A hydrogen exchange study of the open segment in a DNA double helix

The kinetics of the hydrogen-deuterium exchange reactions of double-helical poly[d(A-T)] X poly[d(A-T)], poly(dA) X poly(dT), and constituent nucleosides (deoxyadenosine and thymidine) have been examined at various temperatures by stopped-flow ultraviolet spectrophotometry, in the spectral region 240-300 nm. The results were interpreted on the basis of a mechanism of the hydrogen exchange reaction of a helical polynucleotide, proposed by Englander and colleagues as well as by the Tsuboi and Nakanishi group. It was concluded that the rates of the base-pair opening reactions are nearly equal to one another in double-helical DNAs, irrespective of the base sequence. On the other hand, the free energy required for bringing the open segment at a particular base-pair was found to be much greater for poly(dA) X poly(dT) than for poly[d(A-T)] X poly[d(A-T)].