DNA, RNA and hybrid RNA-DNA oligomers of identical sequence: structural and dynamic differences

A 27-mer sequence was synthesised as DNA duplex (DD), RNA duplex (RR), and RNA-DNA (RD) hybrid in order to characterise their structural and dynamic f eatures, The hydrodynamic radius (R-h) and the rise (b) values of the three samples were consistent with the conformations predicted by CD analysis. T he value of the torsional constant (alpha) of the samples containing RNA wa s approximately twice that of the DD sample and followed the order: DD < RD < RR. The same order was observed in the thermodynamic stability and in th e reduction of the electrophoretic mobility. gamma-Ray footprinting analysi s was carried out to resolve the individual strand conformation in the hybr id. The RNA strand preserved its conformation, while the DNA strand showed local deformations mainly at TA and TG steps. (C) 2000 Elsevier Science B.V . All rights reserved.