Single-stranded DNA: Replacement of canonical by base-modified nucleosides in the minihairpin 5 `-d(GCGAAGC)-3 ` and constructs with the aptamer 5 `-d(GGTTGGTGTGGTTGG)-3 `)

Abstract

The minihairpin 5'-d(GCGAAGC)-3'(1) was modified either in the loop region, in the base-paired stem, or at the 5'-terminus by incorporation of base-modified nucleosides. The thermal melting was correlated to the structural changes induced by the various donor-acceptor properties of the nucleosides. Overhanging nonpaired nucleosides at the 5'-terminus stabilized the hairpin, while a reverse of the dG(3) (.) dA(5) sheared base pair to dA(3) (.) dG(5) severely affected the stability. The combination of the minihairpin 5'-d(GCGAAGC)-3' (1) and the thrombin-binding aptamer 5'-d(GGTTGGTGTGGFTGG)-3' (2 (=46)) resulted in the new construct 5'd(GGTTGGGCGAAGCGGTTGG)-3' (43) arising by replacement of the 5'-d(TGT)-3' loop of 2 by the minihairpin. The fused oligonucleotide 43 exhibits a two-phase thermal transition indicating the presence of the two unaltered moieties. According to slight changes of the T-m values of the construct 43 as compared to the separate units 1 and 2, cooperative distorsions are discussed.