On the propeller structure of isolated Watson-Crick base pairs.

The nucleotide sequence dependence of the DNA and RNA secondary structure is a problem of current interest in molecular biophysics. The key role of stacking interactions in determining this dependence is widely accepted [1, 2], It is be­ lieved that the propeller twisting of base pairs, ob­ served in the structure of both nucleic acids and crystals of nucleosides and nucleotides is a direct manifestation of these interactions. Earlier we have revealed a nonplanar structure (with respect to the amino group) of adenine, guanine and cytosine molecules [3] using the quantum-chemical PCILO method. In these com­ pounds the stable sp3-hybridized character of the N atom valence bonds of the NHU-group is respon­ sible for the slope of the HNH plane of — 40 to the molecule plane. The aim of this note is to dem­ onstrate in terms of usual H-bonding how the pro­ peller structure of the complementary base pairs can be realized without any stacking, only due to this feature of nitrous base geometry. The conformation study of single Watson-Crick adenine-thymine (A-T) and guanine-cytosine (G-C) pairs has been carried out by the PCILO method. The variations of (i) the inter-base dis­ tances along the central hydrogen bond N-H--N and (ii) angle 0 of the rotation of purine and pyr­ imidine base planes around this bond were consid­ ered. The main result is plotted in Fig. 1.