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

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 dG3⋅dA5 sheared base pair to dA3⋅dG5 severely affected the stability. The combination of the minihairpin 5′‐d(GCGAAGC)‐3′ (1) and the thrombin‐binding aptamer 5′‐d(GGTTGGTGTGGTTGG)‐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 Tm values of the construct 43 as compared to the separate units 1 and 2, cooperative distorsions are discussed.