S A Benner

Summary

Affiliation: University of Florida
Country: USA

Publications

  1. pmc Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family
    Eric A Gaucher
    Foundation for Applied Molecular Evolution, Gainesville, FL, USA
    BMC Genomics 7:44. 2006
  2. pmc Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example
    Michael E Bradley
    Department of Chemistry, University of Florida P, O, Box 117200, Gainesville, FL 32611 7200, USA
    BMC Evol Biol 5:22. 2005
  3. pmc The planetary biology of cytochrome P450 aromatases
    Eric A Gaucher
    Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville FL 32601 4256, USA
    BMC Biol 2:19. 2004
  4. pmc The missing organic molecules on Mars
    S A Benner
    Departments of Chemistry, Anatomy, and Cell Biology, University of Florida, Gainesville, FL 32611, USA
    Proc Natl Acad Sci U S A 97:2425-30. 2000
  5. ncbi Chemistry. Redesigning genetics
    Steven A Benner
    Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
    Science 306:625-6. 2004
  6. ncbi Expanding the genetic alphabet: non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern
    Daniel Hutter
    Department of Chemistry and Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32611 7200
    J Org Chem 68:9839-42. 2003
  7. ncbi Understanding nucleic acids using synthetic chemistry
    Steven A Benner
    Department of Chemistry, University of Florida, Gainesville, Florida 32611 7200, USA
    Acc Chem Res 37:784-97. 2004
  8. ncbi 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
  9. ncbi Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics
    S A Benner
    Department of Chemistry, University of Florida, Gainesville, USA
    Res Microbiol 151:97-106. 2000
  10. ncbi Synthetic biology
    Steven A Benner
    Department of Chemistry, University of Florida, Gainesville, FL 32611 7200, USA
    Nat Rev Genet 6:533-43. 2005

