Structural and Energetic Consequences of Noncomplementary Base Oppositions in Nucleic Acid Helices

Abstract

Publisher Summary This chapter describes that secondary structure in nucleic acids generally consists of double-stranded helical regions that are stabilized by a variety of interbase forces. Bases in the opposing strands are regularly oriented with respect to the long axis of the helix by at least two hydrogen bonds, and only certain oppositions seem to be allowed, usually a purine and a pyrimidine. In the chapter, the variety of codon-anticodon interactions observed in protein synthesis suggests that there can be some flexibility in these requirements, such that pairing need not be restricted to base oppositions that are precisely accommodated by the one-dimensional lattice of a long double helix. The conformational possibilities of base oppositions that fall outside these complementary categories also merit definition, particularly in view of several recent indications that noncomplementary residues may have important functional roles in naturally occurring nucleic acids. The conformational alternatives available to noncomplementary residues within helical regions logically fall into two general categories, one being intrahelical and the other extrahelical or “looped-out’’. The conformational class that is adopted in a particular case depends upon the interplay of some factors, such as: (1) the degree of local stereochemical distortion of the helix when the non-complementary residue is left intrahelical, (2) conformatianal entropy, (3) solvation, (4) charge effects, and (5) the relative stacking tendency of the noncomplementary base