 
Chemistry University of Florida, Gainesville, Gainesville, FL, United States 
Area:
"synthetic biology"
Website:
http://www.ffame.org/sbenner.php

230 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Benner SA, Kim HJ, Biondi E. Prebiotic Chemistry that Could Not Have Happened. Life (Basel, Switzerland). 9. PMID 31739415 DOI: 10.3390/life9040084  0.44
2019 Zhang L, Wang S, Yang Z, Hoshika S, Xie S, Li J, Chen X, Wan S, Li L, Benner SA, Tan W. An Aptamer-Nanotrain Assembled from 6-Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells. Angewandte Chemie (International Ed. in English). PMID 31650689 DOI: 10.1002/anie.201909691  0.76
2019 Glushakova LG, Alto BW, Kim MS, Hutter D, Bradley A, Bradley KM, Burkett-Cadena ND, Benner SA. Multiplexed kit based on Luminex technology and achievements in synthetic biology discriminates Zika, chikungunya, and dengue viruses in mosquitoes. Bmc Infectious Diseases. 19: 418. PMID 31088375 DOI: 10.1186/s12879-019-3998-z  0.52
2019 Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins NE, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia J, Georgiadis MM, ... Benner SA, et al. Hachimoji DNA and RNA: A genetic system with eight building blocks. Science (New York, N.Y.). 363: 884-887. PMID 30792304 DOI: 10.1126/science.aat0971  0.84
2018 Ziegler EW, Kim HJ, Benner SA. Molybdenum(VI)-Catalyzed Rearrangement of Prebiotic Carbohydrates in Formamide, a Candidate Prebiotic Solvent. Astrobiology. 18: 1159-1170. PMID 30204496 DOI: 10.1089/ast.2017.1742  0.44
2018 Hoshika S, Singh I, Switzer C, Molt RW, Leal NA, Kim MJ, Kim MS, Kim HJ, Georgiadis MM, Benner SA. "Skinny" and "Fat" DNA: Two New Double Helices. Journal of the American Chemical Society. PMID 30148365 DOI: 10.1021/jacs.8b05042  0.52
2018 Singh I, Laos R, Hoshika S, Benner SA, Georgiadis MM. Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide. Nucleic Acids Research. PMID 29986111 DOI: 10.1093/nar/gky552  0.44
2018 Yang Z, Kim HJ, Le JT, McLendon C, Bradley KM, Kim MS, Hutter D, Hoshika S, Yaren O, Benner SA. Nucleoside analogs to manage sequence divergence in nucleic acid amplification and SNP detection. Nucleic Acids Research. PMID 29800323 DOI: 10.1093/nar/gky392  0.76
2018 Koirala D, Shelke SA, Dupont M, Ruiz S, DasGupta S, Bailey LJ, Benner SA, Piccirilli JA. Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography. Nucleic Acids Research. PMID 29309709 DOI: 10.1093/nar/gkx1292  0.84
2017 Kim HJ, Benner SA. A Direct Prebiotic Synthesis of Nicotinamide Nucleotide. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 29194806 DOI: 10.1002/chem.201705394  0.44
2017 Kim HJ, Benner SA. Prebiotic stereoselective synthesis of purine and noncanonical pyrimidine nucleotide from nucleobases and phosphorylated carbohydrates. Proceedings of the National Academy of Sciences of the United States of America. 114: 11315-11320. PMID 29073050 DOI: 10.1073/pnas.1710778114  0.44
2017 Singh I, Kim MJ, Molt RW, Hoshika S, Benner SA, Georgiadis MM. Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K). Acs Synthetic Biology. PMID 28752992 DOI: 10.1021/acssynbio.7b00150  0.44
2017 Yaren O, Alto BW, Gangodkar PV, Ranade SR, Patil KN, Bradley KM, Yang Z, Phadke N, Benner SA. Point of sampling detection of Zika virus within a multiplexed kit capable of detecting dengue and chikungunya. Bmc Infectious Diseases. 17: 293. PMID 28427352 DOI: 10.1186/s12879-017-2382-0  0.76
2017 Chen F, Zhang Y, Daugherty AB, Yang Z, Shaw R, Dong M, Lutz S, Benner SA. Biological phosphorylation of an Unnatural Base Pair (UBP) using a Drosophila melanogaster deoxynucleoside kinase (DmdNK) mutant. Plos One. 12: e0174163. PMID 28323896 DOI: 10.1371/journal.pone.0174163  1
2017 Wang X, Hoshika S, Peterson RJ, Kim MJ, Benner SA, Kahn JD. The 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). Acs Synthetic Biology. PMID 28094993 DOI: 10.1021/acssynbio.6b00224  0.44
2016 Matsuura MF, Winiger CB, Shaw RW, Kim MJ, Kim MS, Daugherty AB, Chen F, Moussatche P, Moses JD, Lutz S, Benner SA. A Single Deoxynucleoside Kinase Variant from Drosophila melanogaster Synthesizes Monophosphates of Nucleosides That Are Components of an Expanded Genetic System. Acs Synthetic Biology. PMID 27935283 DOI: 10.1021/acssynbio.6b00228  1
2016 Matsuura MF, Kim HJ, Takahashi D, Abboud KA, Benner SA. Crystal structures of deprotonated nucleobases from an expanded DNA alphabet. Acta Crystallographica. Section C, Structural Chemistry. 72: 952-959. PMID 27918296 DOI: 10.1107/S2053229616017071  0.44
2016 Kim HJ, Furukawa Y, Kakegawa T, Bita A, Scorei R, Benner SA. Evaporite Borate-Containing Mineral Ensembles Make Phosphate Available and Regiospecifically Phosphorylate Ribonucleosides: Borate as a Multifaceted Problem Solver in Prebiotic Chemistry. Angewandte Chemie (International Ed. in English). PMID 27862722 DOI: 10.1002/anie.201608001  0.44
2016 Biondi E, Lane JD, Das D, Dasgupta S, Piccirilli JA, Hoshika S, Bradley KM, Krantz BA, Benner SA. Laboratory evolution of artificially expanded DNA gives redesignable aptamers that target the toxic form of anthrax protective antigen. Nucleic Acids Research. PMID 27701076 DOI: 10.1093/nar/gkw890  0.84
2016 Benner SA, Karalkar NB, Hoshika S, Laos R, Shaw RW, Matsuura M, Fajardo D, Moussatche P. Alternative Watson-Crick Synthetic Genetic Systems. Cold Spring Harbor Perspectives in Biology. PMID 27663774 DOI: 10.1101/cshperspect.a023770  0.44
2016 Winiger CB, Shaw RW, Kim MJ, Moses JD, Matsuura MF, Benner SA. Expanded Genetic Alphabets. Managing Nucleotides that Lack Tautomeric, Protonated, or Deprotonated Versions Complementary to Natural Nucleotides. Acs Synthetic Biology. PMID 27648724 DOI: 10.1021/acssynbio.6b00193  0.44
2016 Zhang L, Yang Z, Le Trinh T, Teng IT, Wang S, Bradley KM, Hoshika S, Wu Q, Cansiz S, Rowold DJ, McLendon C, Kim MS, Wu Y, Cui C, Liu Y, ... ... Benner SA, et al. Aptamers against Cells Overexpressing Glypican 3 from Expanded Genetic Systems Combined with Cell Engineering and Laboratory Evolution. Angewandte Chemie (International Ed. in English). PMID 27601357 DOI: 10.1002/anie.201605058  1
2016 Yaren O, Bradley KM, Moussatche P, Hoshika S, Yang Z, Zhu S, Karst SM, Benner SA. A Norovirus Detection Architecture Based on Isothermal Amplification and Expanded Genetic Systems. Journal of Virological Methods. PMID 27546345 DOI: 10.1016/j.jviromet.2016.08.012  0.76
