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C→G base mutations in the CArG box of c‐ fos serum response element alter its bending flexibility
Author(s) -
Stepanek Josef,
Vincent Michel,
Turpin PierreYves,
Paulin Denise,
Fermandjian Serge,
Alpert Bernard,
Zentz Christian
Publication year - 2007
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/j.1742-4658.2007.05768.x
Subject(s) - serum response element , serum response factor , oligonucleotide , dna , microbiology and biotechnology , chemistry , base pair , dimer , biophysics , crystallography , gene , stereochemistry , biology , physics , nuclear magnetic resonance , transcription factor , biochemistry
By binding to the CArG box sequence, the serum response factor (SRF) activates several muscle‐specific genes, as well as genes that respond to mitogens. The core domain of the SRF (core‐SRF) binds as a dimer to the CArG box C −5 C −4 A −3 T −2 A −1 T +1 T +2 A +3 G +4 G +5 of the c‐ fos serum response element (SRE fos ). However, previous studies using 20‐mer DNAs have shown that the binding stoichiometry of core‐SRF is significantly altered by mutations C −5 →G (SRE Gfos ) and C −5 C −4 →GG (SRE GGfos ) of the CArG box [A Huet, A Parlakian, M‐C Arnaud, J‐M Glandières, P Valat, S Fermandjian, D Paulin, B Alpert & C Zentz (2005) FEBS J 272 , 3105–3119]. To understand these effects, we carried out a comparative analysis of the three 20‐mer DNAs SRE fos , SRE Gfos and SRE GGfos in aqueous solution. Their CD spectra were of the B‐DNA type with small differences generated by variations in the mutual arrangement of the base pairs. Analysis by singular value decomposition of a set of Raman spectra recorded as a function of temperature, revealed a premelting transition associated with a conformational shift in the DNA double helices from a bent to a linear form. Time‐resolved fluorescence anisotropy shows that the fluorescein reporter linked to the oligonucleotide 5′‐ends experiences twisting motions of the double helices related to the interconversion between bent and linear conformers. The three SREs present various bent populations submitted, however, to particular internal dynamics, decisive for the mutual adjustment of binding partners and therefore specific complex formation.