Research Topics
| Steven BennerSummaryAffiliation: Foundation for Applied Molecular Evolution Country: USA Publications
Research Grants
| Collaborators
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Detail Information
Publications
Asphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNASteven A Benner
Foundation for Applied Molecular Evolution, Gainesville, Florida 32604, USA
Acc Chem Res 45:2025-34. 2012..Well-known chemistry transforms these structures into nucleosides, nucleotides, and partially formylated oligomeric RNA...
Setting the stage: the history, chemistry, and geobiology behind RNASteven A Benner
Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, USA
Cold Spring Harb Perspect Biol 4:a003541. 2012....- Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metricsTang Li
Foundation for Applied Molecular Evolution, Gainesville, FL 32604, USA
BMC Evol Biol 6:25. 2006..Multiple transitions at synonymous sites may cause equilibration and loss of information. Further, to be useful to correlate events in the genomic record, different genes within a genome must suffer transitions at similar rates... - Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteinsMichael E Bradley
Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
BMC Bioinformatics 7:89. 2006..This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use... - Labeled nucleoside triphosphates with reversibly terminating aminoalkoxyl groupsDaniel Hutter
Foundation for Applied Molecular Evolution, Gainesville, FL 32604, USA
Nucleosides Nucleotides Nucleic Acids 29:879-95. 2010..Multiple extension-cleavage-extension cycles were demonstrated on an Intelligent Bio-Systems Sequencer, showing the potential of the 3'-ONHâ‚‚ blocking group in "next generation sequencing.".. - Defining lifeSteven A Benner
Foundation for Applied Molecular Evolution and The Westheimer Institute for Science and Technology, Gainesville, Florida32601, USA
Astrobiology 10:1021-30. 2010..Last, we ask what chemical structures might support Darwinian evolution universally; these structures might be universal biosignatures... - Comment on "A bacterium that can grow by using arsenic instead of phosphorus"Steven A Benner
The Westheimer Institute for Science and Technology, 720 South 2nd Avenue, Gainesville, FL 32601, USA
Science 332:1149; author reply 1149. 2011..If such arseno-DNA exists, then much of the past century of work with arsenate and phosphate chemistry, as well as much of what we think we know about metabolism, will need rewriting... - Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family exampleMichael E Bradley
Department of Chemistry, University of Florida P, O, Box 117200, Gainesville, FL 32611 7200, USA
BMC Evol Biol 5:22. 2005.... - The planetary biology of cytochrome P450 aromatasesEric A Gaucher
Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville FL 32601 4256, USA
BMC Biol 2:19. 2004..This strategy expands systems biology to a planetary context, necessary for a notion of fitness to underlie (as it must) any discussion of function within a biomolecular system... - Dynamic assembly of primers on nucleic acid templatesNicole A Leal
Foundation for Applied Molecular Evolution, Ayers Medical Plaza, Suite 208, 720 SW 2nd Avenue, Gainesville, FL 32601, USA
Nucleic Acids Res 34:4702-10. 2006..Several polymerases were found that achieve this combination, permitting the implementation of the dynamic combinatorial chemical strategy... - Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene familyEric A Gaucher
Foundation for Applied Molecular Evolution, Gainesville, FL, USA
BMC Genomics 7:44. 2006..Tools that do this will become increasingly important for those seeking to use human genome sequence data to predict disease, make prognoses, and customize therapy to individual patients... 