2016 Yaren O, Glushakova LG, Bradley KM, Hoshika S, Benner SA. Standard and AEGIS nicking molecular beacons detect amplicons from the Middle East respiratory syndrome coronavirus. Journal of Virological Methods. 236: 54-61. PMID 27421627 DOI: 10.1016/j.jviromet.2016.07.008  0.36
2016 Winiger CB, Kim MJ, Hoshika S, Shaw RW, Moses JD, Matsuura MF, Gerloff DL, Benner SA. Polymerase Interactions with Wobble Mismatches in Synthetic Genetic Systems and their Evolutionary Implications. Biochemistry. PMID 27347689 DOI: 10.1021/acs.biochem.6b00533  0.44
2016 Karalkar NB, Leal NA, Kim MS, Bradley KM, Benner SA. Synthesis and Enzymology of 2'-Deoxy-7-deazaisoguanosine Triphosphate and Its Complement: A Second Generation Pair in an Artificially Expanded Genetic Information System. Acs Synthetic Biology. PMID 26914388 DOI: 10.1021/acssynbio.5b00276  0.52
2016 Matsuura MF, Shaw RW, Moses JD, Kim HJ, Kim MJ, Kim MS, Hoshika S, Karalkar N, Benner SA. Assays To Detect the Formation of Triphosphates of Unnatural Nucleotides: Application to Escherichia coli Nucleoside Diphosphate Kinase. Acs Synthetic Biology. PMID 26829203 DOI: 10.1021/acssynbio.5b00172  0.44
2015 Scharf C, Virgo N, Cleaves HJ, Aono M, Aubert-Kato N, Aydinoglu A, Barahona A, Barge LM, Benner SA, Biehl M, Brasser R, Butch CJ, Chandru K, Cronin L, Danielache S, et al. A Strategy for Origins of Life Research. Astrobiology. 15: 1031-42. PMID 26684503 DOI: 10.1089/ast.2015.1113  1
2015 Glushakova LG, Sharma N, Hoshika S, Bradley AC, Bradley KM, Yang Z, Benner SA. Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA. Analytical Biochemistry. 489: 62-72. PMID 26299645 DOI: 10.1016/j.ab.2015.08.015  0.76
2015 Hernandez AR, Shao Y, Hoshika S, Yang Z, Shelke SA, Herrou J, Kim HJ, Kim MJ, Piccirilli JA, Benner SA. A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair. Angewandte Chemie (International Ed. in English). PMID 26223188 DOI: 10.1002/anie.201504731  1
2015 Zhang L, Yang Z, Sefah K, Bradley KM, Hoshika S, Kim MJ, Kim HJ, Zhu G, Jiménez E, Cansiz S, Teng IT, Champanhac C, McLendon C, Liu C, Zhang W, ... ... Benner SA, et al. Evolution of functional six-nucleotide DNA. Journal of the American Chemical Society. 137: 6734-7. PMID 25966323 DOI: 10.1021/jacs.5b02251  1
2015 Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner SA, Richards NG. Structural basis for a six nucleotide genetic alphabet. Journal of the American Chemical Society. 137: 6947-55. PMID 25961938 DOI: 10.1021/jacs.5b03482  0.44
2015 Yang Z, McLendon C, Hutter D, Bradley KM, Hoshika S, Frye CB, Benner SA. Helicase-Dependent Isothermal Amplification of DNA and RNA by Using Self-Avoiding Molecular Recognition Systems. Chembiochem : a European Journal of Chemical Biology. 16: 1365-70. PMID 25953623 DOI: 10.1002/cbic.201500135  1
2015 Kim HJ, Benner SA. Prebiotic glycosylation of uracil with electron-donating substituents. Astrobiology. 15: 301-6. PMID 25860300 DOI: 10.1089/ast.2014.1264  1
2015 Furukawa Y, Kim HJ, Hutter D, Benner SA. Abiotic regioselective phosphorylation of adenosine with borate in formamide. Astrobiology. 15: 259-67. PMID 25826074 DOI: 10.1089/ast.2014.1209  1
2015 McLendon C, Opalko FJ, Illangkoon HI, Benner SA. Solubility of polyethers in hydrocarbons at low temperatures. A model for potential genetic backbones on warm titans. Astrobiology. 15: 200-6. PMID 25761113 DOI: 10.1089/ast.2014.1212  1
2015 Glushakova LG, Bradley A, Bradley KM, Alto BW, Hoshika S, Hutter D, Sharma N, Yang Z, Kim MJ, Benner SA. High-throughput multiplexed xMAP Luminex array panel for detection of twenty two medically important mosquito-borne arboviruses based on innovations in synthetic biology. Journal of Virological Methods. 214: 60-74. PMID 25680538 DOI: 10.1016/j.jviromet.2015.01.003  0.76
2015 Carrigan MA, Uryasev O, Frye CB, Eckman BL, Myers CR, Hurley TD, Benner SA. Hominids adapted to metabolize ethanol long before human-directed fermentation. Proceedings of the National Academy of Sciences of the United States of America. 112: 458-63. PMID 25453080 DOI: 10.1073/pnas.1404167111  0.88
2015 Leal NA, Kim HJ, Hoshika S, Kim MJ, Carrigan MA, Benner SA. Transcription, reverse transcription, and analysis of RNA containing artificial genetic components. Acs Synthetic Biology. 4: 407-13. PMID 25137127 DOI: 10.1021/sb500268n  0.88
2015 Benner SA, Kim HJ, Merritt KB, Yang Z, McLendon DC, Hoshika S, Hutter D. Next-generation DNA in pathogen detection, surveillance, and CLIA-waivable diagnostics Proceedings of Spie - the International Society For Optical Engineering. 9490. DOI: 10.1117/12.2183481  1
2015 Glushakova LG, Sharma N, Hoshika S, Bradley AC, Bradley KM, Yang Z, Benner SA. Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA Analytical Biochemistry. 489: 62-72. DOI: 10.1016/j.ab.2015.08.015  1
2014 Benner SA. Paradoxes in the origin of life. Origins of Life and Evolution of the Biosphere : the Journal of the International Society For the Study of the Origin of Life. 44: 339-43. PMID 25608919 DOI: 10.1007/s11084-014-9379-0  1
2014 Laos R, Thomson JM, Benner SA. DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides. Frontiers in Microbiology. 5: 565. PMID 25400626 DOI: 10.3389/fmicb.2014.00565  1
2014 Merritt KK, Bradley KM, Hutter D, Matsuura MF, Rowold DJ, Benner SA. Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance. Beilstein Journal of Organic Chemistry. 10: 2348-60. PMID 25383105 DOI: 10.3762/bjoc.10.245  1
2014 Sharma N, Hoshika S, Hutter D, Bradley KM, Benner SA. Recombinase-based isothermal amplification of nucleic acids with self-avoiding molecular recognition systems (SAMRS). Chembiochem : a European Journal of Chemical Biology. 15: 2268-74. PMID 25209570 DOI: 10.1002/cbic.201402250  1
2014 Bradley KM, Benner SA. 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. Beilstein Journal of Organic Chemistry. 10: 1826-33. PMID 25161743 DOI: 10.3762/bjoc.10.192  1
2014 Kim HJ, Leal NA, Hoshika S, Benner SA. Ribonucleosides for an artificially expanded genetic information system. The Journal of Organic Chemistry. 79: 3194-9. PMID 24597611 DOI: 10.1021/jo402665d  1
2014 Sefah K, Yang Z, Bradley KM, Hoshika S, Jiménez E, Zhang L, Zhu G, Shanker S, Yu F, Turek D, Tan W, Benner SA. In vitro selection with artificial expanded genetic information systems. Proceedings of the National Academy of Sciences of the United States of America. 111: 1449-54. PMID 24379378 DOI: 10.1073/pnas.1311778111  1