Collaborators

Detail Information

Publications60

  1. pmc Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family
    Eric 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...
  2. pmc Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example
    Michael E Bradley
    Department of Chemistry, University of Florida P, O, Box 117200, Gainesville, FL 32611 7200, USA
    BMC Evol Biol 5:22. 2005
    ....
  3. pmc The planetary biology of cytochrome P450 aromatases
    Eric 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...
  4. pmc The missing organic molecules on Mars
    S A Benner
    Departments of Chemistry, Anatomy, and Cell Biology, University of Florida, Gainesville, FL 32611, USA
    Proc Natl Acad Sci U S A 97:2425-30. 2000
    ..Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life...
  5. ncbi Chemistry. Redesigning genetics
    Steven A Benner
    Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
    Science 306:625-6. 2004
  6. ncbi Expanding the genetic alphabet: non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern
    Daniel Hutter
    Department of Chemistry and Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32611 7200
    J Org Chem 68:9839-42. 2003
    ..These results make nucleoside 4 a promising candidate for an expanded genetic alphabet...
  7. ncbi Understanding nucleic acids using synthetic chemistry
    Steven 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...
  8. ncbi 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...
  9. ncbi Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics
    S A Benner
    Department of Chemistry, University of Florida, Gainesville, USA
    Res Microbiol 151:97-106. 2000
    ....
  10. ncbi Synthetic biology
    Steven 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...
  11. ncbi Planetary biology--paleontological, geological, and molecular histories of life
    Steven 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...
  12. ncbi Evolution, language and analogy in functional genomics
    S A Benner
    Dept of Chemistry, NASA Astrobiology Institute, University of Florida, Gainesville, FL 32611 7200, USA
    Trends Genet 17:414-8. 2001
    ..If this is true, until these paradoxes are recognized and addressed, functional genomics will continue to be limited in its ability to extrapolate information from genomic sequences...
  13. pmc The past as the key to the present: resurrection of ancient proteins from eosinophils
    Steven A Benner
    Department of Chemistry, University of Florida, Gainesville, FL 32611 7200, USA
    Proc Natl Acad Sci U S A 99:4760-1. 2002
  14. ncbi Phosphates, DNA, and the search for nonterrean life: a second generation model for genetic molecules
    Steven 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...
  15. ncbi The Adaptive Evolution Database (TAED)
    D A Liberles
    Department of Chemistry, University of Florida, Gainesville, FL 32611 USA
    Genome Biol 2:PREPRINT0003. 2001
    ....
  16. pmc The adaptive evolution database (TAED)
    D A Liberles
    Departments of Chemistry, University of Florida, Gainesville, FL 32611, USA
    Genome Biol 2:RESEARCH0028. 2001
    ....
  17. ncbi Nucleobase pairing in expanded Watson-Crick-like genetic information systems
    C 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...
  18. pmc Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors
    E A Gaucher
    Department of Chemistry and Molecular Cell Biology Program, College of Medicine, University of Florida, Gainesville, FL 32611 7200, USA
    Proc Natl Acad Sci U S A 98:548-52. 2001
    ..We illustrate this in the elongation factor family of proteins as a paradigm for applications of this type of analysis in functional genomics generally...
  19. pmc PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1
    A 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...
  20. pmc Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern
    Zunyi Yang
    Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville, FL 32601, USA
    Nucleic Acids Res 34:6095-101. 2006
    ....
  21. ncbi Oligodeoxyribonucleotide analogues with bridging dimethylene sulfide, sulfoxide, and sulfone groups. Toward a second-generation model of nucleic acid structure
    Zhen 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...
  22. pmc 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
    ....
  23. pmc Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages
    Zunyi 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...
  24. pmc The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular disease
    Richard 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
    ....
  25. pmc The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system
    A 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...
  26. pmc Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics
    Tang 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...
  27. ncbi Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection
    Matthew 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...
  28. ncbi Predicting functional divergence in protein evolution by site-specific rate shifts
    Eric 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...
  29. pmc Challenging artificial genetic systems: thymidine analogs with 5-position sulfur functionality
    Heike 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...
  30. pmc Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein
    Eric A Gaucher
    NASA Astrobiology Institute and Foundation for Applied Molecular Evolution, University of Florida, Gainesville, Florida, 32611 7200, USA
    Genetics 163:1549-53. 2003
    ....
  31. ncbi Interpretive proteomics--finding biological meaning in genome and proteome databases
    Steven A Benner
    Department of Chemistry, University of Florida, Gainesville FL 32611, USA
    Adv Enzyme Regul 43:271-359. 2003
  32. ncbi Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
    Eric 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...
  33. pmc Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection
    Fei 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...
  34. ncbi 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
    ....
  35. pmc Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteins
    Michael 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...
  36. ncbi A review: synthesis of aryl C-glycosides via the heck coupling reaction
    Kevin 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...
  37. pmc Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosine
