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Ranking ligand affinity for the DNA minor groove by experiment and simulation

Wittayanarakul, Kitiyaporn and Anthony, N.G. and Treesuwan, Witcha and Hannongbua, Supa and Alniss, Hasan and Khalaf, A.I. and Suckling, C.J. and Parkinson, J.A. and Mackay, Simon P. and , Royal Golden Jubilee Ph.D. Program (Funder) and , Thailand Research Fund (Funder) and , W.T. and EPSRC (Funder) and , Scottish Funding Council (Funder) (2010) Ranking ligand affinity for the DNA minor groove by experiment and simulation. Medicinal Chemistry Letters, 1 (8). pp. 376-680. ISSN 1948-5875

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Abstract

The structural and thermodynamic basis for the strength and selectivity of the interactions of minor-groove binders (MGBs) with DNA is not fully understood. In 2003 we reported the first example of a thiazole containing MGB that bound in a phase shifted pattern that spanned 6 base-pairs rather than the usual 4 (for tricyclic distamycin-like compounds). Since then, using DNA footprinting, nuclear magnetic resonance spectroscopy, isothermal titration calorimetry and molecular dynamics, we have established that the flanking bases around the central 4 being read by the ligand have subtle effects on recognition. We have investigated the effect of these flanking sequences on binding and the reasons for the differences and established a computational method to rank ligand affinity against varying DNA sequences.