7-Deaza-2′-deoxyadenosine and 3-deaza-2′-deoxyadenosine replacing dA within d(A6)-tracts: differential bending at 3′- and 5′-junctions of d(A6)·d(T6) and B-DNA

7-Deaza-2′-deoxyadenosine (1, c⁷A_d) and 3-deaza-2′-deoxyadenosine (2, c³A_d) have been incorporated into d(AAAAAA) tracts replacing dA at various positions within oligonucleotides. For this purpose suitably protected phosphonates have been prepared and oligonucleotides were synthsized on solid-phase. The oligomers were hybridized with their cognate strands. The duplexes were phosphorylated at OH-5′ by polynucleotide kinase and self-ligated to multimers employing T4 DNA ligase. Oligomerized DNA-fragments were analyzed by polyacrylamide gel electrophoresis and the bending was determined from anomalies of electrophoretic mobility. Replacement of dA by c³A_d decreased the bending more than replacement by c⁷A_d. Reduction of bending was much stronger when the modified nucleosides replaced one or several dA residues at the 3′-site of an d(AAAAAA)-tract whereas replacement at the 5′-site showed no significant influence [1, 2].