The heminucleotide scheme: an effective probe in the analysis and description of ordered polynucleotide structures

Abstract

The heminucleotide scheme formulated recently permits treatments of the repeating nucleotide backbone in terms of two conformationally similar moieties of constant magnitude spanning its 5' and 3' halves. The scheme is utilized in describing the conformational features of the ordered poly(mononucleotide) helices of A-, B-, and D-DNA, polyadenylic acid, and poly(dinucleotide) helices of Z_I and Z_II types through distance diagonal plots. The unique feature of these diagonal plots lies in the fact that the variations in the observed patterns can be directly correlated with pairs of backbone bond rotations ψ ,ψ ' (C5'-C4' and C4'-C3'), of the sugar residue and ω ,ω' (P-O3' and P-O5') of the phosphodiester, which determine the relative orientations of the heminucleotides and, therefore, the variety in the secondary structures. Thus, the heminucleotide scheme through its constant P.C4' and C4'.P separations provides common premises for characterization and comparison of the observed secondary structures. It is not feasible otherwise through a distance plot of nucleotide P.P separations or between any other atoms, since they vary depending on the backbone torsions, especially (ψ ,ψ ') of the sugar residue. The plots afford identification at a glance of the secondary structural features such as the differences in the widths of the major and minor grooves, regions of closer separation, the parallel and antiparallel nature of the helical strand, and even the characteristic of the repeating motif, whether mono- or dinucleotide. A simple description such as the above may aid in better understanding the binding of metals, salts, solvents, etc., and hence of the conformational transitions among the different secondary structures.