Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

Proton Exchange and Base Opening in Two DNA Triple Helices

DNA triple helices form by binding of a third strand in the major groove of a double-helical DNA molecule. In YRY triple helices, the third strand in pyrimidine rich and binds in a parallel orientation relative to the purine strand of the double helix. A protonated cytosine in the third strand can recognize the guanine in a Watson-Crick GC base pair. Similarly, a thymine in the third strand can recognize the adenine in a Watson-Crick AT base pair. Work from other laboratories has demonstrated that introducing a guanine in the third strand can extend this recognition code: the guanine can recognize the thymine in a Watson-Crick TA base pair by forming a GTA triad.

In the present work, we have used proton exchange and nuclear magnetic resonance (NMR) spectroscopy to characterize the stability of individual base triads in a triple-helical DNA containing a GTA triad. The DNA molecule investigated is 5'-d(AGATAGAA-CCCC-TTCTATCT-TATA-TCTGTCTT)-3' in which the highlighted bases form the GTA triad (1). We have measured the solvent exchange rates of imino protons in both Watson-Crick and Hoogsteen base pairs in this triple helix as a function of temperature in the range from 1 to 50¼C. As a control, we have also characterized the DNA triple helix 5'-d(AGAGAGAA-CCCC-TTCTCTCT-TTT-TCTCTCTT)-3' in which the GTA triad is replaced by a canonical C+GC triad (2). Comparison of the imino proton exchange rates and the exchange activation parameters in these two DNA triple helices allows us to define the energetic effects of GTA triads upon the stability of the DNA triple helix.

Supported by a grant from the National Science Foundation

References and Footnotes
  1. Wang, E., Malek, S., and Feigon, J. Biochemistry 31, 4838-4846 (1992).
  2. Macaya, R., Wang, E., Sklenar, P.S.V., and Feigon, J. J. Mol. Biol. 225, 755-773 (1992).

Lihong Jiang (1), and Irina M. Russu (2),

Department of Molecular Biology and Biochemistry (1), and Department of Chemistry (2), Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA.
E-mail: irussu@wesleyan.edu. Phone: (860)-685-2428