Effect of sodium ions on RNA duplex stability and structural characterization of RNA dinucleotide bulges

It is widely known that RNA needs to fold into its proper 3D structure so that it can function correctly. Due to the fact that the number of solved RNA 3D structures is far less than the number of RNA sequences newly found in the cell, structure prediction has become one of the most efficient ways to elucidate RNA 3D structure. RNA secondary structure prediction is the intermediate step to predict RNA 3D structure. Currently, the most widely used method for predicting RNA secondary structure is free energy minimization, which utilizes the nearest neighbor model. However, the parameters used in the nearest neighbor model were derived from optical melting experiments whose buffer conditions are far different from the monovalent cation concentrations in the cell and what is used in many molecular biology techniques. Thus, the predictions of the nearest neighbor model may not be accurate for other salt conditions. Here, RNA thermodynamic parameter correction factors were derived based on thermodynamic data from optical melting experiments for 18 RNA duplexes, each melted in a wide range of sodium ion concentrations. These correction factors proposed here can be incorporated into RNA secondary structure prediction software to accurately predict RNA thermodynamic parameters in different sodium concentrations. About half the bases in RNA are actually in motif regions, not in helical regions. Thus, a better understanding of structure features found in common RNA secondary structure motifs should help researchers interpret the relationship between RNA structure and function. One common secondary structure motif is dinucleotide bulges, which are widely distributed and play important roles in cells. Here, all available RNA dinucleotide bulges in all available RNA 3D structures deposited in the PDB through the end of January 2013 were found. 187 different dinucleotide bulge sequences were found, and representative structures were identified. General patterns of base pairing, base stacking, and sugar conformations were analyzed and some interesting structural phenomena were found. This work should give insight into the structural features of known dinucleotide bulges and help predict the structures of dinucleotide bulges whose structures are not yet represented in the PDB.