Literature DB >> 17967435

Model systems for understanding DNA base pairing.

Andrew T Krueger1, Eric T Kool.   

Abstract

The fact that nucleic acid bases recognize each other to form pairs is a canonical part of the dogma of biology. However, they do not recognize each other well enough in water to account for the selectivity and efficiency that is needed in the transmission of biological information through a cell. Thus proteins assist in this recognition in multiple ways, and recent data suggest that these mechanisms of recognition can vary widely with context. To probe how the chemical differences of the four nucleobases are defined in various biological contexts, chemists and biochemists have developed modified versions that differ in their polarity, shape, size, and functional groups. This brief review covers recent advances in this field of research.

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Year:  2007        PMID: 17967435      PMCID: PMC2175026          DOI: 10.1016/j.cbpa.2007.09.019

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  48 in total

1.  RNA recognition by fluor-aromatic substituted.

Authors:  A Zivković; J W Engels
Journal:  Nucleosides Nucleotides Nucleic Acids       Date:  2005       Impact factor: 1.381

2.  Probing the active site tightness of DNA polymerase in subangstrom increments.

Authors:  Tae Woo Kim; James C Delaney; John M Essigmann; Eric T Kool
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-25       Impact factor: 11.205

3.  Functional evidence for a small and rigid active site in a high fidelity DNA polymerase: probing T7 DNA polymerase with variably sized base pairs.

Authors:  Tae Woo Kim; Luis G Brieba; Tom Ellenberger; Eric T Kool
Journal:  J Biol Chem       Date:  2005-11-27       Impact factor: 5.157

4.  Gene silencing activity of siRNAs with a ribo-difluorotoluyl nucleotide.

Authors:  Jie Xia; Anne Noronha; Ivanka Toudjarska; Feng Li; Akin Akinc; Ravi Braich; Maria Frank-Kamenetsky; Kallanthottathil G Rajeev; Martin Egli; Muthiah Manoharan
Journal:  ACS Chem Biol       Date:  2006-04-25       Impact factor: 5.100

5.  A synthetic nucleoside probe that discerns a DNA adduct from unmodified DNA.

Authors:  Jiachang Gong; Shana J Sturla
Journal:  J Am Chem Soc       Date:  2007-04-03       Impact factor: 15.419

6.  Human DNA polymerase alpha uses a combination of positive and negative selectivity to polymerize purine dNTPs with high fidelity.

Authors:  Jeff Beckman; Kristi Kincaid; Michal Hocek; Thomas Spratt; Joachim Engels; Richard Cosstick; Robert D Kuchta
Journal:  Biochemistry       Date:  2007-01-16       Impact factor: 3.162

7.  DNA--metal base pairs.

Authors:  Guido H Clever; Corinna Kaul; Thomas Carell
Journal:  Angew Chem Int Ed Engl       Date:  2007       Impact factor: 15.336

8.  Selective pairing of polyfluorinated DNA bases.

Authors:  Jacob S Lai; Eric T Kool
Journal:  J Am Chem Soc       Date:  2004-03-17       Impact factor: 15.419

9.  Exploration of factors driving incorporation of unnatural dNTPS into DNA by Klenow fragment (DNA polymerase I) and DNA polymerase alpha.

Authors:  Kristi Kincaid; Jeff Beckman; Aleksandra Zivkovic; Randall L Halcomb; Joachim W Engels; Robert D Kuchta
Journal:  Nucleic Acids Res       Date:  2005-05-06       Impact factor: 16.971

Review 10.  Synthetic biology.

Authors:  Steven A Benner; A Michael Sismour
Journal:  Nat Rev Genet       Date:  2005-07       Impact factor: 53.242

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  24 in total

1.  Importance of steric effects on the efficiency and fidelity of transcription by T7 RNA polymerase.

Authors:  Sébastien Ulrich; Eric T Kool
Journal:  Biochemistry       Date:  2011-11-01       Impact factor: 3.162

2.  Templating efficiency of naked DNA.

Authors:  Eric Kervio; Annette Hochgesand; Ulrich E Steiner; Clemens Richert
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-16       Impact factor: 11.205

3.  Probing the interaction of archaeal DNA polymerases with deaminated bases using X-ray crystallography and non-hydrogen bonding isosteric base analogues.

Authors:  Tom Killelea; Samantak Ghosh; Samuel S Tan; Pauline Heslop; Susan J Firbank; Eric T Kool; Bernard A Connolly
Journal:  Biochemistry       Date:  2010-07-13       Impact factor: 3.162

4.  Measurement and theory of hydrogen bonding contribution to isosteric DNA base pairs.

Authors:  Omid Khakshoor; Steven E Wheeler; K N Houk; Eric T Kool
Journal:  J Am Chem Soc       Date:  2012-02-02       Impact factor: 15.419

5.  Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?

Authors:  Jiří Šponer; Judit E Šponer; Anton I Petrov; Neocles B Leontis
Journal:  J Phys Chem B       Date:  2010-11-04       Impact factor: 2.991

6.  Molecular electrostatic potentials of DNA base-base pairing and mispairing.

Authors:  Ivonne Otero-Navas; Jorge M Seminario
Journal:  J Mol Model       Date:  2011-04-06       Impact factor: 1.810

7.  Encoding phenotype in bacteria with an alternative genetic set.

Authors:  Andrew T Krueger; Larryn W Peterson; Jijumon Chelliserry; Daniel J Kleinbaum; Eric T Kool
Journal:  J Am Chem Soc       Date:  2011-10-21       Impact factor: 15.419

8.  DNA interstrand cross-linking upon irradiation of aryl halide C-nucleotides.

Authors:  Dianjie Hou; Marc M Greenberg
Journal:  J Org Chem       Date:  2014-02-24       Impact factor: 4.354

9.  Mechanistic studies in the synthesis of a series of thieno-expanded xanthosine and guanosine nucleosides.

Authors:  Zhibo Zhang; Orrette R Wauchope; Katherine L Seley-Radtke
Journal:  Tetrahedron       Date:  2008-11-24       Impact factor: 2.457

10.  Unnatural imidazopyridopyrimidine:naphthyridine base pairs: selective incorporation and extension reaction by Deep Vent (exo- ) DNA polymerase.

Authors:  Shintaro Ogata; Mayumi Takahashi; Noriaki Minakawa; Akira Matsuda
Journal:  Nucleic Acids Res       Date:  2009-07-23       Impact factor: 16.971

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