Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments.

Wujie Wang,Daniel M Hinckley,Brianne Z Wiemann,Ishita Mukerji,Laura M Nocka,Francis W Starr

doi:10.1038/srep22863

Wujie Wang, Daniel M Hinckley + Show 4 more

Open Access

https://doi.org/10.1038/srep22863

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Abstract

Holliday junctions play a central role in genetic recombination, DNA repair and other cellular processes. We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions. The model reproduces many experimentally determined aspects of junction structure and stability, including the temperature dependence of melting on salt concentration, the bias between open and stacked conformations, the relative populations of conformers at high salt concentration, and the inter-duplex angle (IDA) between arms. We also obtain a close correspondence between the junction structure evaluated by all-atom and coarse-grained simulations. We predict that, for salt concentrations at physiological and higher levels, the populations of the stacked conformers are independent of salt concentration, and directly observe proposed tetrahedral intermediate sub-states implicated in conformational transitions. Our findings demonstrate that the 3SPN.2 model captures junction properties that are inaccessible to all-atom studies, opening the possibility to simulate complex aspects of junction behavior.

Highlights

DNA four-way or Holliday junctions are central intermediates in the cellular processes of recombination, integration and DNA repair
As a first step to assess the applicability of the 3-site per nucleotide (3SPN).[2] model to predict bulk thermodynamic properties of the Holliday junction, we evaluate the junction melting properties from simulations of the 3SPN.[2] model and compare it with our absorption experiments
We simulate the junction melting via replica-exchange molecular dynamics (REMD, see methods) to improve the sampling of partially melted states

Summary

Introduction

DNA four-way or Holliday junctions are central intermediates in the cellular processes of recombination, integration and DNA repair. Atomic force microscopy studies suggest that these 4-fold symmetric structures have a square, planar configuration[4,5] In this conformation the junction is capable of branch migration between homologous duplexes, an essential step for recombination and repair processes. Spectroscopic studies of immobile junctions prepared from non-homologous sequences suggest that, in the stacked form, the arms adopt an anti-parallel orientation, which does not require a crossing of the strands in the central region[3]. The computational complexity of these highly-detailed models makes it challenging to address many important structural and energetic features, such as conformational transformations and DNA hybridization These challenges are illustrated by a recent study of junction isomerization dynamics, where it was demonstrated that conformational sampling can be non-ergodic over time scales of up to one minute[26]. In this study we combine simulations and experiments to investigate the ability of a coarse-grained model to predict junction thermodynamics and conformational populations

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