Polynucleotide Models. A Correlation Between Helical Parameters and the Radial Position o f the Backbone
A striking result of structural studies on polynucleotides and nucleotides is that two backbone conformations are highly preferred. They differ primarily in whether the sugar conformation is of the C(B')-endo [C(S')-exo] or c(S')-endo
These "standard" backbones imply that the same distances should be found between given atoms in adjacent residues in the backbones of a number of polynucleotides. For example, the same separation should occur between the P atoms of adjacent residues, and a different but constant separation should occur between the C(1') atoms of adjacent residues, and so on. A survey of a wide range of polynucleotide models indicates that this prediction is met to a high degree of accuracy. The C(l')-C(l') distance is seen to be relatively constant, not only in duplex structures, but also in threeor four-stranded polymers, in a hypothetical one-stranded structure, and even between nearest neighbors in a helical aggregate of guanosine 5'-monophosphate monomers (Table I). The average C(1')-C(1') distance in the polyribonucleotides listed is 5.52 8, with an average absolute deviation of 0.12 A. The corresponding distance for the polydeoxyribonucleotide structures listed is 5.06 with an average absolute deviation of 0.14 A. The C(1')-C(1') distance can thus be regarded as a single virtual bond of relatively constant length. A single virtual bond has previously been used to represent a monomer unit in a polynucleotide, in the interpretation of physicalchemical properties of poly(rA) solutions by Eisenberg and Felsenfeld.6 A single virtual bond model has also been used in theoretical studies of polynucleotide conformation by The backbone position is then defined by the length of this bond and its orientation relative to the helix axis. In turn, the orientation of this virtual bond is defined by its radial distance from the helix axis rC(1,) and its inclination to the helix axis. These parameters are all simply related through Eq. (1):