Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases

Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4258-63. doi: 10.1073/pnas.95.8.4258.


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 polymerase in PCRs; no nonspecific amplification was obtained on genomic DNA of C. elegans. Use of P and K can significantly reduce the complexity of degenerate oligonucleotide mixtures, and when used together, P and K can act as a universal base.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Binding Sites
  • Caenorhabditis elegans / enzymology
  • Caenorhabditis elegans / genetics
  • DNA / chemistry
  • DNA / metabolism
  • DNA Primers
  • DNA-Directed DNA Polymerase / metabolism*
  • Genes, Helminth
  • Molecular Sequence Data
  • Oligodeoxyribonucleotides / chemical synthesis
  • Oligodeoxyribonucleotides / chemistry*
  • Oligodeoxyribonucleotides / metabolism*
  • Plasmids
  • Polymerase Chain Reaction
  • Purines
  • Pyrimidines
  • Pyrophosphatases / genetics*
  • Repetitive Sequences, Nucleic Acid
  • Substrate Specificity
  • Taq Polymerase / metabolism*
  • Templates, Genetic


  • DNA Primers
  • Oligodeoxyribonucleotides
  • Purines
  • Pyrimidines
  • DNA
  • Taq Polymerase
  • bacteriophage T7 induced DNA polymerase
  • DNA-Directed DNA Polymerase
  • Pyrophosphatases
  • dUTP pyrophosphatase