Synthesis of formacetal-linked dinucleotides to facilitate dsDNA bending and binding to the homeodomain of Pax6

Two formacetal-linked dinucleotides T<boolean AND>T and T<boolean AND>T were synthesized as phosphoramidite building blocks for solid-phase synthesis. Incorporated in a 29-mer DNA, the oligomers P3(T<boolean AND>T) and P3(T<boolean AND>A) were studied with respect to the binding activity towards the Pax6 homeodomain. Substitution of the negatively charged phosphodiester by a neutral formacetal linker facilitates the bent conformation of double-stranded DNA. The duplex stability was affected more significantly by the T<boolean AND>T formacetal modification, whereas destabilization induced by T<boolean AND>A was less pronounced. Based on CD spectroscopy, the T<boolean AND>A formacetal-modified oligomer P3(T<boolean AND>A) A has mainly B-DNA topology, whereas the P3(T<boolean AND>T) modified oligomet significantly deviated from B-form DNA. The binding affinity of the P3 oligomer towards Pax6 HD was investigated by in vitro EMSA experiments providing even a small increase in binding affinity for the P3(T<boolean AND>A) T oligomer. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008).