Is 3′-nucleotide rigid?

Abstract

Conformational analysis of nucleic acids and polynucleotides is far more complex than that of proteins and polypeptides, due to five single bond rotations in addition to the sugar puckerings in the monomer. Sundaralingam¹ proposed the concept of the ‘rigid’ nucleotides from analysis of crystal structure data, with the flexibility allowed only about the phosphodiester bonds. However, the crystal structure of deoxyguanosine-5′–phosphate^2,3 indicates at gt conformation about the C-4′–C-5′ bond against gg in a conformationally rigid nudeotide¹. Jack et al.⁴ considered the flexibility of nucleotides in tRNA about the C-4′–C-5′ bond, thereby introducing the concept of ‘non-rigid’ ribonucleotides. Conformational flexibility of the f uranose ring in DNA and RNA and their energetics using classical and quantum chemical methods have been reported^5–8. We have examined the flexibility of 3′-nucleotides. α, the most important of the conformational parameters defining the 3′-end of a nucleotide unit⁹, has a value in the range 195°–270° in all the 3′-nucleotides, dinucleoside monophosphates and higher oligomers which have been surveyed. A survey of the proposed structures of polyribonudeotides^10,11 also shows the values of a to be greater than 200°. However, the structures proposed for B-DNA by Arnott and Hukins^12,13 and D-DNA by Arnott et al.¹⁴ have values of α of 155° and 141° respectively, much lower than the lowest observed value. The structure for B-DNA has two strong, short contacts (C-2′…OP-1 = 2.64 Å and HC-2″…OP-1 = 1.79 Å) which lead to an energetically unfavourable conformation. Hence, it is of interest to investigate whether, by allowing flexibility to the sugar moiety in the nucleotide unit, it is possible to make the structure energetically favourable. Here, conformational energy calculations were carried out to determine the range of α which would give rise to energetically favoured conformations with different sugar puckerings. Our analysis has shown that the theoretically obtained range is nearly the same as the preferred range in crystals, indicating the flexibility of the 3′-nucleotides.