Synthesis and Structural Properties of New Oligodeoxynucleotide Analogues Containing a 2′,5′‐Internucleotidic Squaryldiamide Linkage Capable of Formation of a Watson−Crick Base Pair with Adenine and a Wobble Base Pair with Guanine at the 3′‐Downstream Junction Site

A TpT dimer analogue (U2′sq5′T), in which the 3′‐5′ phosphodiester linkage was replaced by a 2′‐5′ squaryldiamide linkage and the 5′‐upstream T was replaced by a 3′‐deoxyuridine, was synthesized in almost quantitative yield from diethyl squarate. This new dimer structural motif was designed to eliminate the squaryldiamide skeleton‐induced overall strain in T3′sq5′T, previously incorporated into DNA fragments as a new TpT mimic, through the change in the connection mode from the 3′‐5′ linkage to a 2′‐5′ linkage. Spectral analyses of U2′sq5′T suggest that the overall structure of this dimer mimic is basically similar to that of TpT. A DNA 10mer 5′‐d(CGCAU2′sq5′TAGCC)‐3′ incorporating this dimer was synthesized. From the CD analysis, it turned out that the overall structure of a DNA duplex of 5′‐d(CGCAU2′sq5′TAGCC)‐3′/3′‐d(GCGTAATCGG)‐5′ is closer to that of the unmodified duplex than the DNA duplex of 5′‐d(CGCAT3′sq5′TAGCC)‐3′/3′‐d(GCGTAATCGG)‐5′. Interestingly, extensive Tm experiments suggest that d(CGCAU2′sq5′TAGCC)‐3′ exhibits intriguing inherent hybridization affinity not only for the completely complementary oligodeoxynucleotide 3′‐d(GCGAATCGG)‐5′, but also for 3′‐d(GCGTAGTCGG)‐5′, with a mismatched dG. The unique property of the 3′‐downstream dT moiety of U2′sq5′T − the ability to recognize both dA and dG − was also supported by more detailed computational analysis of U2′sq5′T and TpT. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)