2013 Laos R, Shaw R, Leal NA, Gaucher E, Benner S. Directed evolution of polymerases to accept nucleotides with nonstandard hydrogen bond patterns. Biochemistry. 52: 5288-94. PMID 23815560 DOI: 10.1021/bi400558c  1
2013 Benner SA, Bains W, Seager S. Models and standards of proof in cross-disciplinary science: the case of arsenic DNA. Astrobiology. 13: 510-3. PMID 23634974 DOI: 10.1089/ast.2012.0954  1
2013 Neveu M, Kim HJ, Benner SA. The "strong" RNA world hypothesis: fifty years old. Astrobiology. 13: 391-403. PMID 23551238 DOI: 10.1089/ast.2012.0868  1
2013 Yang Z, Durante M, Glushakova LG, Sharma N, Leal NA, Bradley KM, Chen F, Benner SA. Conversion strategy using an expanded genetic alphabet to assay nucleic acids. Analytical Chemistry. 85: 4705-12. PMID 23541235 DOI: 10.1021/ac400422r  1
2012 Benner SA. Aesthetics in synthesis and synthetic biology. Current Opinion in Chemical Biology. 16: 581-5. PMID 23196149 DOI: 10.1016/j.cbpa.2012.11.004  1
2012 Carrigan MA, Uryasev O, Davis RP, Zhai L, Hurley TD, Benner SA. The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion. Plos One. 7: e41175. PMID 22859968 DOI: 10.1371/journal.pone.0041175  1
2012 Benner SA, Kim HJ, Carrigan MA. Asphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNA. Accounts of Chemical Research. 45: 2025-34. PMID 22455515 DOI: 10.1021/ar200332w  1
2012 Kim HJ, Chen F, Benner SA. Synthesis and properties of 5-cyano-substituted nucleoside analog with a donor-donor-acceptor hydrogen-bonding pattern. The Journal of Organic Chemistry. 77: 3664-9. PMID 22390337 DOI: 10.1021/jo300230z  1
2012 Blaby IK, Lyons BJ, Wroclawska-Hughes E, Phillips GC, Pyle TP, Chamberlin SG, Benner SA, Lyons TJ, Crécy-Lagard Vd, Crécy Ed. Experimental evolution of a facultative thermophile from a mesophilic ancestor. Applied and Environmental Microbiology. 78: 144-55. PMID 22020511 DOI: 10.1128/AEM.05773-11  1
2012 Benner SA, Kim HJ, Yang Z. Setting the stage: the history, chemistry, and geobiology behind RNA. Cold Spring Harbor Perspectives in Biology. 4: a003541. PMID 20880988 DOI: 10.1101/cshperspect.a003541  1
2012 Benner SA. Use of codon models in molecular dating and functional analysis Codon Evolution: Mechanisms and Models. DOI: 10.1093/acprof:osobl/9780199601165.003.0010  1
2011 Benner SA, Yang Z, Chen F. Synthetic Biology, Tinkering Biology, and Artificial Biology. What are We Learning? Comptes Rendus. Chimie (Print). 14: 372-387. PMID 29983697 DOI: 10.1016/j.crci.2010.06.013  0.76
2011 Yang Z, Chen F, Alvarado JB, Benner SA. Amplification, mutation, and sequencing of a six-letter synthetic genetic system. Journal of the American Chemical Society. 133: 15105-12. PMID 21842904 DOI: 10.1021/ja204910n  1
2011 Benner SA. Comment on "A bacterium that can grow by using arsenic instead of phosphorus". Science (New York, N.Y.). 332: 1149; author reply 1. PMID 21622712 DOI: 10.1126/science.1201304  1
2011 Kim HJ, Ricardo A, Illangkoon HI, Kim MJ, Carrigan MA, Frye F, Benner SA. Synthesis of carbohydrates in mineral-guided prebiotic cycles. Journal of the American Chemical Society. 133: 9457-68. PMID 21553892 DOI: 10.1021/ja201769f  1
2011 Chen F, Yang Z, Yan M, Alvarado JB, Wang G, Benner SA. Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity. Nucleic Acids Research. 39: 3949-61. PMID 21245035 DOI: 10.1093/nar/gkq1274  1
2011 Benner SA, Yang Z, Chen F. Synthetic biology, tinkering biology, and artificial biology. What are we learning? Comptes Rendus Chimie. 14: 372-387. DOI: 10.1016/j.crci.2010.06.013  1
2011 Benner SA, Chen F, Yang Z. Synthetic Biology, Tinkering Biology, and Artificial Biology: A Perspective from Chemistry Chemical Synthetic Biology. 69-106. DOI: 10.1002/9780470977873.ch3  1
2010 Benner SA. Defining life. Astrobiology. 10: 1021-30. PMID 21162682 DOI: 10.1089/ast.2010.0524  1
2010 Hutter D, Kim MJ, Karalkar N, Leal NA, Chen F, Guggenheim E, Visalakshi V, Olejnik J, Gordon S, Benner SA. Labeled nucleoside triphosphates with reversibly terminating aminoalkoxyl groups. Nucleosides, Nucleotides & Nucleic Acids. 29: 879-95. PMID 21128174 DOI: 10.1080/15257770.2010.536191  1
2010 Kim HJ, Benner SA. Comment on "The silicate-mediated formose reaction: bottom-up synthesis of sugar silicates". Science (New York, N.Y.). 329: 902; author reply 90. PMID 20724620 DOI: 10.1126/science.1188697  1
2010 Johnson RJ, Andrews P, Benner SA, Oliver W. Theodore E. Woodward award. The evolution of obesity: insights from the mid-Miocene. Transactions of the American Clinical and Climatological Association. 121: 295-305; discussion . PMID 20697570  1
2010 Benner SA. Q&A: Life, synthetic biology and risk. Bmc Biology. 8: 77. PMID 20594289 DOI: 10.1186/1741-7007-8-77  1
2010 Hoshika S, Chen F, Leal NA, Benner SA. Artificial genetic systems: self-avoiding DNA in PCR and multiplexed PCR. Angewandte Chemie (International Ed. in English). 49: 5554-7. PMID 20586087 DOI: 10.1002/anie.201001977  1
2010 Benner SA, Kim HJ, Kim MJ, Ricardo A. Planetary organic chemistry and the origins of biomolecules. Cold Spring Harbor Perspectives in Biology. 2: a003467. PMID 20504964 DOI: 10.1101/cshperspect.a003467  1
2010 Chen F, Gaucher EA, Leal NA, Hutter D, Havemann SA, Govindarajan S, Ortlund EA, Benner SA. Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection. Proceedings of the National Academy of Sciences of the United States of America. 107: 1948-53. PMID 20080675 DOI: 10.1073/pnas.0908463107  1
2010 Yang Z, Chen F, Chamberlin SG, Benner SA. Expanded genetic alphabets in the polymerase chain reaction. Angewandte Chemie (International Ed. in English). 49: 177-80. PMID 19946925 DOI: 10.1002/anie.200905173  1
2010 Benner SA. Chemistry, life, and the search for aliens Proceedings of Spie - the International Society For Optical Engineering. 7819. DOI: 10.1117/12.866981  1
2009 Wellington KW, Ooi HC, Benner SA. A convenient synthesis of N,N'-dibenzyl-2,4-diaminopyrimidine-2'-deoxyribonucleoside and 1-methyl-2'-deoxypseudoisocytidine. Nucleosides, Nucleotides & Nucleic Acids. 28: 275-91. PMID 20183581 DOI: 10.1080/15257770902946090  1
2009 Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, Vezenov DV. The challenges of sequencing by synthesis. Nature Biotechnology. 27: 1013-23. PMID 19898456 DOI: 10.1038/nbt.1585  1
2009 Kim HJ, Leal NA, Benner SA. 2'-deoxy-1-methylpseudocytidine, a stable analog of 2'-deoxy-5-methylisocytidine. Bioorganic & Medicinal Chemistry. 17: 3728-32. PMID 19394831 DOI: 10.1016/j.bmc.2009.03.047  1
