Nucleic Acids Research, Vol 24, Issue 13 2606-2613, Copyright © 1996 by Oxford University Press
CY Huang, G Bi and PS Miller
Homopurine sequences of duplex DNA are binding sites for triplex- forming
oligodeoxyribopyrimidines. The interactions of synthetic duplex DNA targets
with an oligodeoxyribopyrimidine containing N4-(6-amino-2-
pyridinyl)deoxycytidine (1), a nucleoside designed to interact with a
single C-G base pair interruption of the purine target tract, was studied
by UV melting, circular dichroism spectroscopy and dimethylsulfate
alkylation experiments. Nucleoside 1 supports stable triplex formation at
pH 7.0 with formation of a 1-Y-Z triad, where Y-Z is a base pair in the
homopurine tract of the target. Selective interaction was observed when Y-Z
was C-G, although A-T and, to a lesser extent, T-A and G-C base pairs were
also recognized. The circular dichroism spectra of the triplex having a
1-C-G triad were similar to those of a triplex having a C(+)-G-C triad,
suggesting that the overall structures of the two triplexes are quite
similar. Removal of the 6-amino group from 1 essentially eliminated triplex
formation. Reaction of a triplex having the 1-C-G triad with
dimethylsulfate resulted in a 50% reduction of methylation of the G residue
of this triad. In contrast, the G of a similar triplex containing a U-C-G
triad was not protected from methylation by dimethylsulfate. These results
are consistent with a binding mode in which the 6-amino-2-pyridinyl group
of 1 spans the major groove of the target duplex at the 1-C-G binding site
and forms a hydrogen bond with the O6 of G. An additional stabilizing
hydrogen bond could form between the N4 of the imino tautomer of 1 and the
N4 amino group of C.
ARTICLES
Triplex formation by oligonucleotides containing novel deoxycytidine derivatives [published erratum appears in Nucleic Acids Res 1997 Sep 15;25(18):following 3750]
Department of Biochemistry, School of Hygiene and Public Health, The Johns Hopkins University, Baltimore, MD 21205, USA.
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