Abstract
AbstractTwo formacetal‐linked dinucleotides TT and TA were synthesized as phosphoramidite building blocks for solid‐phase synthesis. Incorporated in a 29‐mer DNA, the oligomers P3TT and P3TA 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 TT formacetal modification, whereas destabilization induced by TA was less pronounced. Based on CD spectroscopy, the TA formacetal‐modified oligomer P3TA has mainly B‐DNA topology, whereas the P3TT modified oligomer 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 P3TT oligomer. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
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