Localized Influence of 2‘-Hydroxyl Groups and Helix Geometry on Protein Recognition in the RNA Major Groove

Propensities for loop structures of RNA & DNA backbones

RNA oligonucleotides exhibit a large tendency to bend and form a loop conformation which is a major motif contributing to their complex three-dimensional structure. This is in contrast to DNA molecules that predominantly form the double-helix structure. In this paper we investigate by molecular dynamics simulation, as well as, by its combination with the replica-exchange method, the propensity of RNA chains containing the GCUAA pentaloop to form spontaneously a hairpin conformation. The results were then compared with those of analogous hybrid oligonucleotides in which the ribose groups in the loop-region were substituted by deoxyriboses. We find that the RNA oligomers exhibit a marginal excess stability to form loop structures. The equilibrium constant for opening the loop to an extended conformation is twice as large in the hybrid than it is in the RNA chain. Analyses of the hydrogen bonds indicate that the excess stability for forming a hairpin is a result of hydrogen bonds the 2'-hydroxyls in the loop region form with other groups in the loop. Of these hydrogen bonds, the most important is the hydrogen bond donated from the 2'-OH at the first position of the loop to N7 of adenine at the forth position. RNA and DNA backbones are characterized by different backbone dihedral angles and sugar puckering that can potentially facilitate or hamper the hydrogen bonds involving the 2'-OH. Nevertheless, the sugar puckerings of all the pentaloop nucleotides were not significantly different between the two chains displaying the C3'-endo conformation characteristic to the A-form double helix. All of the other backbone dihedrals also did not show any considerable difference in the loop-region except of the δ-dihedral. In this case, the RNA loop exhibited bimodal distributions corresponding to, both, the RNA and DNA backbones, whereas the loop of the hybrid chain behaved mostly as that of a DNA backbone. Thus, it is possible that the behavior of the δ-dihedrals in the loop-region of the RNA adopts conformations that facilitate the intra-nucleotide hydrogen bondings of the 2'-hydroxyls, and consequently renders loop structures in RNA more stable.

Ribose 2'-Hydroxyl Groups Stabilize RNA Hairpin Structures Containing GCUAA Pentaloop

The chemical structure of RNA and DNA is very similar; however, the three-dimensional conformation of these two nucleic acids is very different. Whereas the DNA adopts a repetitive structure of a double-stranded helix, RNA is primarily single stranded with a complex three-dimensional structure in which the hairpin is the most common secondary structure. Apart from the difference between uracil and thymine, the difference in the chemical structure between RNA and DNA is the presence of a hydroxyl group at position 2' of the sugar (ribose) instead of a hydrogen (deoxyribose). In this paper, we present molecular dynamics simulations addressing the contribution of 2'-hydroxyls to the stability of a GCUAA pentaloop motif. The results indicate that the 2'-hydroxyls stabilize the hairpin conformation of the GCUAA pentaloop relative to an analogous oligonucleotide in which the ribose sugars in the loop region were substituted with deoxyriboses. The magnitude of the stabilization was found to be 23.8 ± 4.1 kJ/mol using an alchemical mutations free energy method and 4.2 ± 6.5 kJ/mol using potential of mean force calculations. The latter indicates that in addition to its larger thermodynamic stability the RNA hairpin is also kinetically more stable. We find that the excess stability is a result of intrahairpin hydrogen bonds in the loop region between the 2'-hydroxyls and sugars, bases, and phosphates. The hydrogen bonds with the sugars and phosphates involve predominantly interactions with adjacent nucleotides. However, the hydrogen bonds with the bases involve also interactions between groups on opposite sides of the loop or with the middle base of the loop and are therefore likely to contribute significantly to the stability of the loop. Of these hydrogen bonds, the most frequent is observed between the 2'-hydroxyl at the first position of the pentaloop with N6/N7 of adenine at the forth position, as well as between the 2'-hydroxyl at position -1 with N6 of adenine at the fifth position. Our results contribute to the notion that one of the important roles of the ribose sugars in RNA is to facilitate hairpin formation.

Single-Molecule Study of the Inhibition of HIV-1 Transactivation Response Region DNA/DNA Annealing by Argininamide

Single-molecule spectroscopy was used to examine how a model inhibitor of HIV-1, argininamide, modulates the nucleic acid chaperone activity of the nucleocapsid protein (NC) in the minus-strand transfer step of HIV-1 reverse transcription, in vitro. In minus-strand transfer, the transactivation response region (TAR) RNA of the genome is annealed to the complementary "TAR DNA" generated during minus-strand strong-stop DNA synthesis. Argininamide and its analogs are known to bind to the hairpin bulge region of TAR RNA as well as to various DNA loop structures, but its ability to inhibit the strand transfer process has only been implied. Here, we explore how argininamide modulates the annealing kinetics and secondary structure of TAR DNA. The studies reveal that the argininamide inhibitory mechanism involves a shift of the secondary structure of TAR, away from the NC-induced "Y" form, an intermediate in reverse transcription, and toward the free closed or "C" form. In addition, more potent inhibition of the loop-mediated annealing pathway than stem-mediated annealing is observed. Taken together, these data suggest a molecular mechanism wherein argininamide inhibits NC-facilitated TAR RNA/DNA annealing in vitro by interfering with the formation of key annealing intermediates.