A universal nucleoside for use at ambiguous sites in DNA primers View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1994-06

AUTHORS

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

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-beta-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 (Tm range 3 degrees C). More... »

PAGES

492-493

Journal

TITLE

Nature

ISSUE

6480

VOLUME

369

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/369492a0

    DOI

    http://dx.doi.org/10.1038/369492a0

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1042362221

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/8202140


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