2009 Davies PC, Benner SA, Cleland CE, Lineweaver CH, McKay CP, Wolfe-Simon F. Signatures of a shadow biosphere. Astrobiology. 9: 241-9. PMID 19292603 DOI: 10.1089/ast.2008.0251  1
2009 Johnson RJ, Sautin YY, Oliver WJ, Roncal C, Mu W, Gabriela Sanchez-Lozada L, Rodriguez-Iturbe B, Nakagawa T, Benner SA. Lessons from comparative physiology: could uric acid represent a physiologic alarm signal gone awry in western society? Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology. 179: 67-76. PMID 18649082 DOI: 10.1007/s00360-008-0291-7  1
2008 Sheng P, Yang Z, Kim Y, Wu Y, Tan W, Benner SA. Design of a novel molecular beacon: modification of the stem with artificially genetic alphabet. Chemical Communications (Cambridge, England). 5128-30. PMID 18956044 DOI: 10.1039/b811159f  1
2008 Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, Di Ventra M, Garaj S, Hibbs A, Huang X, Jovanovich SB, Krstic PS, Lindsay S, Ling XS, Mastrangelo CH, et al. The potential and challenges of nanopore sequencing. Nature Biotechnology. 26: 1146-53. PMID 18846088 DOI: 10.1038/nbt.1495  1
2008 Benner SA, Hoshika S, Sukeda M, Hutter D, Leal N, Yang Z, Chen F. Synthetic biology for improved personalized medicine. Nucleic Acids Symposium Series (2004). 243-4. PMID 18776344 DOI: 10.1093/nass/nrn123  1
2008 Hoshika S, Chen F, Leal NA, Benner SA. Self-Avoiding Molecular Recognition Systems (SAMRS). Nucleic Acids Symposium Series (2004). 129-30. PMID 18776287 DOI: 10.1093/nass/nrn066  1
2008 Borg LE, Des Marais DJ, Beaty DW, Aharonson O, Benner SA, Bogard DD, Bridges JC, Budney CJ, Calvin WN, Clark BC, Eigenbrode JL, Grady MM, Head JW, Hemming SR, Hinners NW, et al. Science priorities for Mars sample return Astrobiology. 8: 489-535. PMID 18688946 DOI: 10.1089/ast.2008.0759  1
2008 Johnson RJ, Gaucher EA, Sautin YY, Henderson GN, Angerhofer AJ, Benner SA. The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular disease. Medical Hypotheses. 71: 22-31. PMID 18331782 DOI: 10.1016/j.mehy.2008.01.017  1
2008 Havemann SA, Hoshika S, Hutter D, Benner SA. Incorporation of multiple sequential pseudothymidines by DNA polymerases and their impact on DNA duplex structure. Nucleosides, Nucleotides & Nucleic Acids. 27: 261-78. PMID 18260010 DOI: 10.1080/15257770701853679  1
2008 Kim HJ, Kim MJ, Karalkar N, Hutter D, Benner SA. Synthesis of pyrophosphates for in vitro selection of catalytic RNA molecules. Nucleosides, Nucleotides & Nucleic Acids. 27: 43-56. PMID 18188769 DOI: 10.1080/15257770701571867  1
2008 Sassi SO, Benner SA. The resurrection of ribonucleases from mammals: from ecology to medicine Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.003.0018  1
2008 Benner SA. The early days of paleogenetics: Connecting molecules to the planet Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.003.0001  1
2007 Johnson RJ, Segal MS, Sautin Y, Nakagawa T, Feig DI, Kang DH, Gersch MS, Benner S, Sánchez-Lozada LG. Potential role of sugar (fructose) in the epidemic of hypertension, obesity and the metabolic syndrome, diabetes, kidney disease, and cardiovascular disease. The American Journal of Clinical Nutrition. 86: 899-906. PMID 17921363  1
2007 Yang Z, Sismour AM, Sheng P, Puskar NL, Benner SA. Enzymatic incorporation of a third nucleobase pair. Nucleic Acids Research. 35: 4238-49. PMID 17576683 DOI: 10.1093/nar/gkm395  1
2007 Yang Z, Sismour AM, Benner SA. Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages. Nucleic Acids Research. 35: 3118-27. PMID 17452363 DOI: 10.1093/nar/gkm168  1
2007 Sassi SO, Braun EL, Benner SA. The evolution of seminal ribonuclease: pseudogene reactivation or multiple gene inactivation events? Molecular Biology and Evolution. 24: 1012-24. PMID 17267422 DOI: 10.1093/molbev/msm020  1
2007 Benner SA, Sassi SO, Gaucher EA. Molecular paleoscience: systems biology from the past. Advances in Enzymology and Related Areas of Molecular Biology. 75: 1-132, xi. PMID 17124866 DOI: 10.1002/9780471224464.ch1  1
2006 Ricardo A, Frye F, Carrigan MA, Tipton JD, Powell DH, Benner SA. 2-Hydroxymethylboronate as a reagent to detect carbohydrates: application to the analysis of the formose reaction. The Journal of Organic Chemistry. 71: 9503-5. PMID 17137382 DOI: 10.1021/jo061770h  1
2006 Yang Z, Hutter D, Sheng P, Sismour AM, Benner SA. Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern. Nucleic Acids Research. 34: 6095-101. PMID 17074747 DOI: 10.1093/nar/gkl633  1
2006 Wellington KW, Benner SA. A review: synthesis of aryl C-glycosides via the heck coupling reaction. Nucleosides, Nucleotides & Nucleic Acids. 25: 1309-33. PMID 17067955 DOI: 10.1080/15257770600917013  1
2006 Leal NA, Sukeda M, Benner SA. Dynamic assembly of primers on nucleic acid templates. Nucleic Acids Research. 34: 4702-10. PMID 16963776 DOI: 10.1093/nar/gkl625  1
2006 Li T, Chamberlin SG, Caraco MD, Liberles DA, Gaucher EA, Benner SA. Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics. Bmc Evolutionary Biology. 6: 25. PMID 16545144 DOI: 10.1186/1471-2148-6-25  1
2006 Gaucher EA, De Kee DW, Benner SA. Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family. Bmc Genomics. 7: 44. PMID 16522197 DOI: 10.1186/1471-2164-7-44  1
2006 Bradley ME, Benner SA. Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteins. Bmc Bioinformatics. 7: 89. PMID 16504077 DOI: 10.1186/1471-2105-7-89  1
2006 Wang L, Yang CJ, Medley CD, Benner SA, Tan W. Locked nucleic acid molecular beacons for intracellular mRNA monitoring Progress in Biomedical Optics and Imaging - Proceedings of Spie. 6095. DOI: 10.1117/12.644649  1
2005 Wang L, Yang CJ, Medley CD, Benner SA, Tan W. Locked nucleic acid molecular beacons. Journal of the American Chemical Society. 127: 15664-5. PMID 16277483 DOI: 10.1021/ja052498g  1
2005 Sismour AM, Benner SA. Synthetic biology. Expert Opinion On Biological Therapy. 5: 1409-14. PMID 16255644 DOI: 10.1517/14712598.5.11.1409  1
2005 Sismour AM, Benner SA. The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system. Nucleic Acids Research. 33: 5640-6. PMID 16192575 DOI: 10.1093/nar/gki873  1
2005 Li Q, Ricardo A, Benner SA, Winefordner JD, Powell DH. Desorption/ionization on porous silicon mass spectrometry studies on pentose-borate complexes. Analytical Chemistry. 77: 4503-8. PMID 16013866 DOI: 10.1021/ac050258d  1
2005 Benner SA, Sismour AM. Synthetic biology. Nature Reviews. Genetics. 6: 533-43. PMID 15995697 DOI: 10.1038/nrg1637  1
2005 Thomson JM, Gaucher EA, Burgan MF, De Kee DW, Li T, Aris JP, Benner SA. Resurrecting ancestral alcohol dehydrogenases from yeast. Nature Genetics. 37: 630-5. PMID 15864308 DOI: 10.1038/ng1553  1
