FTIR spectroscopic studies of oligonucleotides that model a triple-helical domain in self-splicing group I introns

Fourier Transform infrared (FTIR) spectroscopy was used to characterize the Mg2+ dependent association of a 23-mer mixed ribo-deoxyribonucleotide (23-mer RNA) and a 7-mer oligoribonucleotide (7-mer RNA) that models the triple-helical domain of a self-splicing group I intron [Sarkar et al. (1996) Biochemistry 35, 4678-4688]. To elucidate the effect of deoxyribose substitution in the entire backbone, as well as at specific positions, in the assembly of the triple-helical domain, parallel studies were carried out on the association of pure deoxyribonucleotides having base sequences corresponding to the oligoribonucleotides and also between 23-mer RNA and two 7-mer RNA variants. In the variants, either the ribose attached to G451 or the ribose attached to U453 was changed to deoxyribose. FTIR-monitored thermal denaturation of the two 23-mer hairpins shows two distinct melting regions in 1 M NaCl, in case of the RNA hairpin but not for the 23-mer DNA. Triple-helix association between the two strands (7-mer and 23-mer) studied by FTIR show that only when both strands are RNA, association takes place with the formation of the P6 helix. Our results also show that the interactions between the two RNA strands involve some participation of the riboses, which could also involve the 2'-OH groups of the RNA backbone. The assembly of the triple-helical domain is not possible with a deoxyribose backbone and is completely perturbed even when only one ribose at either G451 or U453 position is substituted by deoxyribose.