Synthesis and properties of 4'-ThioDNA: unexpected RNA-like behavior of 4'-ThioDNA

Abstract

The synthesis and properties of fully modified 4′-thioDNAs, oligonucleotides consisting of 2′-deoxy-4′-thionucleosides, were examined. In addition to the known literature properties (preferable hybridization with RNA and resistance to endonuclease hydrolysis), we also observed higher resistance of 4′-thioDNA to 3′-exonuclease cleavage. Furthermore, we found that fully modified 4′-thioDNAs behaved like RNA molecules in their hybridization properties and structural aspect, at least in the case of the 4′-thioDNA duplex. This observation was confirmed by experiments using groove binders, in which a 4′-thioDNA duplex interacts with an RNA major groove binder, lividomycin A, but not with DNA groove binders, to give an increase in its thermal stability. Since a 4′-thioDNA duplex competitively inhibited the hydrolysis of an RNA duplex by RNase V1, it was not only the physical properties but also this biological data suggested that a 4′-thioDNA duplex has an RNA-like structure.

2′-Fluoro-4′-thioarabino-modified oligonucleotides: conformational switches linked to siRNA activity

“…Given that the nucleoside favors a northern conformation, and that the II :RNA hybrid does display an A-like conformation (CD studies described below), the second option seems more likely. It is interesting to observe that 2′-fluoroarabino (40), 4′-thio-RNA (23) and 4′thio-DNA (25) modifications, taken alone, usually provide an increase in stability toward complementary strands. Thus it may be that the ‘combination’ of the longer S4′–C1′ bond (and the larger van der Waals radius of S versus O) with the top-face fluorine is responsible for the destabilization of the hybrid structure.…”

“…4′-Thio-RNA is accepted by the RNAi machinery (24). The 4′-thiolation of DNA (25) or 2′F-ANA (19) induces a conformational switch to the north (RNA-like), and we would thus expect that duplexes containing 4′S-FANA would adopt an A-form helix and also be accepted by the RNAi machinery (26). Furthermore, evaluation of hybrids containing 4′S-FANA would help elucidate the structural factors that provide the optimal AON–RNA substrate for RNase H. While 2′-deoxy-2′-fluoro-4′-thioarabinonucleosides have previously been synthesized (19,27–30), they have not, to the best of our knowledge, been incorporated into oligonucleotides.…”

Insights from Crystallographic Studies into the Structural and Pairing Properties of Nucleic Acid Analogs and Chemically Modified DNA and RNA Oligonucleotides

“…Pallan, unpublished data). Recently, the synthesis and pairing properties of all 4 -thioDNAs have been published (47). Accordingly, 4 -thio-DNA exhibits excellent resistance to degradation by exo-and endonucleases, and its hybridization and structural properties resemble those of RNA.…”

Chemistry, Properties, and in Vitro and in Vivo Applications of 2′‐O‐Methoxyethyl‐4′‐thioRNA, a Novel Hybrid Type of Chemically Modified RNA

“…Concerning hybridization with cDNA, MOE-SRNA15 (36.1 8C; DT m = À15.9 8C) and Me-SRNA15 (44.9 8C; DT m = À7.1 8C) formed less-stable duplexes, unlike MOERNA15 and MeRNA15. This property is characteristic of 4'-thionucleic acid derivatives [5,20,21] and was significantly enhanced by methoxyethylation of the 2'-OH group.…”