Literature DB >> 11410649

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

D Loakes1.   

Abstract

A universal base analogue forms 'base pairs' with each of the natural DNA/RNA bases with little discrimination between them. A number of such analogues have been prepared and their applications as biochemical tools investigated. Most of these analogues are non-hydrogen bonding, hydrophobic, aromatic 'bases' which stabilise duplex DNA by stacking interactions. This review of the literature of universal bases (to 2000) details the analogues investigated, and their uses and limitations are discussed.

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Year:  2001        PMID： 11410649      PMCID： PMC55727          DOI： 10.1093/nar/29.12.2437

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


  65 in total

1.  Melting studies of short DNA hairpins containing the universal base 5-nitroindole.

Authors:  P M Vallone; A S Benight
Journal:  Nucleic Acids Res       Date:  1999-09-01       Impact factor: 16.971

2.  Optimal reconstruction of a sequence from its probes.

Authors:  A M Frieze; F P Preparata; E Upfal
Journal:  J Comput Biol       Date:  1999 Fall-Winter       Impact factor: 1.479

3.  Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication.

Authors: 
Journal:  Angew Chem Int Ed Engl       Date:  2000-03       Impact factor: 15.336

4.  Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability.

Authors:  P M Vallone; T M Paner; J Hilario; M J Lane; B D Faldasz; A S Benight
Journal:  Biopolymers       Date:  1999-10-05       Impact factor: 2.505

5.  Universal bases for hybridization, replication and chain termination.

Authors:  M Berger; Y Wu; A K Ogawa; D L McMinn; P G Schultz; F E Romesberg
Journal:  Nucleic Acids Res       Date:  2000-08-01       Impact factor: 16.971

6.  The N(8)-(2'-deoxyribofuranoside) of 8-aza-7-deazaadenine: a universal nucleoside forming specific hydrogen bonds with the four canonical DNA constituents.

Authors:  F Seela; H Debelak
Journal:  Nucleic Acids Res       Date:  2000-09-01       Impact factor: 16.971

7.  Nucleotide analogs facilitate base conversion with 3' mismatch primers.

Authors:  J P Day; D Bergstrom; R P Hammer; F Barany
Journal:  Nucleic Acids Res       Date:  1999-04-15       Impact factor: 16.971

8.  Nitroazole universal bases in peptide nucleic acids.

Authors:  H Challa; M L Styers; S A Woski
Journal:  Org Lett       Date:  1999-11-18       Impact factor: 6.005

9.  Quantification of syntrophic fatty acid-beta-oxidizing bacteria in a mesophilic biogas reactor by oligonucleotide probe hybridization.

Authors:  K H Hansen; B K Ahring; L Raskin
Journal:  Appl Environ Microbiol       Date:  1999-11       Impact factor: 4.792

10.  Recognition of nonhybridizing base pairs during nucleotide excision repair of DNA.

Authors:  N Buschta-Hedayat; T Buterin; M T Hess; M Missura; H Naegeli
Journal:  Proc Natl Acad Sci U S A       Date:  1999-05-25       Impact factor: 11.205
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  35 in total

1.  DNA computing using single-molecule hybridization detection.

Authors:  Kristiane A Schmidt; Christiaan V Henkel; Grzegorz Rozenberg; Herman P Spaink
Journal:  Nucleic Acids Res       Date:  2004-09-23       Impact factor: 16.971

2.  Unlocking hidden genomic sequence.

Authors:  Jonathan M Keith; Duncan A E Cochran; Gita H Lala; Peter Adams; Darryn Bryant; Keith R Mitchelson
Journal:  Nucleic Acids Res       Date:  2004-02-18       Impact factor: 16.971

3.  Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution.

Authors:  Tuck Seng Wong; Kang Lan Tee; Berhard Hauer; Ulrich Schwaneberg
Journal:  Nucleic Acids Res       Date:  2004-02-10       Impact factor: 16.971

4.  Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.

Authors:  Samra Obeid; Wolfram Welte; Kay Diederichs; Andreas Marx
Journal:  J Biol Chem       Date:  2012-02-07       Impact factor: 5.157

5.  Solution structure of a dsDNA:LNA triplex.

Authors:  Jesper J Sørensen; Jakob T Nielsen; Michael Petersen
Journal:  Nucleic Acids Res       Date:  2004-11-18       Impact factor: 16.971

6.  A hydrophobic similarity analysis of solvation effects on nucleic acid bases.

Authors:  Jordi Muñoz-Muriedas; Xavier Barril; José María López; Modesto Orozco; Francisco Javier Luque
Journal:  J Mol Model       Date:  2006-09-21       Impact factor: 1.810

7.  Canonical nucleosides can be utilized by T4 DNA ligase as universal template bases at ligation junctions.

Authors:  Rashada C Alexander; Ashley K Johnson; Jeffrey A Thorpe; Travis Gevedon; Stephen M Testa
Journal:  Nucleic Acids Res       Date:  2003-06-15       Impact factor: 16.971

8.  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

9.  Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog.

Authors:  Alexander M Spring-Connell; Marina G Evich; Harald Debelak; Frank Seela; Markus W Germann
Journal:  Nucleic Acids Res       Date:  2016-08-26       Impact factor: 16.971

10.  Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs.

Authors:  Alrun N Koller; Jelena Bozilovic; Joachim W Engels; Holger Gohlke
Journal:  Nucleic Acids Res       Date:  2010-01-15       Impact factor: 16.971
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