Investigations into the unfolding of a DNA quadruplex: Effect of loop sequence

Understanding of the human telomere and telomerase is expected to provide major insights into genome stability, cancer, and telomere-related diseases. Quadruplexes have been received as a potential target for anti-cancer therapy because of their ability to inhibit telomerase. Hence, it is very important to have a firm understanding of the different structures that they can form as well as their respective stabilities in order to use quadruplexes in developing new cancer therapeutics. Previous studies have indicated that the unfolding of the DNA quadruplex formed from (TTAGGG)4 in potassium solution proceeds via a three state mechanism. Our interest is the nature of the intermediate and the mechanism of the unfolding. Results of circular dichroism (CD) suggest that unknown intermediate is a double hairpin which would form if the backside loop of the folded quadruplex, which corresponds to the third TTA segment of (TTAGGG)4, acts as a "hinge." To investigate this further, we characterized the unfolding of DNA quadruplexes formed where each loop of the quadruplex was permuted to all possible combinations of A and T.