Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model

The analysis and prediction of non-canonical structural motifs in RNA is of great importance for an understanding of the function and design of RNA st ructures. A hierarchical method has been employed to generate a large varie ty of sterically possible conformations for a single-base adenine bulge str ucture in A-form DNA and RNA. A systematic conformational search was perfor med on the isolated bulge motif and neighboring nucleotides under the const raint to fit into a continuous helical structure. These substructures were recombined with double-stranded DNA or RNA. Energy minimization resulted in more than 300 distinct bulge conformations. Energetic evaluation using a s olvation model based on the finite-difference Poisson-Boltzmann method iden tified three basic classes of low-energy structures. The three classes corr espond to conformations with the bulge base stacked between flanking nucleo tides (I), location of the bulge base in the minor groove (II) and conforma tions with a continuous stacking of the flanking helices and a looped out b ulge base (III). For the looped out class, two subtypes (ma and IIIb) with different backbone geometries at the bulge site could be distinguished. The conformation of lowest calculated energy was a class I structure with back bone torsion angles close to those in standard A-form RNA. Conformations ve ry close to the extra-helical looped out bulge structure determined by X-ra y crystallography were also among the low-energy structures. In addition, t opologies observed in other experimentally determined bulge structures have been found among low-energy conformers. The implicit solvent model was fur ther tested by comparing an uridine and adenine bulge flanked by guanine:cy tosine base-pairs, respectively. Ln agreement with the experimental observa tion, a looped out form was found as the energetically most favorable form for the uridine bulge and a stacked conformation in case of the adenine bul ge. The inclusion of solvation effects especially electrostatic reaction fi eld contributions turned out to be critically important in order to select realistic low-energy bulge structures from a large number of sterically pos sible conformations. The results indicate that the approach might be useful to model the three-dimensional structure of non-canonical motifs embedded in double-stranded RNA, in particular, to restrict the number of possible c onformations to a manageable number of conformers with energies below a cer tain threshold. (C) 1999 Academic Press.