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Synthesis of Formacetal‐Linked Dinucleotides to Facilitate dsDNA Bending and Binding to the Homeodomain of Pax6
Author(s) -
Pitulescu Marian,
Grapp Marcel,
Krätzner Ralph,
Knepel Willhart,
Diederichsen Ulf
Publication year - 2008
Publication title -
european journal of organic chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.825
H-Index - 155
eISSN - 1099-0690
pISSN - 1434-193X
DOI - 10.1002/ejoc.200701178
Subject(s) - oligomer , chemistry , dna , linker , stereochemistry , phosphodiester bond , phosphoramidite , oligonucleotide , solid phase synthesis , crystallography , histone octamer , rna , biochemistry , polymer chemistry , gene , peptide , operating system , nucleosome , histone , computer science
Two formacetal‐linked dinucleotides TT and TA were synthesized as phosphoramidite building blocks for solid‐phase synthesis. Incorporated in a 29‐mer DNA, the oligomers P3 TT and P3 TA 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 P3 TA has mainly B‐DNA topology, whereas the P3 TT 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 P3 TT oligomer. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)