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Heterogeneous DNA binding modes of berenil

AuthorsBarceló, Francisca; Ortiz-Lombardía, Miguel; Portugal, José
Issue Date28-Jun-2001
CitationBiochimica et Biophysica Acta - Gene Structure and Expression 1519(3): 175-184 (2001)
AbstractIsothermal titration calorimetry (ITC) profiles of berenil bound to different DNAs show that, despite the strong preference of berenil for AT-rich regions in DNA, it can bind to other DNA sequences significantly. The ITC results were used to quantify the binding of berenil, and the thermodynamic profiles were obtained using natural DNAs as well as synthetic polynucleotides. ITC binding isotherms cannot be simply described when a single set of identical binding sites is considered, except for poly[d(A-T)2]. Ultraviolet melting of DNA and differential scanning calorimetry were also used to quantify several aspects of the binding of berenil to salmon testes DNA. We present evidence for secondary binding sites for berenil in DNA, corresponding to G+C rich sites. Berenil binding to poly[d(G-C)2] is also observed. Circular dichroism experiments showed that binding to GC-rich sites involves drug intercalation. Using a molecular modeling approach we demonstrate that intercalation of berenil into CpG steps is sterically feasible. © 2001 Elsevier Science B.V.
Publisher version (URL)http://dx.doi.org/10.1016/S0167-4781(01)00233-0
Identifiersdoi: 10.1016/S0167-4781(01)00233-0
issn: 0167-4781
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