RNA bulges and the helical periodicity of double-stranded RNA

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Abstract
RNA MOLECULES typically exhibit extensive secondary structure, including double-stranded duplex, hairpins, internal loops, bulged bases and pseudoknotted1,2 structures (reviewed in refs 3 and 4). This is intimately connected with biological function, including splicing reactions5,6 and ribozyme activity7,8. The formation of RNA–DNA hybrids is important in the transcription of DNA, reverse transcription of viral RNA, and DNA replication. Bulged bases in RNA helices are potentially significant in RNA folding and in providing sites for specific protein–RNA interactions, as illustrated by TFIIIA of Xenopus9and the coat protein of phage R17 (ref. 10). Most information about the structure of RNA derives from fibre diffraction11,12 or crystallography of natural molecules, notably transfer RNA13–17, but until recently there have been few systematic studies of RNA structure using designed sequences18–22. We have used gel electrophoresis to investigate the properties of bulged bases in both RNA and RNA–DNA duplexes in solution. As in DNA helices23–25, bulges introduce pronounced kinks into RNA and into RNA–DNA helices, depending on the number and types of bases in the bulge and its position in the fragment. By varying the spacing between two bulge-induced kinks, we have measured the periodicity of RNA and RNA–DNA helices in solution.