Occurrence and stability of anion–π interactions between phosphate and nucleobases in functional RNA molecules

Abstract

We present a systematic structural and energetic characterization of phosphate(OP)–nucleobase anion…π stacking interactions in RNAs. We observed OP–nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from the stacking between a phosphate and a guanine or a uracil two-residue upstream in specific U-turns, such interactions in RNA have been scarcely characterized to date. Our QM calculations showed an energy minimum at a distance between the OP atom and the nucleobase plane centroid slightly below 3 Å for all the nucleobases. By sliding the OP atom over the nucleobase plane we localized the optimal mutual positioning of the stacked moieties, corresponding to an energy minimum below -6 kcal•mol−1, for all the nucleobases, consistently with the projections of the OP atoms over the different π-rings we observed in experimental occurrences. We also found that the strength of the interaction clearly correlates with its electrostatic component, pointing to it as the most relevant contribution. Finally, as OP–uracil and OP–guanine interactions represent together 86% of the instances we detected, we also proved their stability under dynamic conditions in model systems simulated by state-of-the art DFT-MD calculations.

Structural aspects of dehydration and rehydration in the adenosine 5′-diphosphate (ADP)–potassium–water system

“…As shown in Table S14,† ribose O4′ atoms participate in lp⋯π contacts even shorter than those of the diphosphate groups (atom–centroid distances below 3 Å). Systems of this type, although important from the point of view of nucleic acid stabilization, 52–54 are still not well understood. Analysis of the Hirshfeld surface (with the geometric d norm function mapped on it) and fingerprint plots generated for the ADP − anions in I–IVb , apart from IVa , due to disorder of the ribose ring (Fig.…”

“…As shown in Table S14, † ribose O4′ atoms participate in lp⋯π contacts even shorter than those of the diphosphate groups (atom-centroid distances below 3 Å). Systems of this type, although important from the point of view of nucleic acid stabilization, [52][53][54] are still not well understood. Analysis of the Hirshfeld surface (with the S3.…”

Polyoxometalate Archetype-Boosted Stability and Charge Storage of 2D Graphene Nanosheets

“…In addition, the phosphate moiety of the impregnated PTA may interact with the π electron of graphene. 94 Therefore, the stability of graphene nano-sheets would be achieved by these nonspecific interactions with the metal atom (tungsten) and/or addenda atom (phosphate group) of PTA to form a rigid lifted-up shade structure, wherein the PTA archetype stands as a pillar, with ion-accessible pores. In graphite, the distance between two adjacent graphene sheets is 3.4 Å (0.34 nm).…”

Toward α‐1,3/4 fucosyltransferases targeted drug discovery: In silico uncovering of promising natural inhibitors of fucosyltransferase 6

“…The systems were equilibrated for 200 ps and further subjected to a production run of 100 ns. MD simulations have been widely used to evaluate the structural stability of proteins and nucleic acids, 8,[36][37][38][39][40][41][42] and to investigate conformational changes in proteins upon ligand binding along with the protein-ligand binding energies. [43][44][45][46] Here, we applied MD simulation to assess the FUT6-ligand complexes stability, by monitoring the root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg) and solvent accessible surface area (SASA), using the GROMACS inbuilt utility: gmx rms, gmx rmsf, gmx_gyrate and gmx_sasa, respectively.…”