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 (U 2′ sq 5′ 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 T 3′ sq 5′ 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 U 2′ sq 5′ T suggest that the overall structure of this dimer mimic is basically similar to that of TpT. A DNA 10mer 5′‐d(CGCA U 2′ sq 5′ T AGCC)‐3′ incorporating this dimer was synthesized. From the CD analysis, it turned out that the overall structure of a DNA duplex of 5′‐d(CGCA U 2′ sq 5′ T AGCC)‐3′/3′‐d(GCGT AA TCGG)‐5′ is closer to that of the unmodified duplex than the DNA duplex of 5′‐d(CGCA T 3′ sq 5′ T AGCC)‐3′/3′‐d(GCGT AA TCGG)‐5′. Interestingly, extensive Tm experiments suggest that d(CGCA U 2′ sq 5′ T AGCC)‐3′ exhibits intriguing inherent hybridization affinity not only for the completely complementary oligodeoxynucleotide 3′‐d(GCG AA TCGG)‐5′, but also for 3′‐d(GCGT A G TCGG)‐5′, with a mismatched dG. The unique property of the 3′‐downstream dT moiety of U 2′ sq 5′ T − the ability to recognize both dA and dG − was also supported by more detailed computational analysis of U 2′ sq 5′ T and TpT. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)