The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution

The Journal of Biological Chemistry
Jeffrey M Vargason, P Shing Ho

Abstract

The single crystal structure of the methylated sequence d(CCGGTACm(5)CGG) has been solved as an antiparallel stacked X Holliday junction to 1.5 A resolution. When compared with the parent nonmethylated d(CCGGTACCGG) structure, the duplexes are translated by 3.4 A along the helix axis and rotated by 10.8 degrees relative to each other, rendering the major grooves more accessible overall. A Ca(2+) complex is seen in the minor groove opposite the junction but is related to the B conformation of the stacked arms. At the junction itself, the hydrogen bond from the N4 nitrogen of cytosine C8 to the C7 phosphate at the crossover in the parent structure has been replaced by a water bridge. Thus, this direct interaction is not absolutely required to stabilize the junction at the previously defined ACC trinucleotide core. The more compact methylated junction forces the Na(+) of the protected central cavity of the nonmethylated junction into a solvent cluster that spans the space between the junction crossover and the stacked arms. A series of void volumes within the methylated and the nonmethylated structures suggests that small monovalent cations can fill and vacate this central cavity without the need to unfold the four-stranded Hollid...Continue Reading

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Citations

Jul 20, 2002·Journal of Molecular Biology·Brandt F EichmanPui Shing Ho
Jul 5, 2011·Nature Structural & Molecular Biology·Subhajyoti De, Franziska Michor
Feb 14, 2013·Molecular BioSystems·Aradhita BaralShantanu Chowdhury
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Jun 3, 2004·Nucleic Acids Research·Jeffrey WatsonP Shing Ho
Mar 24, 2007·Proceedings of the National Academy of Sciences of the United States of America·Andrea Regier VothP Shing Ho
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Dec 29, 2020·Chembiochem : a European Journal of Chemical Biology·Pallabi SenguptaSubhrangsu Chatterjee
Aug 13, 2003·Biochemistry·Franklin A HaysP Shing Ho

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