2005 Bradley ME, Benner SA. Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example. Bmc Evolutionary Biology. 5: 22. PMID 15752422 DOI: 10.1186/1471-2148-5-22  1
2005 Benner SA, Ricardo A. Planetary systems biology. Molecular Cell. 17: 471-2. PMID 15721248 DOI: 10.1016/j.molcel.2005.02.005  1
2004 Benner SA, Ricardo A, Carrigan MA. Is there a common chemical model for life in the universe? Current Opinion in Chemical Biology. 8: 672-89. PMID 15556414 DOI: 10.1016/j.cbpa.2004.10.003  1
2004 Benner SA. Chemistry. Redesigning genetics. Science (New York, N.Y.). 306: 625-6. PMID 15499002 DOI: 10.1126/science.1101104  1
2004 Benner SA. Understanding nucleic acids using synthetic chemistry. Accounts of Chemical Research. 37: 784-97. PMID 15491125 DOI: 10.1021/ar040004z  1
2004 Carrigan MA, Ricardo A, Ang DN, Benner SA. Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection. Biochemistry. 43: 11446-59. PMID 15350131 DOI: 10.1021/bi049898l  1
2004 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, et al. Multiplexed genetic analysis using an expanded genetic alphabet. Clinical Chemistry. 50: 2019-27. PMID 15319316 DOI: 10.1373/clinchem.2004.034330  1
2004 Gaucher EA, Graddy LG, Li T, Simmen RC, Simmen FA, Schreiber DR, Liberles DA, Janis CM, Benner SA. The planetary biology of cytochrome P450 aromatases. Bmc Biology. 2: 19. PMID 15315709 DOI: 10.1186/1741-7007-2-19  1
2004 Chang MS, Benner SA. Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments. Journal of Molecular Biology. 341: 617-31. PMID 15276848 DOI: 10.1016/j.jmb.2004.05.045  1
2004 Martinot TA, Benner SA. Artificial genetic systems: exploiting the "aromaticity" formalism to improve the tautomeric ratio for isoguanosine derivatives. The Journal of Organic Chemistry. 69: 3972-5. PMID 15153036 DOI: 10.1021/jo0497959  1
2004 Hendrickson CL, Devine KG, Benner SA. Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosine. Nucleic Acids Research. 32: 2241-50. PMID 15107492 DOI: 10.1093/nar/gkh542  1
2004 Roychowdhury A, Illangkoon H, Hendrickson CL, Benner SA. 2'-deoxycytidines carrying amino and thiol functionality: synthesis and incorporation by Vent (exo-) polymerase. Organic Letters. 6: 489-92. PMID 14961605 DOI: 10.1021/ol0360290  1
2004 Sismour AM, Lutz S, Park JH, Lutz MJ, Boyer PL, Hughes SH, Benner SA. PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1. Nucleic Acids Research. 32: 728-35. PMID 14757837 DOI: 10.1093/nar/gkh241  1
2004 Ricardo A, Carrigan MA, Olcott AN, Benner SA. Borate minerals stabilize ribose. Science (New York, N.Y.). 303: 196. PMID 14716004 DOI: 10.1126/science.1092464  1
2003 Geyer CR, Battersby TR, Benner SA. Nucleobase pairing in expanded Watson-Crick-like genetic information systems. Structure (London, England : 1993). 11: 1485-98. PMID 14656433 DOI: 10.1016/j.str.2003.11.008  1
2003 Hutter D, Benner SA. Expanding the genetic alphabet: non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern. The Journal of Organic Chemistry. 68: 9839-42. PMID 14656120 DOI: 10.1021/jo034900k  1
2003 Des Marais DJ, 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, et al. The NASA Astrobiology Roadmap. Astrobiology. 3: 219-35. PMID 14577870 DOI: 10.1089/153110703769016299  1
2003 Benner SA, Hutter D, Sismour AM. Synthetic biology with artificially expanded genetic information systems. From personalized medicine to extraterrestrial life. Nucleic Acids Research. Supplement (2001). 125-6. PMID 14510412  1
2003 Gaucher EA, Thomson JM, Burgan MF, Benner SA. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature. 425: 285-8. PMID 13679914 DOI: 10.1038/nature01977  1
2003 Held HA, Roychowdhury A, Benner SA. C-5 modified nucleosides: direct insertion of alkynyl-thio functionality in pyrimidines. Nucleosides, Nucleotides & Nucleic Acids. 22: 391-404. PMID 12885121 DOI: 10.1081/NCN-120022030  1
2003 Benner SA. Interpretive proteomics--finding biological meaning in genome and proteome databases. Advances in Enzyme Regulation. 43: 271-359. PMID 12791396 DOI: 10.1016/S0065-2571(02)00024-9  1
2003 Gaucher EA, Miyamoto MM, Benner SA. Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein. Genetics. 163: 1549-53. PMID 12702697  1
2003 Benner SA. Synthetic biology: Act natural. Nature. 421: 118. PMID 12520282 DOI: 10.1038/421118a  1
2003 Eschgfäller B, Schmidt JG, König M, Benner SA. Synthesis and properties of oligodeoxynucleotide analogs with bis(methylene) sulfone bridges Helvetica Chimica Acta. 86: 2959-2997. DOI: 10.1002/hlca.200390244  1
2003 Schmidt J, Eschgfäller B, Benner SA. A direct synthesis of nucleoside analogs homologated at the 3′- and 5′-positions Helvetica Chimica Acta. 86: 2937-2958. DOI: 10.1002/hlca.200390243  1
2002 Wigger M, Eyler JR, Benner SA, Li W, Marshall AG. 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. Journal of the American Society For Mass Spectrometry. 13: 1162-9. PMID 12387321 DOI: 10.1016/S1044-0305(02)00439-7  1
2002 Held HA, Benner SA. Challenging artificial genetic systems: thymidine analogs with 5-position sulfur functionality. Nucleic Acids Research. 30: 3857-69. PMID 12202771  1
2002 Beintema JJ. Ribonucleases in ruminants. Science (New York, N.Y.). 297: 1121-2; author reply. PMID 12192657  1
2002 Gaucher EA, Gu X, Miyamoto MM, Benner SA. Predicting functional divergence in protein evolution by site-specific rate shifts. Trends in Biochemical Sciences. 27: 315-21. PMID 12069792 DOI: 10.1016/S0968-0004(02)02094-7  1
2002 Huang Z, Benner SA. Oligodeoxyribonucleotide analogues with bridging dimethylene sulfide, sulfoxide, and sulfone groups. Toward a second-generation model of nucleic acid structure. The Journal of Organic Chemistry. 67: 3996-4013. PMID 12054932 DOI: 10.1021/jo0003910  1
2002 Fukami-Kobayashi K, Schreiber DR, Benner SA. Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. Journal of Molecular Biology. 319: 729-43. PMID 12054866 DOI: 10.1016/S0022-2836(02)00239-5  1
2002 Benner SA, Caraco MD, Thomson JM, Gaucher EA. Planetary biology--paleontological, geological, and molecular histories of life. Science (New York, N.Y.). 296: 864-8. PMID 11988562 DOI: 10.1126/science.1069863  1
2002 Benner SA. The past as the key to the present: resurrection of ancient proteins from eosinophils. Proceedings of the National Academy of Sciences of the United States of America. 99: 4760-1. PMID 11959927 DOI: 10.1073/pnas.092143699  1
