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Nucleic Acids Research, Vol 27, Issue 16 3371-3379, Copyright © 1999 by Oxford University Press

ARTICLES

Evidence from CD spectra and melting temperatures for stable Hoogsteen- paired oligomer duplexes derived from DNA and hybrid triplexes

GM Hashem, JD Wen, Q Do and DM Gray
Department of Molecular and Cell Biology, Mail Stop FO31, The University of Texas at Dallas, Box 830688, Richardson, TX 75083-0688, USA.

The pyr*pur.pyr type of nucleic acid triplex has a purine strand that is Hoogsteen-paired with a parallel pyrimidine strand (pyr*pur pair) and that is Watson-Crick-paired with an antiparallel pyrimidine strand (pur.pyr pair). In most cases, the Watson-Crick pair is more stable than the Hoogsteen pair, although stable formation of DNA Hoogsteen- paired duplexes has been reported. Using oligomer triplexes of repeating d(AG)12 and d(CT)12 or r(CU)12 sequences that were 24 nt long, we found that hybrid RNA*DNA as well as DNA*DNA Hoogsteen-paired strands of triplexes can be more stable than the Watson-Crick-paired strands at low pH. The structures and relative stabilities of these duplexes and triplexes were evaluated by circular dichroism (CD) spectroscopy and UV absorption melting studies of triplexes as a function of pH. The CD contributions of Hoogsteen-paired RNA*DNA and DNA*DNA duplexes were found to dominate the CD spectra of the corresponding pyr*pur.pyr triplexes.
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