PMID: 9539724May 16, 1998Paper

Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases

Proceedings of the National Academy of Sciences of the United States of America
F HillD M Brown

Abstract

A universal base that is capable of substituting for any of the four natural bases in DNA would be of great utility in both mutagenesis and recombinant DNA experiments. This paper describes the properties of oligonucleotides incorporating two degenerate bases, the pyrimidine base 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one and the purine base N6-methoxy-2,6-diaminopurine, designated P and K, respectively. An equimolar mixture of the analogues P and K (called M) acts, in primers, as a universal base. The thermal stability of oligonucleotide duplexes were only slightly reduced when natural bases were replaced by P or K. Templates containing the modified bases were copied by Taq polymerase; P behaved as thymine in 60% of copying events and as cytosine in 40%, whereas K behaved as if it were guanine (13%) or adenine (87%). The dUTPase gene of Caenorhabditis elegans, which we have found to contain three nonidentical homologous repeats, was used as a model system to test the use of these bases in primers for DNA synthesis. A pair of oligodeoxyribonucleotides, each 20 residues long and containing an equimolar mixture of P and K at six positions, primed with high specificity both T7 DNA polymerase in sequencing reactions and Taq ...Continue Reading

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Citations

May 9, 2002·Mutation Research·Chie OtsukaKazuo Negishi
Dec 12, 2001·Bioorganic & Medicinal Chemistry Letters·Akimitsu OkamotoIsao Saito
Feb 24, 2001·Nucleosides, Nucleotides & Nucleic Acids·D LoakesS Nampalli
Apr 2, 1999·Nucleic Acids Research·J P DayF Barany
Jul 25, 2000·Nucleic Acids Research·M BergerF E Romesberg
Aug 10, 2010·Nucleic Acids Research·Katherine L Petrie, Gerald F Joyce
Aug 10, 2007·Journal of Virology·Jason D GraciCraig E Cameron
Jun 22, 2012·Journal of Nucleic Acids·Jason M Walsh, Penny J Beuning
Feb 14, 2006·Journal of Virological Methods·Thomas Bruun RasmussenMonserrat Agüero
Oct 3, 2003·Chemistry & Biology·Natasha PaulV Jo Davisson
Sep 13, 2005·Structure·Nicolas TarbouriechWim P Burmeister
Oct 1, 1998·Journal of Molecular Biology·G S SchuermanS A Salisbury
Apr 13, 2004·Antiviral Chemistry & Chemotherapy·Jason D Graci, Craig E Cameron
Apr 23, 2008·Current Protocols in Nucleic Acid Chemistry·D E Bergstrom
Jun 3, 2009·Current Protocols in Nucleic Acid Chemistry·Donald E Bergstrom

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