Optical Spectroscopic Study of the Effects of a Single Deoxyribose Substitution in a Ribose Backbone:  Implications in RNA−RNA Interaction

Abstract

The 2'-OH group in the ribose sugars of an RNA molecule plays an important role in guiding tertiary interactions that stabilize different RNA structural motifs. Deoxyribose, or 2'-OH by 2'-H, substitution in both the single-stranded and the duplex part of an RNA backbone has been routinely used to evaluate what role the 2'-OH plays in different tertiary interactions that guide an RNA-RNA contact. A deoxyribose substitution not only has the effect of removing a hydrogen bond donating group, but also introduces a sugar moiety with a preference for C2'-endo pucker in a backbone of predominantly C3'-endo sugars. This study evaluates the effects of a single deoxyribose substitution in both single-stranded and double-helical forms of RNA oligomers. A single-stranded, nonrepetitive 7-mer oligoribonucleotide (7-mer RNA) and four different variants having the same base sequence but with a single deoxyribose sugar at different positions in the strands have been studied by ultraviolet (UV) absorption, circular dichroism (CD), and Fourier transform infrared (FTIR) spectroscopy. Duplexes were formed by association with the complementary strand of the 7-mer RNA. The results show that both RNA and DNA single strands have preorganized conformations with spectral properties resembling those of A- and B-form helices, respectively, with RNA being more heterogeneous than its DNA counterpart. A single deoxyribose substitution perturbs the structure of the RNA backbone, with the effect being more pronounced in the single-stranded than in the duplex structure. The perturbation depends on the position of the 2'-H substitution in the strand.

Translesion synthesis DNA polymerase η exhibits a specific RNA extension activity and a transcription-associated function

“…These results indicate that if Polη participated in RNA synthesis in vivo , it could insert both rNTPs and dNTPs on undamaged templates, and it would most probably insert dNTPs opposite DNA lesions. This would have severe consequences by leading to the accumulation of dNTPs in RNA causing miscoding, affecting RNA structure 55 , RNA-protein interactions 56 , and RNA packaging 57 . To resolve this problem we presume that cellular factors can modify the kinetics of the reactions.…”

A nature of conformational changes of yeast tRNAPhe

“…2b). The band around 1459 cm −1 was assigned to purine imidazolic ring vibrations and any changes in the position or intensity correspond to the interactions on N7 sites in the case of triple helix formation or the changes in hydration in major groove [55,58,[62][63][64]. It seems that this band is sensitive to the interaction between guanines with water molecules [62].…”

“…Transition of water structure from the hexagonal arrangement of tetrahedrally connected molecule (low density) to cubic octamers (higher density) leads to a more economical hydration of tRNA [64]. As a result, higher energetic structure appears, which is displayed by the bands shift towards shorter wavelengths…”

Effects of Base Substitutions in an RNA Hairpin from Molecular Dynamics and Free Energy Simulations

“…The application of a thermodynamic cycle requires the structure of an unfolded single RNA strand. There is little experimental data concerning single-stranded RNA, but there are indications of the existence of a preorganized A-like backbone conformation (Lindqvist et al, 2000). We examined several models of single-stranded RNA which differ in size, initial structure, or sequence.…”