NMR Structure of a Cyclic Polyamide-DNA Complex
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- 作者：Qing Zhang ; Tammy J. Dwyer ; Vickie Tsui ; David A. Case ; Junhyeong Cho ; Peter B. Dervan ; and David E. Wemmer
- 刊名：Journal of the American Chemical Society
- 出版年：2004
- 出版时间：June 30, 2004
- 年：2004
- 卷：126
- 期：25
- 页码：7958 - 7966
- 全文大小：384K
- 年卷期：v.126,no.25(June 30, 2004)
- ISSN：1520-5126
文摘
The solution structure of a cyclic polyamide ligand complexed to a DNA oligomer, derived fromNMR restrained molecular mechanics, is presented. The polyamide, cyclo-
-ImPyPy--PyPyPy*-, bindsto target DNA with a nanomolar dissociation constant as characterized by quantitative footprinting previouslyreported. 2D 1H NMR data were used to generate distance restraints defining the structure of this cyclicpolyamide with the DNA duplex d(5'-GCCTGTTAGCG-3'):d(5'-CGCTAACAGGC-3'). Data interpretationused complete relaxation matrix analysis of the NOESY cross-peak intensities with the programMARDIGRAS. The NMR-based distance restraints (276 total) were applied in restrained molecular dynamicscalculations using a solvent model, yielding structures with an rmsd for the ligand and binding site of ~1Å. The resulting structures indicate some distortion of the DNA in the binding site. The constraints fromcyclization lead to altered stacking of the rings in the halves of the cyclic ligand relative to unlinked complexes.Despite this, the interactions with DNA are very similar to what has been found in unlinked complexes.Measurements of ligand amide and DNA imino proton exchange rates indicate very slow dissociation ofthe ligand and show that the DNA can undergo opening fluctuations while the ligand is bound although thepresence of the ligand decreases their frequency relative to the free DNA.
-ImPyPy--PyPyPy*-, bindsto target DNA with a nanomolar dissociation constant as characterized by quantitative footprinting previouslyreported. 2D 1H NMR data were used to generate distance restraints defining the structure of this cyclicpolyamide with the DNA duplex d(5'-GCCTGTTAGCG-3'):d(5'-CGCTAACAGGC-3'). Data interpretationused complete relaxation matrix analysis of the NOESY cross-peak intensities with the programMARDIGRAS. The NMR-based distance restraints (276 total) were applied in restrained molecular dynamicscalculations using a solvent model, yielding structures with an rmsd for the ligand and binding site of ~1Å. The resulting structures indicate some distortion of the DNA in the binding site. The constraints fromcyclization lead to altered stacking of the rings in the halves of the cyclic ligand relative to unlinked complexes.Despite this, the interactions with DNA are very similar to what has been found in unlinked complexes.Measurements of ligand amide and DNA imino proton exchange rates indicate very slow dissociation ofthe ligand and show that the DNA can undergo opening fluctuations while the ligand is bound although thepresence of the ligand decreases their frequency relative to the free DNA.