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.

Figure 1

Structure of 2′-deoxy-4′-thionucleosides.

Figure 2

Sequences of DNA, 4′-thioDNA and RNA.

Figure 3

CD spectra of duplexes consist of ON1:ON2.

Figure 4

CD spectra of self-complementary duplexes consist of ON3.

Figure 5

CD spectra of duplexes consist of ON4:ON5.

Figure 6

Inhibition assay of DNase I digestion. Errors reflect standard deviation from three independent experiments.

Figure 7

Inhibition assay of RNase V₁ digestion. Errors reflect standard deviation from three independent experiments.

Figure 8

Hanes–Woolf plots of RNase V₁ and RNA1:RNA2 without (square) and with thioDNA3 (circle). Errors reflect standard deviation from three independent experiments.