A universal nucleoside for use at ambiguous sites in DNA primers

R. Nichols, P. C. Andrews, Peiming Zhang, D. E. Bergstrom

Research output: Contribution to journalArticle

95 Citations (Scopus)

Abstract

A NON-DISCRIMINATORY base analogue, or universal base, would be an invaluable component of oligonucleotide probes and primers for solving the design problems that arise as a result of the degeneracy of the genetic code, or when only fragmentary peptide sequence data are available. We have designed an alternative to previous universal nucleoside candidates, a new analogue, 1-(2'-deoxy-β-D-ribofuranosyl)-3-nitropyrrole (designated M; Fig. 1), which maximizes stacking while minimizing hydrogen-bonding interactions without sterically disrupting a DNA duplex. Oligonucleotides containing M at several sites were used as primers for sequencing and the polymerase chain reaction. The sequencing primer d(5'-CGT AAM CAM AAM ACM AT-3') is as effective as the exact match d(5'-CGT AAT CAG AAA ACA AT-3'). It is also possible to sequence using a primer containing M at several contiguous positions, for example d(5'-CGT AAT MMM MMM MMM AT-3'). Melting curves show that duplexes formed on hybridization of the sequences d(5'-CCT TTT TMT TTT TGG-3') and d(5'-CCA AAA AXA AAA AGG-3'), where X is A, C, G or T, melted at a lower temperature than the corresponding duplexes containing only d(A·T) and d(C·G) base pairs, but showing little variation among different X bases (T(m) range 3 °C).

Original languageEnglish (US)
Pages (from-to)492-493
Number of pages2
JournalNature
Volume369
Issue number6480
DOIs
StatePublished - Jun 9 1994
Externally publishedYes

Fingerprint

DNA Primers
Nucleosides
Genetic Code
Oligonucleotide Probes
Hydrogen Bonding
Oligonucleotides
Base Pairing
Freezing
Polymerase Chain Reaction
Peptides
Temperature
DNA
deoxy(cytidylyl-guanylyl-thymidylic acid)

ASJC Scopus subject areas

  • General

Cite this

Nichols, R., Andrews, P. C., Zhang, P., & Bergstrom, D. E. (1994). A universal nucleoside for use at ambiguous sites in DNA primers. Nature, 369(6480), 492-493. https://doi.org/10.1038/369492a0

A universal nucleoside for use at ambiguous sites in DNA primers. / Nichols, R.; Andrews, P. C.; Zhang, Peiming; Bergstrom, D. E.

In: Nature, Vol. 369, No. 6480, 09.06.1994, p. 492-493.

Research output: Contribution to journalArticle

Nichols, R, Andrews, PC, Zhang, P & Bergstrom, DE 1994, 'A universal nucleoside for use at ambiguous sites in DNA primers', Nature, vol. 369, no. 6480, pp. 492-493. https://doi.org/10.1038/369492a0
Nichols R, Andrews PC, Zhang P, Bergstrom DE. A universal nucleoside for use at ambiguous sites in DNA primers. Nature. 1994 Jun 9;369(6480):492-493. https://doi.org/10.1038/369492a0
Nichols, R. ; Andrews, P. C. ; Zhang, Peiming ; Bergstrom, D. E. / A universal nucleoside for use at ambiguous sites in DNA primers. In: Nature. 1994 ; Vol. 369, No. 6480. pp. 492-493.
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