The evolution of seminal ribonuclease: pseudogene reactivation or multiple gene inactivation events?Slim O Sassi
Foundation for Applied Molecular Evolution, Gainesville, Florida, USA
Mol Biol Evol 24:1012-24. 2007....- Predicting functional divergence in protein evolution by site-specific rate shiftsEric A Gaucher
NASA Astrobiology Institute, University of Florida, Gainesville, FL 32611, USA
Trends Biochem Sci 27:315-21. 2002..Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs... - Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detectionFei Chen
Foundation for Applied Molecular Evolution, 720 SW 2nd Avenue, Suite 201, Gainesville, FL 32601, USA
Proc Natl Acad Sci U S A 107:1948-53. 2010..This work provides polymerases for DNA analyses and shows how evolutionary analyses help explore relationships between structure and function in proteins... - Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignmentsMike S S Chang
Foundation for Applied Molecular Evolution, Gainesville, FL 32601, USA
J Mol Biol 341:617-31. 2004..By providing mechanisms to identify errors, the tools will enhance the value of genome sequence databases in support of integrated paleogenomics strategies used to extract functional information in a post-genomic environment... - Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosineCynthia L Hendrickson
Department of Chemistry and Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32611-7200, USA
Nucleic Acids Res 32:2241-50. 2004..Each interpretation is significant for understanding the planetary biology of polymerases... - Challenging artificial genetic systems: thymidine analogs with 5-position sulfur functionalityHeike A Held
Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
Nucleic Acids Res 30:3857-69. 2002..This remains curious, as the ability of the polymerase to replicate natural DNA with high fidelity and its propensity to exclude unnatural analogs are presumed to be correlated... - Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity proteinEric A Gaucher
NASA Astrobiology Institute and Foundation for Applied Molecular Evolution, University of Florida, Gainesville, Florida, 32611 7200, USA
Genetics 163:1549-53. 2003.... - Nucleobase pairing in expanded Watson-Crick-like genetic information systemsC Ronald Geyer
Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
Structure 11:1485-98. 2003..The experiments also demonstrate that expanded genetic systems can be constructed using size complementary nucleobase pairs that contain three hydrogen bonds... - PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1A Michael Sismour
Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
Nucleic Acids Res 32:728-35. 2004..This work also illustrates a research strategy that combines in clinico pre-evolution of proteins followed by rational design to obtain an enzyme that meets a particular technological specification... - A review: synthesis of aryl C-glycosides via the heck coupling reactionKevin W Wellington
Foundation for Applied Molecular Evolution, Gainesville, Florida 32604, USA
Nucleosides Nucleotides Nucleic Acids 25:1309-33. 2006..The subsequent conversion of the Heck products to the corresponding target molecules and the application of the target molecules are also described... - Enzymatic incorporation of a third nucleobase pairZunyi Yang
Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville, FL 32601, USA
Nucleic Acids Res 35:4238-49. 2007..The dZ:dP pair and these polymerases, should be useful in dynamic architectures for sequencing, molecular-, systems- and synthetic-biology... - Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteinsEric A Gaucher
NASA Astrobiology Institute, Gainesville, Florida 32611 7200, USA
Nature 425:285-8. 2003..The study illustrates the use of experimental palaeobiochemistry and assumptions about deep phylogenetic relationships between bacteria to explore the character of ancient life... - The past as the key to the present: resurrection of ancient proteins from eosinophilsSteven A Benner
Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
Proc Natl Acad Sci U S A 99:4760-1. 2002 - Chemistry. Redesigning geneticsSteven A Benner
Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
Science 306:625-6. 2004 - Lessons from comparative physiology: could uric acid represent a physiologic alarm signal gone awry in western society?Richard J Johnson
Division of Nephrology, Hypertension and Transplantation, University of Florida, Gainesville, FL 32610, USA
J Comp Physiol B 179:67-76. 2009.... - 2'-deoxycytidines carrying amino and thiol functionality: synthesis and incorporation by Vent (exo-) polymeraseAbhijit Roychowdhury
Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, USA
Org Lett 6:489-92. 2004..The ability of Vent (exo(-)) polymerase to amplify oligonucleotides containing these functionalized cytidine derivatives in a polymerase chain reaction (PCR) was demonstrated for the amino-functionalized derivative... - Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding patternZunyi Yang
Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville, FL 32601, USA
Nucleic Acids Res 34:6095-101. 2006.... - Understanding nucleic acids using synthetic chemistrySteven A Benner
Department of Chemistry, University of Florida, Gainesville, Florida 32611 7200, USA
Acc Chem Res 37:784-97. 2004..A new field, synthetic biology, is emerging on the basis of these experiments, where chemistry mimics biological processes as complicated as Darwinian evolution... - Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkagesZunyi Yang
Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville, FL 32604 1174, USA
Nucleic Acids Res 35:3118-27. 2007..Furthermore, these results provide constraints on how exonuclease III-thiotriphosphate-polymerase combinations can be used to analyze the behavior of the components of a synthetic biology... - Is there a common chemical model for life in the universe?Steven A Benner
Department of Chemistry, University of Florida, Gainesville, FL 32611 7200, USA
Curr Opin Chem Biol 8:672-89. 2004..If we constrain life to water, more specific criteria can be proposed, including soluble metabolites, genetic materials with repeating charges, and a well defined temperature range... - Locked nucleic acid molecular beaconsLin Wang
Center for Research at Bio/nano Interface, Department of Chemistry, UF Genetics Institute, Gainesville, Florida 32611-7200, USA
J Am Chem Soc 127:15664-5. 2005..The LNA-MB will be widely useful in a variety of areas, especially for in vivo hybridization studies... - Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selectionMatthew A Carrigan
Foundation for Applied Molecular Evolution, Incorporated, Post Office Box 13174, Gainesville, Florida 32604, USA
Biochemistry 43:11446-59. 2004..This study of a specific catalytically active DNAzyme is an example of studies that will be necessary generally to permit in vitro selection to help us understand the distribution of function in sequence space... - The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological systemA Michael Sismour
Department of Chemistry, University of Florida, Gainesville, FL 32611 7200, USA
Nucleic Acids Res 33:5640-6. 2005..The analogous PCR employing TTP had a fidelity-per-round of only approximately 93%. Thus, the A, 2-thioT, G, C, isoC, isoG alphabet is an artificial genetic system capable of Darwinian evolution... - Synthetic biologySteven A Benner
Department of Chemistry, University of Florida, Gainesville, FL 32611 7200, USA
Nat Rev Genet 6:533-43. 2005..Synthetic biology has generated diagnostic tools that improve the care of patients with infectious diseases, as well as devices that oscillate, creep and play tic-tac-toe... - Resurrecting ancestral alcohol dehydrogenases from yeastJ Michael Thomson
Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32610, USA
Nat Genet 37:630-5. 2005..These results help to connect the chemical behavior of these enzymes through systems analysis to a time of global ecosystem change, a small but useful step towards a planetary systems biology... - Planetary biology--paleontological, geological, and molecular histories of lifeSteven A Benner
Department of Chemistry, University of Florida, Gainesville FL, 32611 7200, USA
Science 296:864-8. 2002..Together, planetary analysis of genome and proteome databases is providing an enhanced understanding of how life interacts with the biosphere and adapts to global change... - Interpretive proteomics--finding biological meaning in genome and proteome databasesSteven A Benner
Department of Chemistry, University of Florida, Gainesville FL 32611, USA
Adv Enzyme Regul 43:271-359. 2003 - Multiplexed genetic analysis using an expanded genetic alphabetScott C Johnson
Eragen Biosciences, Inc, Madison, WI 53717, USA
Clin Chem 50:2019-27. 2004..CONCLUSIONS: The unique genetic multiplexing platform was successfully able to test for 31 targets within the CFTR gene and provides accurate genotype assignments in a clinical setting... - The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factorsEric A Gaucher
Mol Biol Evol 19:569-73. 2002 - Incorporation of multiple sequential pseudothymidines by DNA polymerases and their impact on DNA duplex structureStephanie A Havemann
Department of Microbiology and Cell Science, Space Life Sciences Laboratory, Kennedy Space Center, University of Florida, FL, USA
Nucleosides Nucleotides Nucleic Acids 27:261-78. 2008..These results constrain architectures for sequencing, quantitating, and analyzing DNA analogs that exploit C-glycosides, and define better the challenge of creating a synthetic biology using these with natural polymerases... - 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 libraryMaria Wigger
J Am Soc Mass Spectrom 13:1162-9. 2002.... - Oligodeoxyribonucleotide analogues with bridging dimethylene sulfide, sulfoxide, and sulfone groups. Toward a second-generation model of nucleic acid structureZhen Huang
Department of Chemistry, University of Florida, Gainesville 32611, USA
J Org Chem 67:3996-4013. 2002..Features of the second-generation model are important for many areas of nucleic acid chemistry, from the design of nucleic acid therapeutic agents to the search for life on other planets... - Phosphates, DNA, and the search for nonterrean life: a second generation model for genetic moleculesSteven A Benner
Department of Chemistry, University of Florida, P O Box 117200, Gainesville 32611 7200, USA
Bioorg Chem 30:62-80. 2002..quot; The polyelectrolyte structure therefore may be a universal signature of life, regardless of its genesis, and unique to living forms as well... - The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular diseaseRichard J Johnson
Division of Nephrology, Hypertension and Transplantation, University of Florida, and the Foundation of Applied Molecular Evolution, Gainesville, FL 32610 0224, United States
Med Hypotheses 71:22-31. 2008....
