X-ray crystallographic study of the possible binding sites of the monovalent cations in the Z-DNA structure.
Determination of the binding positions of light metal ions in the structure of oligonucleotides remains a challenge owing to their irregular coordination geometries, low electron densities and mobility in the crystals. To study the interactions between monovalent cations and DNA, the heavier alkali metal ion Rb(+) was used to replace Na(+) and K(+) in the Z-DNA crystal and the structure was analyzed using X-ray cryocrystallography. The resolution of the Rb-d(CGCGCG)(2) crystal data set is 1.76 A, with an R(merge) of 0.061. The final residual factor (R factor) for the crystal structure is 0.175. The positions of 16 Rb(+) ions were tentatively assigned, with most of them having partial occupancies. Three rubidium ions with full occupancies coordinated to two DNA double strands were located in the Z-DNA crystal. The results of this work suggest that there are numerous relatively low-energy sites for binding of monovalent cations to Z-DNA and that these sites are cation-water hybrid positions.
Dong
Xiangchao
X
Department of Chemistry, Hunter College of The City University of New York, New York, NY 10071, USA. xcdong@nankai.edu.cn
D001665:Binding Sites; D002414:Cations, Monovalent / Q000737:chemistry*; D003080:Cold Temperature; D003460:Crystallization; D018360:Crystallography, X-Ray; D043542:DNA, Z-Form / Q000737:chemistry*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D012413:Rubidium / Q000737:chemistry
D002414:Cations, Monovalent; D043542:DNA, Z-Form; D009838:Oligodeoxyribonucleotides; D012413:Rubidium