Stabilities of nearest‐neighbor doublets in double‐helical DNA determined by fitting calculated melting profiles to observed profiles

Abstract

Abstract Melting profiles were calculated for restriction fragments of ϕX174 and fd phage DNAs and compared with experimental profiles. The algorithm of Fixman and Freire was slightly modified so that a stability parameter was assigned not to a base pair but to each nearest‐neighbor doublet. Stabilities of the 10 kinds of nearest‐neighbor doublets were estimated by fitting the calculated profiles to the observed ones. Agreement of the calculated and observed profiles was much improved by this modification. The most interesting finding was that purine (3′‐5′) pyrimidine stackings are much more stable than their respective reverses. The order of nearest‐neighbor stabilities is in excellent agreement with that of negative stacking energies calculated by Rein and coworkers by a quantum‐chemical method.