Research Grants
- Artificial Genetic SystemsSteven Benner; Fiscal Year: 2007..Multiplexed PCR is the rate limiting step in many genomics analyses. Our long term, highly ambitious goal is to develop a "synthetic biology", a chemical system capable of Darwinian evolution, based on AEGIS components. ..
- Near Term Development of Reagents and Enzymes for Genome SequencingSteven Benner; Fiscal Year: 2009..This proposal, from a laboratory with a track record of innovation in structures, reagents, and enzymes to manipulate nucleic acids, is focused on near term development of these to enable NHGRI cost-reduction sequencing goals. ..
- Chemistry to Improve Human Genomic Array Analysis ArchitecturesSteven A Benner; Fiscal Year: 2010..This proposal seeks funds to benchmark the improvements in array performance generated by these new technologies, improve them by a cycle of test and redesign, and provide them to the genomics community. ..
- Near Term Development of Reagents and Enzymes for Genome SequencingSteven A Benner; Fiscal Year: 2010..This proposal, from a laboratory with a track record of innovation in structures, reagents, and enzymes to manipulate nucleic acids, is focused on near term development of these to enable NHGRI cost-reduction sequencing goals. ..
- Alcohol Metabolism,Primate Evolution and Paleogenetics. An Inclusive ParadigmSteven A Benner; Fiscal Year: 2010..This research will be the first collaboration between Steven Benner, who initiated experimental paleogenetics as a field and has developed planetary and systems biology in many ..
- Artificial Genetic SystemsSteven A Benner; Fiscal Year: 2010..Multiplexed PCR is the rate limiting step in many genomics analyses. Our long term, highly ambitious goal is to develop a "synthetic biology", a chemical system capable of Darwinian evolution, based on AEGIS components. ..
- Near Term Development of Reagents and Enzymes for Genome SequencingSteven Benner; Fiscal Year: 2009..This proposal, from a laboratory with a track record of innovation in structures, reagents, and enzymes to manipulate nucleic acids, is focused on near term development of these to enable NHGRI cost-reduction sequencing goals. ..
- DNA Sequencing using NanoporesSteven Benner; Fiscal Year: 2007..These will then be targeted against specific sequences extracted from mammalian genomes. ..
- Polymerases for Sequencing by SynthesisSteven Benner; Fiscal Year: 2007....
- NON-STANDARD BASE PAIRS AS BIOMEDICAL RESEARCH TOOLSSteven Benner; Fiscal Year: 1999....
- EVOLUTION OF THE RIBONUCLEASE SUPERFAMILYSteven Benner; Fiscal Year: 2001....
- Targeted Assisted Combinational SynthesisSteven Benner; Fiscal Year: 2004..abstract_text> ..
- NON-STANDARD BASE PAIRS AS BIOMEDICAL RESEARCH TOOLSSteven Benner; Fiscal Year: 2004....
- Dynamic combinatorial chemistry for nucleic acidsSteven Benner; Fiscal Year: 2007..The proposed work will develop another platform technology, this one allowing the detection of nucleic acid targets through a novel combination of dynamic combinatorial chemistry, enzymology, and nucleic acid science. ..
- Chemistry to Improve Human Genomic Array Analysis ArchitecturesSteven Benner; Fiscal Year: 2009..This proposal seeks funds to benchmark the improvements in array performance generated by these new technologies, improve them by a cycle of test and redesign, and provide them to the genomics community. ..