2002 Benner SA, Hutter D. Phosphates, DNA, and the search for nonterrean life: a second generation model for genetic molecules. Bioorganic Chemistry. 30: 62-80. PMID 11955003 DOI: 10.1006/bioo.2001.1232  1
2002 Gaucher EA, Das UK, Miyamoto MM, Benner SA. The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factors. Molecular Biology and Evolution. 19: 569-73. PMID 11919299  1
2002 Hutter D, Blaettler MO, Benner SA. From phosphate to bis(methylene) sulfone: Non-ionic backbone linkers in DNA Helvetica Chimica Acta. 85: 2777-2806. DOI: 10.1002/1522-2675(200209)85:9<2777::AID-HLCA2777>3.0.CO;2-1  1
2001 Liberles DA, Schreiber DR, Govindarajan S, Chamberlin SG, Benner SA. The adaptive evolution database (TAED). Genome Biology. 2: RESEARCH0028. PMID 11532212  1
2001 Rao P, Benner SA. Fluorescent charge-neutral analogue of xanthosine: synthesis of a 2'-deoxyribonucleoside bearing a 5-aza-7-deazaxanthine base. The Journal of Organic Chemistry. 66: 5012-5. PMID 11463249 DOI: 10.1021/jo005743h  1
2001 Benner SA, Gaucher EA. Evolution, language and analogy in functional genomics. Trends in Genetics : Tig. 17: 414-8. PMID 11418223 DOI: 10.1016/S0168-9525(01)02320-4  1
2001 Liberles DA, Schreiber DR, Govindarajan S, Chamberlin SG, Benner SA. The Adaptive Evolution Database (TAED). Genome Biology. 2: PREPRINT0003. PMID 11305934  1
2001 Gaucher EA, Miyamoto MM, Benner SA. Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors. Proceedings of the National Academy of Sciences of the United States of America. 98: 548-52. PMID 11209054 DOI: 10.1073/pnas.98.2.548  1
2001 Benner SA. Natural progression. Nature. 409: 459. PMID 11206523 DOI: 10.1038/35054149  1
2000 Benner SA. Unite efforts and conquer mysteries of artificial genetics. Science (New York, N.Y.). 290: 1506. PMID 11185506  1
2000 Peltier MR, Raley LC, Liberles DA, Benner SA, Hansen PJ. Evolutionary history of the uterine serpins. The Journal of Experimental Zoology. 288: 165-74. PMID 10931499 DOI: 10.1002/1097-010X(20000815)288:2<165::AID-JEZ7>3.0.CO;2-R  1
2000 Benner SA, Chamberlin SG, Liberles DA, Govindarajan S, Knecht L. Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics. Research in Microbiology. 151: 97-106. PMID 10865954 DOI: 10.1016/S0923-2508(00)00123-6  1
2000 Benner SA, Devine KG, Matveeva LN, Powell DH. The missing organic molecules on Mars. Proceedings of the National Academy of Sciences of the United States of America. 97: 2425-30. PMID 10706606 DOI: 10.1073/pnas.040539497  1
2000 Jurczyk SC, Horlacher J, Devined KG, Benner SA, Battersby TR. Synthesis and characterization of oligonucleotides containing 2'- deoxyxanthosine using phosphoramidite chemistry Helvetica Chimica Acta. 83: 1517-1524. DOI: 10.1002/1522-2675(20000705)83:7<1517::AID-HLCA1517>3.0.CO;2-S  1
1999 Zepik HH, Benner SA. Catalysts, Anticatalysts, and Receptors for Unactivated Phosphate Diesters in Water. The Journal of Organic Chemistry. 64: 8080-8083. PMID 11674719 DOI: 10.1021/jo982418+  1
1999 Battersby TR, Ang DN, Burgstaller P, Jurczyk SC, Bowser MT, Buchanan DD, Kennedy RT, Benner SA. Quantitative analysis of receptors for adenosine nucleotides obtained via in vitro selection from a library incorporating a cationic nucleotide analog. Journal of the American Chemical Society. 121: 9781-9. PMID 11543572 DOI: 10.1021/ja9816436  1
1999 Soucek J, Raines RT, Haugg M, Raillard-Yoon SA, Benner SA. Structural changes to ribonuclease A and their effects on biological activity. Comparative Biochemistry and Physiology. Part C, Pharmacology, Toxicology & Endocrinology. 123: 103-11. PMID 10442819 DOI: 10.1016/S0742-8413(99)00005-5  1
1999 Lutz MJ, Will DW, Breipohl G, Benner SA, Uhlmann E. Synthesis of a monocharged peptide nucleic acid (PNA) analog and its recognition as substrate by DNA polymerases. Nucleosides & Nucleotides. 18: 393-401. PMID 10408922  1
1999 Lutz S, Burgstaller P, Benner SA. An in vitro screening technique for DNA polymerases that can incorporate modified nucleotides. Pseudo-thymidine as a substrate for thermostable polymerases. Nucleic Acids Research. 27: 2792-8. PMID 10373598 DOI: 10.1093/nar/27.13.2792  1
1999 Lutz S, Benner SA. Simple one-pot synthesis of a 2'-tritium labeled C-deoxynucleoside. Bioorganic & Medicinal Chemistry Letters. 9: 723-6. PMID 10201836 DOI: 10.1016/S0960-894X(99)00068-2  1
1999 Vatzaki EH, Allen SC, Leonidas DD, Trautwein-Fritz K, Stackhouse J, Benner SA, Acharya KR. Crystal structure of a hybrid between ribonuclease A and bovine seminal ribonuclease--the basic surface, at 2.0 A resolution. European Journal of Biochemistry / Febs. 260: 176-82. PMID 10091597 DOI: 10.1046/j.1432-1327.1999.00142.x  1
1999 Gerloff DL, Cannarozzi GM, Joachimiak M, Cohen FE, Schreiber D, Benner SA. Evolutionary, mechanistic, and predictive analyses of the hydroxymethyldihydropterin pyrophosphokinase family of proteins. Biochemical and Biophysical Research Communications. 254: 70-6. PMID 9920734 DOI: 10.1006/bbrc.1998.9884  1
1999 Jurczyk SC, Kodra JT, Park JH, Benner SA, Battersby TR. Synthesis of 2'-deoxyisoguanosine 5'-triphosphate and 2'-deoxy-5 methylisocytidine 5'-triphosphate Helvetica Chimica Acta. 82: 1005-1015. DOI: 10.1002/(SICI)1522-2675(19990707)82:7<1005::AID-HLCA1005>3.0.CO;2-5  1
1998 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, et al. Redesigning nucleic acids. Pure and Applied Chemistry. Chimie Pure Et AppliquéE. 70: 263-6. PMID 11542721  1
1998 Lutz MJ, Horlacher J, Benner SA. Recognition of a non-standard base pair by thermostable DNA polymerases. Bioorganic & Medicinal Chemistry Letters. 8: 1149-52. PMID 9871725 DOI: 10.1016/S0960-894X(98)00177-2  1
1998 Lutz MJ, Horlacher J, Benner SA. Recognition of 2'-deoxyisoguanosine triphosphate by HIV-1 reverse transcriptase and mammalian cellular DNA polymerases. Bioorganic & Medicinal Chemistry Letters. 8: 499-504. PMID 9871606 DOI: 10.1016/S0960-894X(98)00057-2  1
1998 Gerloff DL, Joachimiak M, Cohen FE, Cannarozzi GM, Chamberlin SG, Benner SA. Structure prediction in a post-genomic environment: a secondary and tertiary structural model for the initiation factor 5A family. Biochemical and Biophysical Research Communications. 251: 173-81. PMID 9790926 DOI: 10.1006/bbrc.1998.9198  1
1998 Benner SA, Trabesinger N, Schreiber D. Post-genomic science: Converting primary structure into physiological function Advances in Enzyme Regulation. 38: 155-180. PMID 9762352 DOI: 10.1016/S0065-2571(97)00019-8  1
