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Nucleic Acids Research, 2000, Vol. 28, No. 3 770-775
© 2000 Oxford University Press

Stabilities of intrastrand pyrimidine motif DNA and RNA triple helices

Paula Rodrigues Hoyne, A. Marquis Gacy1, Cynthia T. McMurray1 and L. James Maher III*

Department of Biochemistry and Molecular Biology, Mayo Foundation, Rochester, MN 55905, USA and 1Department of Pharmacology, Mayo Foundation, Rochester, MN 55905, USA

Nucleic acid triple helices have provoked interest since their discovery more than 40 years ago, but it remains unknown whether such structures occur naturally in cells. To pursue this question, it is important to determine the stabilities of representative triple helices at physiological temperature and pH. Previous investigations have concluded that while both DNA and RNA can participate in the pyrimidine triplex motif under mildly acidic conditions, these structures are often relatively unstable at neutral pH. We are now explorin g the stability of intrastrand DNA and RNA pyrimidine motif triplexes at physiological temperature and pH. Duplex and triplex formation were monitored by thermal denaturation analysis, circular dichroism spectroscopy and gel shift experi­ments. Short intrastrand triplexes were observed to form in the pyrimidine motif in both DNA and RNA. In the presence of physiological concentrations of Mg2+ and at physiological pH, all detected triplexes were sufficiently stable to persist at physiological temperature. If sequences specifying such intrastrand triplexes are encoded in genomes, the potential exists for the formation of stable structures in RNA or DNA in vivo.

* To whom correspondence should be addressed. Tel: +1 507 284 9041; Fax: +1 507 284 2053; Email: maher@mayo.edu


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