VIBRATIONAL NORMAL-MODES AND DYNAMICAL STABILITY OF DNA TRIPLEX POLY(DA)CENTER-DOT-2POLY(DT) - S-TYPE STRUCTURE IS MORE STABLE AND IN BETTER AGREEMENT WITH OBSERVATIONS IN SOLUTION

A normal-mode and statistical mechanical calculation was carried out t o determine the vibrational normal modes, contribution of internal flu ctuations to the free energy, and hydrogen bond disruption of DNA trip ler poly(dA). 2poly(dT). The calculation was performed on both the x-r ay fiber diffraction model with a N-type sugar conformation, and a new ly proposed model with a S-type sugar conformation. Our calculated nor mal modes for the S-type structure are in better agreement with observ ed IR spectra for samples in D2O solution. We also find that the contr ibution of internal fluctuations to free energy, premelting hydrogen b ond disruption probability, and hydrogen bond melting temperatures for the Hoogsteen and Watson-Crick hydrogen bonds all show that the S-typ e structure is dynamically more stable than the N-type structure in a nominal solution environment. Therefore our calculation supports exper imental findings that the tripler d(T)(n) . d(A)(n)d(T)(n), most likel y adopts a S-type sugar conformation in solution or at high humidity. Our calculations, however, do not preclude the possibility of an N-typ e conformation at lower humidities.