1998 Huang Z, Benner SA. Functionalization of nucleoside analogs: Regiospecific conversion of 4'- hydroxyl groups to thioesters and deoxygenation of 3'-hydroxyl groups Nucleosides and Nucleotides. 17: 895-899. PMID 9708330  1
1998 Chelvanayagam G, Knecht L, Jenny T, Benner SA, Gonnet GH. A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure Folding and Design. 3: 149-160. PMID 9562545 DOI: 10.1016/S1359-0278(98)00023-6  1
1998 Eschgfäller B, König M, Boess F, Boelsterli UA, Benner SA. Synthesis and biodistribution of a short nonionic oligonucleotide analogue in mouse with a potential to mimic peptides Journal of Medicinal Chemistry. 41: 276-283. PMID 9464358 DOI: 10.1021/jm970538o  1
1998 Blattler MO, Wenz C, Pingoud A, Benner SA. Distorting duplex DNA by dimethylenesulfone substitution: A new class of 'transition state analog' inhibitors for restriction enzymes [13] Journal of the American Chemical Society. 120: 2674-2675. DOI: 10.1021/ja972768y  1
1998 Jurczyk SC, Kodra JT, David Rozzell J, Benner SA, Battersby TR. Synthesis of Oligonucleotides Containing 2′-Deoxyisoguanosine and 2′-Deoxy-5-methylisocytidine Using Phosphoramidite Chemistry Helvetica Chimica Acta. 81: 793-811.  1
1998 Giger T, Wigger M, Audétat S, Benner SA. Libraries for Receptor-Assisted Combinatorial Synthesis (RACS). The olefin metathesis reaction Synlett. 688-691.  1
1997 Wigger M, Nawrocki JP, Watson CH, Eyler JR, Benner SA. Assessing enzyme substrate specificity using combinatorial libraries and electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry. Rapid Communications in Mass Spectrometry : Rcm. 11: 1749-52. PMID 9375409 DOI: 10.1002/(SICI)1097-0231(19971030)11:16<1749::AID-RCM91>3.0.CO;2-G  1
1997 Chelvanayagam G, Eggenschwiler A, Knecht L, Gonnet GH, Benner SA. An analysis of simultaneous variation in protein structures Protein Engineering. 10: 307-316. PMID 9194155  1
1997 Gerloff DL, Cohen FE, Korostensky C, Turcotte M, Gonnet GH, Benner SA. A predicted consensus structure for the N-terminal fragment of the heat shock protein HSP90 family. Proteins. 27: 450-8. PMID 9094746 DOI: 10.1002/(SICI)1097-0134(199703)27:3<450::AID-PROT12>3.0.CO;2-K  1
1997 Gerloff DL, Cohen FE, Benner SA. A predicted consensus structure for the C terminus of the beta and gamma chains of fibrinogen. Proteins. 27: 279-89. PMID 9061791 DOI: 10.1002/(SICI)1097-0134(199702)27:2<279::AID-PROT13>3.0.CO;2-J  1
1997 Tauer A, Benner SA. The B12-dependent ribonucleotide reductase from the archaebacterium Thermoplasma acidophila: An evolutionary solution to the ribonucleotide reductase conundrum Proceedings of the National Academy of Sciences of the United States of America. 94: 53-58. PMID 8990160 DOI: 10.1073/pnas.94.1.53  1
1997 Lutz MJ, Benner SA, Hein S, Breipohl G, Uhlmann E. Recognition of uncharged polyamide-linked nucleic acid analogs by DNA polymerases and reverse transcriptases Journal of the American Chemical Society. 119: 3177-3178. DOI: 10.1021/ja9637457  1
1997 Benner SA, Cannarozzi G, Gerloff D, Turcotte M, Chelvanayagam G. Bona fide predictions of protein secondary structure using transparent analyses of multiple sequence alignments Chemical Reviews. 97: 2725-2843.  1
1997 Kodra JT, Benner SA. Synthesis of an N-Alkyl Derivative of 2′-Deoxywoguanosine Synlett. 1997: 939-940.  1
1996 Baeschlin DK, Hyrup B, Benner SA, Richert C. Chimera of Dimethylene Sulfone-, Methyl Sulfide-, and Methyl Sulfoxide-Linked Ribonucleotides and DNA. The Journal of Organic Chemistry. 61: 7620-7626. PMID 11667701 DOI: 10.1021/jo960669h  1
1996 Benner SA, Geroff DL, Rozzell JD. Protein structure prediction [2] Science. 274: 1448-1449. PMID 8966608  1
1996 Nawrocki JP, Wigger M, Watson CH, Hayes TW, Senko MW, Benner SA, Eyler JR. Analysis of combinatorial libraries using electrospray Fourier transform ion cyclotron resonance mass spectrometry. Rapid Communications in Mass Spectrometry : Rcm. 10: 1860-4. PMID 8953790 DOI: 10.1002/(SICI)1097-0231(199611)10:14<1860::AID-RCM770>3.0.CO;2-#  1
1996 Benner SA, Jermann TM, Opitz JG, Raillard SA, Zankel TR, Trautwein-Fritz K, Stackhouse J, Ciglic MI, Haugg M, Trabesinger-Rüf N, Weinhold EG. Developing new synthetic catalysts. How nature does it Acta Chemica Scandinavica. 50: 243-248. PMID 8901176  1
1996 Lutz MJ, Held HA, Hottiger M, Hübscher U, Benner SA. Differential discrimination of DNA polymerase for variants of the non-standard nucleobase pair between xanthosine and 2,4-diaminopyrimidine, two components of an expanded genetic alphabet. Nucleic Acids Research. 24: 1308-13. PMID 8614635  1
1996 Trabesinger-Ruef N, Jermann T, Zankel T, Durrant B, Frank G, Benner SA. Pseudogenes in ribonuclease evolution: A source of new biomacromolecular function? Febs Letters. 382: 319-322. PMID 8605993 DOI: 10.1016/0014-5793(96)00191-3  1
1996 Richert C, Roughton AL, Benner SA. Nonionic analogs of RNA with dimethylene sulfone bridges Journal of the American Chemical Society. 118: 4518-4531. DOI: 10.1021/ja952322m  1
1996 Baeschlin DK, Daube M, Blättler MO, Benner SA, Richert C. Four step synthesis of a 5′-deoxy-5′-iodomethylthymidine Tetrahedron Letters. 37: 1591-1592. DOI: 10.1016/0040-4039(96)00090-1  1
1996 Voegel JJ, Benner SA. 156. 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 Helvetica Chimica Acta. 79: 1881-1898.  1
1996 Voegel JJ, Benner SA. 155. Synthesis and characterization of non-standard nucleosides and nucleotides bearing the acceptor-donor-donor pyrimidine analog 6-amino-3-methylpyrazin-2(1H)-one Helvetica Chimica Acta. 79: 1863-1880.  1
1996 Benner SA. Catalysis: The omnipresent phenomenon Faseb Journal. 10: A968.  1
1996 Gonnet GH, Benner SA. Probabilistic ancestral sequences and multiple alignments Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1097: 380-391.  1
1995 Benner SA, Gerloff D, Chelvanayagam G. The phospho-β-galactosidase and synaptotagmin predictions Proteins: Structure, Function and Genetics. 23: 446-453. PMID 8710837 DOI: 10.1002/prot.340230318  1
1995 Weinhold EG, Benner SA. Engineering yeast alcohol dehydrogenase. Replacing Trp54 by leu broadens substrate specificity Protein Engineering. 8: 457-461. PMID 8532667 DOI: 10.1093/protein/8.5.457  1
1995 Jenny TF, Gerloff DL, Cohen MA, Benner SA. Predicted secondary and supersecondary structure for the serine-threonine-specific protein phosphatase family. Proteins. 21: 1-10. PMID 7716164 DOI: 10.1002/prot.340210102  1
1995 Benner SA. Predicting the conformation of proteins from sequences. Progress and future progress Journal of Molecular Recognition : Jmr. 8: 9-28. PMID 7598957  1
