Kinking of DNA and RNA by base bulges.

Base bulges are features of nucleic acid structure where a duplex section is interrupted by one or more formally singlestranded bases on one strand that are unopposed by bases on the other strand. Base bulges are very common features of folded RNA structures, where they can present highly recognizable features for specific protein binding; a good example is the binding of the human immunodeficiency virus transactivator protein Tat to the three-pyrimidine bulge in the response element TAR (1, 2). Bulges may be created in heteroduplex DNA arising from recombination between imperfectly homologous sequences, where they become features to be recognized by the repair machinery. In general, base bulges in nucleic acids are an important feature in the repertoire of folding elements, and one that can be exploited for specific recognition by proteins of various kinds. It is clear that base bulges have a rather major effect on local geometry, because their inclusion brings about a significant destabilization of DNA or RNA duplexes (3-6). Analysis of the molecular geometries of branchpoints within nucleic acids in solution provides an interesting challenge. Because of the elongated, sequential construction of nucleic acids, both short-range and long-range information is required, and neither alone can fully define the structure of the molecule. NMR can provide a wealth of information on the stereochemistry of nucleic acids, but the information is essentially short-range. The absence of longer distances makes global features such as kinks difficult to estimate with assurance. For these reasons a combined approach exploiting a number of different biophysical methods has evolved for the analysis of these features. One of the simplest techniques used to study branched nucleic acid structures is gel electrophoresis, yet the approach is perhaps surprisingly powerful. The mobilities of duplex species that are bent or kinked in some manner are retarded in polyacrylamide gels, as is well known in the case of DNA that is curved by the presence of phased oligoadenine tracts (7, 8). Although the physical basis of this effect is not fully understood, these experiments can usually be set up so that the relative mobilities of a series of related molecules are compared. The electrophoretic mobilities of DNA (9-11) and A ~~~An