Use of cross-links to study the conformational dynamics of triplex DNA

The conformational dynamics of a 34-base-long pyrimidine purine-pyrimidine motif intramolecular DNA triple helix possessing three cytosine residues in the Hoogsteen strand (1) and a disulfide cross-linked analog (2) were studied by two-dimensional exchange and NOE spectroscopy and by measuring base-catalyzed imino proton exchange rates. Under acidic conditions that stabilize triplexes containing Hoogsteen strand cytosines (pH 6.0 and 1 degree C), sequences 1 and 2 exhibit a small and identical degree of conformational heterogeneity. However, at a higher temperature (pH 6.0 and 37 degrees C), 1 exhibits much more extensive conformational heterogeneity than 2. The exchange times for Watson-Crick imino protons are approximately 1 h for both triplexes. However, the Hoogsteen base-pair lifetimes of 1 could not be measured because this sequence is conformationally labile under the alkaline conditions necessary to conduct these experiments. Because of the extraordinary pH stability conferred by the cross-link, it is possible to estimate the base-pair lifetimes for 2. The lifetimes of the Hoogsteen base pairs range from about 3 to 370 ms, and in all cases are shorter than that of the Watson-Crick base pair contained in the same triplet. These experiments represent the first measurement of base-pair lifetimes within Hoogsteen triplets. The ability to measure individual base-pair lifetimes may prove useful in studies that attempt to modulate triplex properties through rational design.