Literature DB >> 10908353

Universal bases for hybridization, replication and chain termination.

M Berger1, Y Wu, A K Ogawa, D L McMinn, P G Schultz, F E Romesberg.   

Abstract

Several unnatural, predominantly hydrophobic nucleobases that pack efficiently in duplex DNA without hydrogen bonding functionalities are reported to circumvent the hydrogen bonding-based specificity, both during oligonucleotide hybridization and enzymatic DNA synthesis. The reported nucleoside analogs are efficient 'universal bases' for hybridization, template directed DNA synthesis and chain termination. Moreover, several of the universal bases function in their biological role, hybridization or replication, with an efficiency not significantly reduced relative to their natural counterparts.

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Year:  2000        PMID： 10908353      PMCID： PMC102677          DOI： 10.1093/nar/28.15.2911

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  20 in total

1.  Replication of non-hydrogen bonded bases by DNA polymerases: a mechanism for steric matching.

Authors:  E T Kool
Journal:  Biopolymers       Date:  1998       Impact factor: 2.505

2.  Genetic analysis by peptide nucleic acid affinity MALDI-TOF mass spectrometry.

Authors:  T J Griffin; W Tang; L M Smith
Journal:  Nat Biotechnol       Date:  1997-12       Impact factor: 54.908

Review 3.  DNA sequencing by mass spectrometry.

Authors:  K K Murray
Journal:  J Mass Spectrom       Date:  1996-11       Impact factor: 1.982

4.  How E. coli DNA polymerase I (Klenow fragment) distinguishes between deoxy- and dideoxynucleotides.

Authors:  M Astatke; N D Grindley; C M Joyce
Journal:  J Mol Biol       Date:  1998-04-24       Impact factor: 5.469

5.  A procedure for selective DNA alkylation and detection by mass spectrometry.

Authors:  I G Gut; S Beck
Journal:  Nucleic Acids Res       Date:  1995-04-25       Impact factor: 16.971

Review 6.  Biochemical basis of DNA replication fidelity.

Authors:  M F Goodman; S Creighton; L B Bloom; J Petruska
Journal:  Crit Rev Biochem Mol Biol       Date:  1993       Impact factor: 8.250

7.  Hydrophobic, Non-Hydrogen-Bonding Bases and Base Pairs in DNA.

Authors:  Barbara A Schweitzer; Eric T Kool
Journal:  J Am Chem Soc       Date:  1995-02-22       Impact factor: 15.419

8.  Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases.

Authors:  F Hill; D Loakes; D M Brown
Journal:  Proc Natl Acad Sci U S A       Date:  1998-04-14       Impact factor: 11.205

9.  Comparison of the base pairing properties of a series of nitroazole nucleobase analogs in the oligodeoxyribonucleotide sequence 5'-d(CGCXAATTYGCG)-3'.

Authors:  D E Bergstrom; P Zhang; W T Johnson
Journal:  Nucleic Acids Res       Date:  1997-05-15       Impact factor: 16.971

10.  Effect of the 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole residue on the stability of DNA duplexes and triplexes.

Authors:  O Amosova; J George; J R Fresco
Journal:  Nucleic Acids Res       Date:  1997-05-15       Impact factor: 16.971
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  12 in total

Review 1.  Survey and summary: The applications of universal DNA base analogues.

Authors:  D Loakes
Journal:  Nucleic Acids Res       Date:  2001-06-15       Impact factor: 16.971

2.  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

3.  Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips.

Authors:  V A Vasiliskov; D V Prokopenko; A D Mirzabekov
Journal:  Nucleic Acids Res       Date:  2001-06-01       Impact factor: 16.971

4.  C2'-pyrene-functionalized triazole-linked DNA: universal DNA/RNA hybridization probes.

Authors:  Sujay P Sau; Patrick J Hrdlicka
Journal:  J Org Chem       Date:  2011-11-16       Impact factor: 4.354

5.  Evolving a polymerase for hydrophobic base analogues.

Authors:  David Loakes; José Gallego; Vitor B Pinheiro; Eric T Kool; Philipp Holliger
Journal:  J Am Chem Soc       Date:  2009-10-21       Impact factor: 15.419

6.  The fidelity of replication of the three-base-pair set adenine/thymine, hypoxanthine/cytosine and 6-thiopurine/5-methyl-2-pyrimidinone with T7 DNA polymerase.

Authors:  Harry P Rappaport
Journal:  Biochem J       Date:  2004-08-01       Impact factor: 3.857

7.  Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet.

Authors:  Aaron M Leconte; Gil Tae Hwang; Shigeo Matsuda; Petr Capek; Yoshiyuki Hari; Floyd E Romesberg
Journal:  J Am Chem Soc       Date:  2008-01-25       Impact factor: 15.419

Review 8.  Non-natural nucleotides as probes for the mechanism and fidelity of DNA polymerases.

Authors:  Irene Lee; Anthony J Berdis
Journal:  Biochim Biophys Acta       Date:  2009-09-03

9.  Ambivalent incorporation of the fluorescent cytosine analogues tC and tCo by human DNA polymerase alpha and Klenow fragment.

Authors:  Gudrun Stengel; Byron W Purse; L Marcus Wilhelmsson; Milan Urban; Robert D Kuchta
Journal:  Biochemistry       Date:  2009-08-11       Impact factor: 3.162

10.  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
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