Optical spectroscopic study of the effects of a single deoxyribose substitution in a ribose backbone: Implications in RNA-RNA interaction

The 2'-OH group in the ribose sugars of an RNA molecule plays an important role in guiding tertiary interactions that stabilize different RNA structur al motifs. Deoxyribose, or 2'-OH by 2'-H, substitution in both the single-s tranded and the duplex part of an RNA backbone has been routinely used to e valuate what role the 2'-OH plays in different tertiary interactions that g uide an RNA-RNA contact. A deoxyribose substitution not only has the effect of removing a hydrogen bond donating group, but also introduces a sugar mo iety with a preference for C2'-endo pucker in a backbone of predominantly C 3'-endo sugars. This study evaluates the effects of a single deoxyribose su bstitution in both single-stranded and double-helical forms of RNA oligomer s. A single-stranded, nonrepetitive 7-mer oligoribonucleotide (7-mer RNA) a nd four different variants having the same base sequence but with a single deoxyribose sugar at different positions in the strands have been studied b y ultraviolet (UV) absorption, circular dichroism (CD), and Fourier transfo rm infrared (FTIR) spectroscopy. Duplexes were formed by association with t he complementary strand of the 7-mer RNA. The results show that both RNA an d DNA single strands have preorganized conformations with spectral properti es resembling those of A- and B-form helices, respectively, with RNA being more heterogeneous than its DNA counterpart. A single deoxyribose substitut ion perturbs the structure of the RNA backbone, with the effect being more pronounced in the single-stranded than in the duplex structure. The perturb ation depends on the position of the 2'-H substitution in the strand.