Nucleosides and Nucleotides. 182. Synthesis of Branched Oligodeoxynucleotides with Pentaerythritol at the Branch Point and Their Thermal Stabilization of Triplex Formation1

To find an oligodeoxynucleotide (ODN) with triplex stabilization capability, we designed and synthesized novel branched ODNs 1 and 2 with pentaerythritols at their branch points. Branched ODNs 1 and 2 were synthesized on a solid support using bis(phosphoramidite) 11 . The stability of the triplexes formed by branched ODNs 1 and 2 with (dA) 21 or (dT) 21 was studied by thermal denaturation. Branched ODN 1 formed a stable parallel T·AT-type triplex with (dA) 21 ( T m = 38.9 °C) in a buffer of 0.01 M sodium phosphate (pH 7.0) containing 0.5 M NaCl and 0.02 M MgCl 2, while branched ODN 2 formed a stable antiparallel A·AT-type triplex with (dT) 21 ( T m = 44.2 °C) in the same buffer. The formation of these triplexes was also confirmed by circular dichroism (CD) measurements and a gel retardation assay.