PHYSICOCHEMICAL AND BIOCHEMICAL-PROPERTIES OF 2',5'-LINKED RNA AND 2',5'-RNA-3',5'-RNA HYBRID DUPLEXES

In recent publications, oligonucleotides joined by 2',5'-linkages were found to bind to complementary single-stranded RNA but to bind weakly , or not at all, to single-stranded DNA [e.g., P. A. Giannaris and M. J. Damha (1993) Nucleic Acids Res. 21, 4742-4749]. In this work, the b iochemical and physicochemical properties of 2',5'-linked oligoribonuc leotides containing mixed sequences of the four nucleobases (A, G, C, and U) were evaluated. CD spectra of RNA:2',5'-RNA duplexes were compa red with the spectra of DNA:DNA, RNA:RNA, and DNA:RNA duplexes of the same base sequence. The CD results indicated that the RNA:2',5'-RNA du plex structure more closely resembles the structure of the RNA:DNA hyb rid, being more A-form than B-form in character. The melting temperatu re (T-m) values of the backbone-modified duplexes were compared with t he T-m values of the unmodified duplexes. The order of thermal stabili ty was RNA:RNA > DNA:DNA approximate to RNA:DNA approximate to DNA:RNA > RNA:2',5'-RNA > 2',5'-RNA:2',5'-RNA much greater than DNA:2',5'-RNA (undetected). RNA:2',5'-RNA duplexes are not substrates of the enzyme RNase H (Escherichia coli, or HIV-1 reverse transcriptase), but they can inhibit the RNase H-mediated cleavage of a natural DNA:RNA substra te. Structural models that are consistent with the selective associati on properties of 2',5'-linked oligonucleotides are discussed.