Solvent and Salt Effects on Structural Stability of Human Telomere

The free energy and the solvation structures of the G-quadruplex telomeric DNA in pure water and in the 0.1 M aqueous solutions of sodium and potassium chlorides are calculated on the basis of the 3D-RISM theory. To find the most stable structure of each G-quadruplex in the aqueous solutions, the free energy is minimized in the solutions on the basis of the quasi-Newton method using the analytical derivative of the solvation free energy obtained from 3D-RISM. In pure water, the chair-type conformation was found to be the most stable structure, which is followed by basket-, hybrid-, and propeller-type structures in the order. It is clarified that the order of the stability is determined essentially by the solvation free energy, not by the conformational energy. The order of the stability changes in 0.1 M NaCl solutions from that in pure water. The basket-type structure becomes the most stable one in the electrolyte solution. The theoretical finding is consistent with the experimental observation due to NMR. The reversed order of the conformational stability was attributed to the salt effect, especially, to that from the Na+ ions bound at interstrand spaces of DNA. Concerning the conformational stability in KCl solutions, which has not been clarified yet by experiments, our results predict that the order is not changed from that in pure water; that is, the chair-type is the most stable one. The finding suggests that the effect of the potassium ion upon the structure is not so strong as the sodium ion to change the order of the stability determined in pure water. The result is consistent with our finding for RDFs of the ions bound at the interstrand spaces in DNA, which indicates clearly that the affinity of K+ to the binding site is weaker than that of Na+.