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 biochemical and physicochemical properties of 2',5'-linked oligoribonucleotides containing mixed sequences of the four nucleobases (A, G, C, and U) were evaluated. CD spectra of RNA:2', 5'-RNA duplexes were compared 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 duplex structure more closely resembles the structure of the RNA:DNA hybrid, being more A-form than B-form in character. The melting temperature (Tm) values of the backbone-modified duplexes were compared with the Tm values of the unmodified duplexes. The order of thermal stability was RNA:RNA > DNA:DNA approximately RNA:DNA approximately DNA:RNA > RNA:2',5'-RNA > 2',5'-RNA:2',5'-RNA >> 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 substrate. Structural models that are consistent with the selective association properties of 2',5'-linked oligonucleotides are discussed.
Wasner
M
M
Department of Chemistry, McGill University, Montreal, Quebec, Canada.
Arion
D
D
Borkow
G
G
Noronha
A
A
Uddin
A H
AH
Parniak
M A
MA
Damha
M J
MJ
D002236:Carbohydrate Conformation; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry; D004790:Enzyme Induction / Q000187:drug effects; D006358:Hot Temperature; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D009843:Oligoribonucleotides / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D012313:RNA / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D016914:Ribonuclease H / Q000096:biosynthesis / Q000378:metabolism; D013056:Spectrophotometry, Ultraviolet; D013379:Substrate Specificity / Q000187:drug effects / Q000235:genetics
D009692:Nucleic Acid Heteroduplexes; D009843:Oligoribonucleotides; D012313:RNA; D004247:DNA; D016914:Ribonuclease H