Mismatched base pairing in RNA crystal structures

Non-Watson-Crick base pairs or mismatches in RNA crystal structures have been summarized and their effects on the geometry of RNA molecules and their biological implications have been discussed. The mismatches can distort the helical structures by producing kinks/bends and can increase or decrease the major groove width, depending on the sequence. The helical irregularities may serve as potential sites for interaction with proteins. The different base-stacking patterns of the mismatches together with the flanking Watson-Crick base pairs can also provide unique recognizable surfaces for interaction with ligands. Mismatches are usually more hydrated than the Watson-Crick base pairs. Details of hydration of mismatches show the interaction of water molecules with the appendant functional groups of the mismatches. Mismatches with only one base-base hydrogen bond have been observed, in which bridging water molecules replace-one of the direct base pair hydrogen bonds to stabilize the conformation. (C) 1999 John Wiley & Sons, Inc.