Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts

The fidelity of group II intron self-splicing and retrohoming relies on long-range tertiary interactions between the intron and its flanking exons. By single-molecule FRET, we explore the binding kinetics of the most important, structurally conserved contact, the exon and intron binding site 1 (EBS1/IBS1). A comparison of RNA-RNA and RNA-DNA hybrid contacts identifies transient metal ion binding as a major source of kinetic heterogeneity which typically appears in the form of degenerate FRET states. Molecular dynamics simulations suggest a structural link between heterogeneity and the sugar conformation at the exon-intron binding interface. While Mg2+ ions lock the exon in place and give rise to long dwell times in the exon bound FRET state, sugar puckering alleviates this structural rigidity and likely promotes exon release. The interplay of sugar puckering and metal ion coordination may be an important mechanism to balance binding affinities of RNA and DNA interactions in general.

Crystal structure and sequential dehydration transitions of disodium guanosine 5′-monophosphate tetrahydrate

Disodium guanosine 5′-monophosphate was reported previously to crystallize as both the tetrahydrate and the heptahydrate. We herein report a determination of the molecular and crystal structures of the title tetrahydrated salt, 2Na+·C10H12N5O8P2−·4H2O. It was found that the structure differs markedly from that of the heptahydrate, but greatly resembles that of disodium deoxyguanosine 5′-monophosphate tetrahydrate. The C2′—O2′H moiety of ribose is surrounded by hydrophilic moieties and is disordered over two sites. The sugar puckering mode is O4′-endo-C1′-exo at both sites and the conformation around the C4′—C5′ bond is gauche–trans. Powder X-ray diffraction and thermal analyses revealed that the temperature-controlled transition from the tetrahydrate to the anhydride proceeded through three intermediate phases between 40 and 60 °C at 0% relative humidity. Large induction periods were observed.

Studies on sugar puckering and glycosidic stabilities of 3′-amino-5′-carboxymethyl-3′,5′-dideoxy nucleoside mimics

Nucleoside amino acids and their dimers show a predilection of these backbone modified molecules towards an N-type conformation with a slightly weaker glycosidic linkage.

Protonation induces base rotation of purine nucleotides pdGuo and pGuo

Synergistic IRMPD spectroscopy and computations find that protonation of the guanine nucleotides (pdGuo and pGuo) occurs preferentially at N7 and induces changes in the base orientation and sugar puckering.