Geometry of experimentally observed RNA residues in tRNA and dinucleoside monophosphates: the effect of small variations in the backbone angles

Variability in the geometry of RNA double helices generated from dinucleoside building-blocks

A graphical method is presented for the generation of helical parameters from single-crystal structures of RNA nucleic acid fragments that are minimally dinucleosides. The method is compared with other published procedures, for a number of text examples. The RNA double helices generated from three different salts of the dinucleoside monophosphate GpC are examined in relation to the variations in helix morphology that are produced. It is shown that small differences between these GpC salts can be amplified to very distinct helix characteristics.

Stereochemical details of the side-by-side model for DNA

Coordinates are presented for a refined model of the side-by-side (SBS) structure for the in vivo B-form of duplex DNA. Bond lengths and bond angles are within 0.025A and 2.0 degrees of standard values and there are no non-bonded intramolecular contacts shorter than 2.75 A. These and other details of the refined model indicate that the SBS proposal is stereochemically viable.