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 5β² and 3β² halves. The scheme is utilized in describing the conformational features of the ordered poly(mononucleotide) helices of Aβ, Bβ, and DβDNA, 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 Ο,Οβ² (C5β²βC4β² and C4β²βC3β²), of the sugar residue and Οβ²,Ο (PβO3β² and PβO5β²) 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 PΛC4β² and C4β²ΛP separations provides common premises for characterization and comparison of the observed secondary structures. It is not feasible otherwise through a distance plot of nucleotide PΛP separations or between any other atoms, since they vary depending on the backbone torsions, especially (Ο,Οβ²) 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 monoβ 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.