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Nucleic Acids Research, 1995, Vol. 23, No. 11 1956-1963
© 1995

MOLECULAR BIOLOGY

Effect of competing self-structure on triplex formation with purine-rich oligodeoxynucleotides containing GA repeats

Sarah B. Noonberg1,2,*, Jean-Christophe François1, Thérsèe Garestier1 and Claude Héiène1

1Laboratoire de Biophysique, Musèum National d'Histoire Naturelle INSERM Unité 201-CNRS UA 481, 43 rue Cuvier, 75231 Paris, France 2Cancer Research Institute, University of California at San Francisco Box 0128, San Francisco, CA 94143-0128, USA

* To whom correspondence should be addressed at: Cancer Research Institute, University of California at San Francisco, Box 0128, San Francisco, CA 94143-0128, USA

Received February 10, 1995. Revised April 19, 1995. Accepted April 19, 1995.

Competition between triplex formation with double-stranded DNA and ollgonucleotide self-association was investigated in 23mer GA and GT oligonucleotides containing d(GA)5 or d(GT)5 repeats. Whereas triplex formation with GT oligonucleotides was diminished when temperature increased from 4 to 37°C, triplex formation with GA oligonucleotides was enhanced when temperature Increased within the same range due to the presence of competing Intermolecular GA ollgonucleotide self-structure. This self-structure was determined to be a homoduplex stabilized by the internal GA repeats. UV spectroscopy of these homo-duplexes demonstrated a single sharp transition with rapid kinetics (Tm = 38.5–43.5°C over strand concentrations of 0.5-4 µM, respectively, with transition enthalpy, {Delta}H = –89 ± 7 kcal/mol) in 10 mM MgCl2, 100 mM NaCI, pH 7.0. Homoduplex formation was strongly stabilized by multivalent cations (spermlne > Mg2+ = Ca2+) and destabilized by low concentrations of monovalent cations (K+ = Li+ = Na+) In the presence of divalent cations. However, unlike GA or GT oligo-nucleotide-containlng triplexes, the homoduplex formed even In the absence of multivalent cations, stabilized by only moderate concentrations of monovalent cations (LI+ > Na+ > K+). Through the development of multiple equilibrium states and the resulting depletion of free oligonucteotide, It was found that the presence of competing self-structure could decrease triplex formation under a variety of experimental conditions.


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