We used a combination of spectroscopic and calorimetric techniques to determine complete thermodynamic profiles accompanying the folding of a set of triple helices and control duplexes. Specifically, we studied the sequences: d(A7C5T7C5T7), d(A6C5T6C5T6), d(A6C5T6), d(AGAGAGAC5TCTCTCTC5-TCTCTCT), d(AGAGAC5TCTCTC5TCTCT), d(AGAGAC5TCTCTC2), d(AAGGAC5TCCTTC5TTCCT), d(AGG- AAC5TTCCTC5TCCTT), and d(GAAAGC5CTTTCC5CTTTC). Circular dichroism spectroscopy indicated that all triplexes and duplexes are in the "B" conformation. DSC melting experiments revealed that the formation of triplexes is accompanied by a favorable free energy change, which arises from the compensation of a large and favorable enthalpic contribution with an unfavorable entropic contribution. Comparison of the thermodynamic profiles of these triplexes yielded enthalpic contributions of -24 kcal/mol, -23 kcal/mol, and -22 kcal/mol for the formation of TAT/TAT, TAT/CGC+, and CGC+/CGC+ base triplet stacks, respectively. UV melts as a function of sodium concentration show sodium ions stabilize the triplexes that contain only TAT triplets but destabilize the triplexes that contain CGC+ triplets. UV melts as a function of pH indicate that the protonation of the third strand and loop cytosines stabilizes the triplexes that contain CGC+ and TAT triplets, respectively. Our overall results suggest that the triplex to duplex transition of triplexes that contain CGC+ triplets is accompanied by a release of protons and an uptake of sodium, while their duplex to random coil transition is accompanied by a release of sodium ions. A consequence of this opposite sodium dependence is that their coupled transitions are nearly independent of sodium concentration but are dependent on the experimental pH.
ASJC Scopus subject areas
- Colloid and Surface Chemistry