Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions
Year: 2016
Type: article
Abstract: 5-Hydroxymethylcytosine ( 5hm C) is an epigenetic marker that has recently been shown to promote homologous recombination (HR). In this study, we determine the effects of 5hm C on the structure, thermodynamics, and conformational dynamics of the Holliday junction (the four-stranded DNA intermediate associated with HR) in its native stacked-X form. The hydroxymethyl and the control methyl substituents are placed in the context of an amphimorphic G x CC trinucleotide core sequence (where x C is C, 5hm C, or the methylated 5m C), which is part of a sequence also recognized by endonuclease G to promote HR. The hydroxymethyl group of the 5hm C junction adopts two distinct rotational conformations, with an in-base-plane form being dominant over the competing out-of-plane rotamer that has typically been seen in duplex structures. The in-plane rotamer is seen to be stabilized by a more stable intramolecular hydrogen bond to the junction backbone. Stabilizing hydrogen bonds (H-bonds) formed by the hydroxyl substituent in 5hm C or from a bridging water in the 5m C structure provide approximately 1.5–2 kcal/mol per interaction of stability to the junction, which is mostly offset by entropy compensation, thereby leaving the overall stability of the G 5hm CC and G 5m CC constructs similar to that of the GCC core. Thus, both methyl and hydroxymethyl modifications are accommodated without disrupting the structure or stability of the Holliday junction. Both 5hm C and 5m C are shown to open the structure to make the junction core more accessible. The overall consequences of incorporating 5hm C into a DNA junction are thus discussed in the context of the specificity in protein recognition of the hydroxymethyl substituent through direct and indirect readout mechanisms.
Source: Biochemistry
Institutions: Colorado State University, Oslo University Hospital
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2523687276