    Cynthia 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...
  38. ncbi Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments
    Mike 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...
  39. doi Comment on "The silicate-mediated formose reaction: bottom-up synthesis of sugar silicates"
    Hyo Joong Kim
    Foundation for Applied Molecular Evolution, The Westheimer Institute for Science and Technology, 720 SW 2nd Avenue, Suite 201, Gainesville, FL 32601, USA
    Science 329:902; author reply 902. 2010
    ..Here, we show that silicate has minimal impact in these respects, especially when compared to borate minerals...
  40. doi Incorporation of multiple sequential pseudothymidines by DNA polymerases and their impact on DNA duplex structure
    Stephanie 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...
  41. pmc Enzymatic incorporation of a third nucleobase pair
    Zunyi 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...
  42. ncbi Fluorescent charge-neutral analogue of xanthosine: synthesis of a 2'-deoxyribonucleoside bearing a 5-aza-7-deazaxanthine base
    P Rao
    Department of Chemistry and Department of Anatomy and Molecular Biology, University of Florida, Gainesville, Florida 32611, USA
    J Org Chem 66:5012-5. 2001
    ..5.6. Furthermore, as part of the design, 4 is made capable of presenting an unshared pair of electrons to the DNA minor groove...
  43. ncbi Borate minerals stabilize ribose
    A Ricardo
    Department of Chemistry University of Florida, Gainesville, FL 32611, USA
    Science 303:196. 2004
  44. ncbi Molecular paleoscience: systems biology from the past
    Steven A Benner
    Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville, FL 32601, USA
    Adv Enzymol Relat Areas Mol Biol 75:1-132, xi. 2007
    ..These show how paleogenetics can lead to an understanding of the function of biomolecules, analyze changing function, and put meaning to genomic sequences, all in ways that are not possible with traditional molecular biological studies...
  45. pmc Dynamic assembly of primers on nucleic acid templates
    Nicole 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...
  46. ncbi Locked nucleic acid molecular beacons
    Lin 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...
  47. ncbi Artificial genetic systems: exploiting the "aromaticity" formalism to improve the tautomeric ratio for isoguanosine derivatives
    Theodore A Martinot
    Department of Chemistry, University of Florida, P O Box 117200, Gainesville, Florida 32611 7200, USA
    J Org Chem 69:3972-5. 2004
    ..The replacement of the imidazole ring in 1 with a pyrrole ring in 2 makes the keto form in the latter more favored by 2 orders of magnitude (K(TAUT) for 2 approximately 10(3), as opposed to K(TAUT) for 1 approximately 10)...
  48. ncbi Synthetic biology: Act natural
    Steven A Benner
    Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
    Nature 421:118. 2003
  49. ncbi 2'-deoxycytidines carrying amino and thiol functionality: synthesis and incorporation by Vent (exo-) polymerase
    Abhijit 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...
  50. doi 2'-deoxy-1-methylpseudocytidine, a stable analog of 2'-deoxy-5-methylisocytidine
    Hyo Joong Kim
    Westheimer Institute for Science and Technology, Foundation for Applied Molecular Evolution, PO Box 13174, Gainesville, FL 32604, USA
    Bioorg Med Chem 17:3728-32. 2009
    ..We report here a C-glycoside analog that is more stable and, in oligonucleotides, pairs with 2'-deoxyisoguanosine, contributing to duplex stability about as much as a standard 2'-deoxycytidine and 2'-deoxyguanosine pair...
  51. pmc Planetary organic chemistry and the origins of biomolecules
    Steven A Benner
    Foundation for Applied Molecular Evolution and The Westheimer Institute for Science and Technology, Gainesville, Florida 32601, USA
    Cold Spring Harb Perspect Biol 2:a003467. 2010
    ..We describe here the latest thoughts on how on this challenge, focusing on how it might be resolved using minerals containing borate, silicate, and molybdate, inter alia...
  52. doi Synthesis of pyrophosphates for in vitro selection of catalytic RNA molecules
    Hyo Joong Kim
    Foundation for Applied Molecular Evolution, Gainesville, Florida, USA
    Nucleosides Nucleotides Nucleic Acids 27:43-56. 2008
    ..Two detailed procedures are presented to prepare this new compound, as well as one procedure to prepare the new flavin-2,6-diaminopurine dinucleotide...
  53. ncbi Planetary systems biology
    Steven A Benner
    Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
    Mol Cell 17:471-2. 2005
    ..Combining paleogenetics, protein engineering, synthetic biology, and metabolic modeling, a planetary biology perspective is brought to bear on adaptive evolutionary events in ancient bacteria...
  54. pmc Resurrecting ancestral alcohol dehydrogenases from yeast
    J 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...
  55. ncbi C-5 modified nucleosides: direct insertion of alkynyl-thio functionality in pyrimidines
    Heike A Held
    Department of Chemistry, University of Florida, Gainesville, Florida 32611 7200, USA
    Nucleosides Nucleotides Nucleic Acids 22:391-404. 2003
    ..These products should be useful to support in vitro selection experiments with functionalized DNA...
  56. ncbi The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factors
    Eric A Gaucher
    Mol Biol Evol 19:569-73. 2002
  57. ncbi Synthetic biology
    A Michael Sismour
    Expert Opin Biol Ther 5:1409-14. 2005
    ..Supported by the National Science Foundation as part of its Chemical Bonding program, this work cannot help but generate clarity in our understanding of how biological systems work...
  58. pmc Multiplexed genetic analysis using an expanded genetic alphabet
    Scott C Johnson
    Eragen Biosciences, Inc, Madison, WI 53717, USA
    Clin Chem 50:2019-27. 2004
    ..We describe the development and technical evaluation of a multiplex platform that may foster increased newborn genetic screening...
  59. ncbi The NASA Astrobiology Roadmap
    David J Des Marais
    Space Science Division, NASA Ames Research Center, Moffett Field, California 94035, USA
    Astrobiology 3:219-35. 2003
    ..For each of these goals, Science Objectives outline more specific high-priority efforts for the next 3-5 years. These 18 objectives are being integrated with NASA strategic planning...
  60. ncbi 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
    Maria Wigger
    J Am Soc Mass Spectrom 13:1162-9. 2002
    ....