Conformation of polynucleotides : studies on D-DNA

Abstract

The aim of this thesis has been to critically examine the available experimental data on the D-form of DNA in the solid state and to see what possible structures are consistent with the data. The model-building work reported in this thesis indicates that:

(a) Stereochemically satisfactory helical models of either handedness can be built for D-DNA. (b) Both left- and right-handed models are equally in agreement with the available X-ray data.

Left-handed models for D-DNA have been rejected in the past on the basis of X-ray agreement indices, stereochemistry, and other criteria. The present superior X-ray data and the model-building studies, however, clearly show that one cannot reject left-handed models on the above grounds.

This conclusion is supported by the use of further inputs to model building, in the form of the phosphate orientation angles and g g

derived from IR measurements on oriented DNA films. The binding of cations is also shown to occur with equal facility in the case of both left- and right-handed models. Energy calculations also indicate that models of both handedness are equally stable.

The D-form, while it is similar to other forms of DNA in its conformational flexibility, is in one sense structurally unique. D-DNA has a narrow minor groove of 6-7 Å width, unlike natural forms of DNA. Such a narrow minor groove enables a cation to coordinate to the phosphate oxygens directly across the minor groove. The available evidence indicates that such binding may be an important means of stabilization of the D-form structure. There is also evidence that under certain conditions, the structure can become locked into the D-form.

No single-crystal data are available on the D-form as yet. This is presumably because no long stretches of repeating purine-pyrimidine sequences have been crystallized. It would appear that long stretches (one turn or more) of poly d(A-T) or poly d(I-C) under salt conditions equivalent to about one Na + + ion per phosphate group should crystallize into the D-form. In such experiments, one would expect to find helices of both handedness. Only crystal structure analysis can provide further insights into the problem.

The D-form of DNA is unique in the sense that, while it has a flexible polynucleotide backbone, it can, under certain conditions, become a rigid structure stabilized by cation binding.