GEOMETRY OF EXPERIMENTALLY OBSERVED RNA RESIDUES IN TRANSFER-RNA AND DINUCLEOSIDE MONO-PHOSPHATES - EFFECT OF SMALL VARIATIONS IN THE BACKBONE ANGLES

The polymerization of various experimentally observed conformers of RNA from tRNA and some dinucleoside monophosphates have been examined with a program that computes the basic helix parameters directly from the six backbone torsion angles ω′, ϕ′, ψ′, ψ, ϕ, ω to give n (= 360/θ), the number of residues per turn; h, the rise per residue; and r, the radius of the phosphate atoms from the helix axis. The single‐stranded regions of tRNA that have A‐form residues have a notably lower value of n than the double‐stranded regions. The G‐U “wobble” base pair is shown to be an energetically strained left‐handed form. The A‐form dinucleoside monophosphates also have a low value of n. A model of UpAl polymerized as a fourfold left‐handed helix with the bases on the outside and phosphates on the inside is investigated for its sharp 90° turn angle characteristics. UpA2 cannot be polymerized due to a low values of h (1.31 Å) and r (2.72 Å), which cause steric hindering. An eightfold model of poly(rA) is discussed as are the nonhelical residues of tRNA. Finally, the effects of small changes in dihedral angles and bond lengths and angles on the helical parameters are investigated and discussed by way of explaining this behavior. Copyright © 1979 John Wiley & Sons, Inc.