Purine 3′:5′-cyclic nucleotides with the nucleobase in asynorientation: cAMP, cGMP and cIMP

Purine 3′:5′-cyclic nucleotides are very well known for their role as the secondary messengers in hormone action and cellular signal transduction. Nonetheless, their solid-state conformational details still require investigation. Five crystals containing purine 3′:5′-cyclic nucleotides have been obtained and structurally characterized, namely adenosine 3′:5′-cyclic phosphate dihydrate, C10H12N5O6P·2H2O or cAMP·2H2O, (I), adenosine 3′:5′-cyclic phosphate 0.3-hydrate, C10H12N5O6P·0.3H2O or cAMP·0.3H2O, (II), guanosine 3′:5′-cyclic phosphate pentahydrate, C10H12N5O7P·5H2O or cGMP·5H2O, (III), sodium guanosine 3′:5′-cyclic phosphate tetrahydrate, Na+·C10H11N5O7P−·4H2O or Na(cGMP)·4H2O, (IV), and sodium inosine 3′:5′-cyclic phosphate tetrahydrate, Na+·C10H10N4O7P−·4H2O or Na(cIMP)·4H2O, (V). Most of the cyclic nucleotide zwitterions/anions [two from four cAMP present in total in (I) and (II), cGMP in (III), cGMP−in (IV) and cIMP−in (V)] aresynconformers about the N-glycosidic bond, and this nucleobase arrangement is accompanied by Crib—H...Npurhydrogen bonds (rib = ribose and pur = purine). The base orientation is tuned by the ribose pucker. An analysis of data obtained from the Cambridge Structural Database made in the context ofsyn–anticonformational preferences has revealed that among thesynconformers of various purine nucleotides, cyclic nucleotides and dinucleotides predominate significantly. The interactions stabilizing thesynconformation have been indicated. The inter-nucleotide contacts in (I)–(V) have been systematized in terms of the chemical groups involved. All five structures display three-dimensional hydrogen-bonded networks.

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.

Swi5-Sfr1 protein stimulates Rad51-mediated DNA strand exchange reaction through organization of DNA bases in the presynaptic filament

The Swi5-Sfr1 heterodimer protein stimulates the Rad51-promoted DNA strand exchange reaction, a crucial step in homologous recombination. To clarify how this accessory protein acts on the strand exchange reaction, we have analyzed how the structure of the primary reaction intermediate, the Rad51/single-stranded DNA (ssDNA) complex filament formed in the presence of ATP, is affected by Swi5-Sfr1. Using flow linear dichroism spectroscopy, we observe that the nucleobases of the ssDNA are more perpendicularly aligned to the filament axis in the presence of Swi5-Sfr1, whereas the bases are more randomly oriented in the absence of Swi5-Sfr1. When using a modified version of the natural protein where the N-terminal part of Sfr1 is deleted, which has no affinity for DNA but maintained ability to stimulate the strand exchange reaction, we still observe the improved perpendicular DNA base orientation. This indicates that Swi5-Sfr1 exerts its activating effect through interaction with the Rad51 filament mainly and not with the DNA. We propose that the role of a coplanar alignment of nucleobases induced by Swi5-Sfr1 in the presynaptic Rad51/ssDNA complex is to facilitate the critical matching with an invading double-stranded DNA, hence stimulating the strand exchange reaction.