Structure dynamics and energetics of the d(CGCGAATTCGCG) dodecamer duplex and its selectively modified analogues in solution

Abstract

A great deal of our knowledge concerning the molecular forces that stabilise RNA structures has been obtained from systematic investigations of specially designed and synthesised ribo-oligonucleotides possessing the various structural features found in naturally-occurring RNA molecules. (Uhlenbeck et al., 1971; Craig et al., 1971; Martin et al., 1971; Porschke et al., 1973; Uhlenbeck et al., 1973; Gralla and Crothers 1973a; Borer et al., 1974; Breslauer et al., 1975). Fewer corresponding investigations have been conducted on DNA structures, primarily because of the lack of available deoxyoligomers. (Burd et al., 1975; Seising and Wells, 1979). Most early workers studied complementary homopolymers and self-complementary, alternating copolymers. (Wells and Wartell, 1974; Arnott et al., 1975; Wells et al., 1977; Arnott, 1977; Leslie et al., 1980). Although these studies were important, the lack of sequence heterogeneity caused the information content of these molecules to be somewhat limited. Furthermore, in the absence of controlled sequence modification, it was difficult to correlate a given experimental observation with a specific molecular event. Thus, the effects of mismatches, bulges and internal loops on the stability of DNA structures are just beginning to be understood (Dodgson and Wells, 1977; Early et al., 1977; Selsing et al., 1978; Wallace et al., 1979; Cornells et al., 1979; Haasnoot et al., 1980).