1995 Matousek J, Soucek J, Riha J, Zankel TR, Benner SA. Immunosuppressive activity of angiogenin in comparison with bovine seminal ribonuclease and pancreatic ribonuclease Comparative Biochemistry and Physiology -- Part B: Biochemistry And. 112: 235-241. PMID 7584854 DOI: 10.1016/0305-0491(95)00075-5  1
1995 Gerloff DL, Benner SA. A consensus prediction of the secondary structure for the 6-phospho-β-D- galactosidase superfamily Proteins: Structure, Function and Genetics. 21: 273-281. PMID 7567950 DOI: 10.1002/prot.340210402  1
1995 Hyrup B, Richert C, Schulte-herbrüggen T, Benner SA, Egli M. X-ray crystal struture of a dimethylene sulfone-bridged ribonucleotide dimer in a single-stranded state Nucleic Acids Research. 23: 2427-2433. PMID 7543197 DOI: 10.1093/nar/23.13.2427  1
1995 Horlacher J, Hottiger M, Podust VN, Hübscher U, Benner SA. Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns Proceedings of the National Academy of Sciences of the United States of America. 92: 6329-6333. PMID 7541538 DOI: 10.1073/pnas.92.14.6329  1
1995 Jermann TM, Opitz JG, Stackhouse J, Benner SA. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily Nature. 374: 57-59. PMID 7532788  1
1995 Gerloff DL, Chelvanayagam G, Benner SA. A predicted consensus structure for the protein kinase C2 homology (C2H) domain, the repeating unit of synaptotagmin Proteins: Structure, Function and Genetics. 22: 299-310. PMID 7479705 DOI: 10.1002/prot.340220402  1
1995 Benner SA, Jermann TM, Opitz JG, Stackhouse J, Knecht LJ, Gonnet GH. Uncertainty in ancient phylogenies [7] Nature. 377: 109-110.  1
1995 Roughton AL, Portmann S, Benner SA, Egli M. Crystal structure of a dimethylene sulfone-linked ribodinucleotide analog Journal of the American Chemical Society. 117: 7249-7250.  1
1995 Von Krosigk U, Benner SA. pH-independent triple helix formation by an oligonucleotide containing a pyrazine donor-donor-acceptor base Journal of the American Chemical Society. 117: 5361-5362.  1
1994 Boix E, Nogués MV, Schein CH, Benner SA, Cuchillo CM. Reverse Transphosphorylation by Ribonuclease A Needs an Intact p2-binding Site: Point mutations at LYS-7 and ARG-10 alter the catalytic properties of the enzyme Journal of Biological Chemistry. 269: 2529-2534. PMID 8300580  1
1994 Benner SA, Badcoe I, Cohen MA, Gerloff DL. Bona fide prediction of aspects of protein conformation. Assigning interior and surface residues from patterns of variation and conservation in homologous protein sequences. Journal of Molecular Biology. 235: 926-58. PMID 8289328 DOI: 10.1006/jmbi.1994.1049  1
1994 Jenny TF, Benner SA. Evaluating predictions of secondary structure in proteins Biochemical and Biophysical Research Communications. 200: 149-155. PMID 8166681 DOI: 10.1006/bbrc.1994.1427  1
1994 Gonnet GH, Cohen MA, Benner SA. Analysis of amino acid substitution during divergent evolution: the 400 by 400 dipeptide substitution matrix. Biochemical and Biophysical Research Communications. 199: 489-96. PMID 8135790 DOI: 10.1006/bbrc.1994.1255  1
1994 Benner SA, Gerloff DL, Jenny TF. Predicting protein crystal structures [3] Science. 265: 1642-1644. PMID 8085149  1
1994 Benner SA, Jenny TF, Cohen MA, Gonnet GH. Predicting the conformation of proteins from sequences. Progress and future progress. Advances in Enzyme Regulation. 34: 269-353. PMID 7942279 DOI: 10.1016/0065-2571(94)90021-3  1
1994 Jenny TF, Benner SA. A prediction of the secondary structure of the pleckstrin homology domain Proteins: Structure, Function and Genetics. 20: 1-3. PMID 7824519 DOI: 10.1002/prot.340200102  1
1994 Benner SA. Expanding the genetic lexicon: Incorporating non-standard amino acids into proteins by ribosome-based synthesis Trends in Biotechnology. 12: 158-163. PMID 7764897 DOI: 10.1016/0167-7799(94)90076-0  1
1994 Benner SA, Cohen MA, Gonnet GH. Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Engineering. 7: 1323-32. PMID 7700864  1
1994 Voegel JJ, Benner SA. Nonstandard hydrogen bonding in duplex oligonucleotides. The base pair between an acceptor-donor-donor pyrimidine analog and a donor-acceptor-acceptor purine analog Journal of the American Chemical Society. 116: 6929-6230. DOI: 10.1021/ja00094a055  1
1994 Heeb NV, Benner SA. Guanosine derivatives bearing an N2-3-imidazolepropionic acid Tetrahedron Letters. 35: 3045-3048. DOI: 10.1016/S0040-4039(00)76823-7  1
1993 Johnsson K, Allemann RK, Widmer H, Benner SA. Synthesis, structure and activity of artificial, rationally designed catalytic polypeptides Nature. 365: 530-532. PMID 8413606  1
1993 Arslan T, Benner SA. Reduction of 2-substituted 3-oxoglutarates mediated by baker's yeast. Variation in enantioselectivity without corresponding variation in diastereoselectivity Journal of Organic Chemistry. 58: 2260-2264.  1
1991 Weinhold EG, Glasfeld A, Ellington AD, Benner SA. Structural determinants of stereospecificity in yeast alcohol dehydrogenase. Proceedings of the National Academy of Sciences of the United States of America. 88: 8420-4. PMID 1924300  1
1991 Piccirilli JA, Moroney SE, Benner SA. A C-nucleotide base pair: methylpseudouridine-directed incorporation of formycin triphosphate into RNA catalyzed by T7 RNA polymerase. Biochemistry. 30: 10350-6. PMID 1718418 DOI: 10.1021/bi00106a037  1
1990 Glasfeld A, Leanz GF, Benner SA. The stereospecificities of seven dehydrogenases from Acholeplasma laidlawii. The simplest historical model that explains dehydrogenase stereospecificity. The Journal of Biological Chemistry. 265: 11692-9. PMID 2365693  1
1990 Piccirilli JA, Krauch T, Moroney SE, Benner SA. Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature. 343: 33-7. PMID 1688644 DOI: 10.1038/343033a0  1
1989 Glasfeld A, Benner SA. The stereospecificity of the ferrous-ion-dependent alcohol dehydrogenase from Zymomonas mobilis. European Journal of Biochemistry / Febs. 180: 373-5. PMID 2924772  1
1987 Berkowitz DB, Benner SA. Anomeric specificity of L-fucose dehydrogenase: a stereochemical imperative in aldopyranose dehydrogenases? Biochemistry. 26: 2606-11. PMID 3607036  1
1987 Benner SA, Allemann RK, Ellington AD, Ge L, Glasfeld A, Leanz GF, Krauch T, MacPherson LJ, Moroney S, Piccirilli JA. Natural selection, protein engineering, and the last riboorganism: rational model building in biochemistry. Cold Spring Harbor Symposia On Quantitative Biology. 52: 53-63. PMID 2456885  1
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