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(CGCAU(2),sq(5),TAG CC)-3' incorporating this dimer was synthesized. From the CD analysis, it turned out that the overall structure of a DNA duplex of 5'-d(CGCAU(2),sq(5),TAGCC)-3'/3'-d(GCGTAATCGG)-5' is closer to that of the unmodified duplex than the DNA duplex of 5'-d(CGCAT(3),sq(5),TAGCC)-3'/3'-d(GCGTAATCGG)-5'. Interestingly, extensive Tm experiments suggest that d(CGCAU(2),sq(5),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 U-2,sq(5),T - the ability to recognize both dA and dG - was also supported by more detailed computational analysis of U2,sq5,T and TpT. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004).