How global DNA unwinding causes non-uniform stress distribution and melting of DNA.

Korbinian Liebl,Martin Zacharias

doi:10.1371/journal.pone.0232976

Abstract

DNA unwinding is an important process that controls binding of proteins, gene expression and melting of double-stranded DNA. In a series of all-atom MD simulations on two DNA molecules containing a transcription start TATA-box sequence we demonstrate that application of a global restraint on the DNA twisting dramatically changes the coupling between helical parameters and the distribution of deformation energy along the sequence. Whereas only short range nearest-neighbor coupling is observed in the relaxed case, long-range coupling is induced in the globally restrained case. With increased overall unwinding the elastic deformation energy is strongly non-uniformly distributed resulting ultimately in a local melting transition of only the TATA box segment during the simulations. The deformation energy tends to be stored more in cytidine/guanine rich regions associated with a change in conformational substate distribution. Upon TATA box melting the deformation energy is largely absorbed by the melting bubble with the rest of the sequences relaxing back to near B-form. The simulations allow us to characterize the structural changes and the propagation of the elastic energy but also to calculate the associated free energy change upon DNA unwinding up to DNA melting. Finally, we design an Ising model for predicting the local melting transition based on empirical parameters. The direct comparison with the atomistic MD simulations indicates a remarkably good agreement for the predicted necessary torsional stress to induce a melting transition, for the position and length of the melted region and for the calculated associated free energy change between both approaches.

Highlights

In living cells DNA is under permanent torsional stress due to supercoiling and packing by proteins
Molecular Dynamics (MD) simulations were performed on two 50 bp-long dsDNA sequences, one (AT) with approximately 50% randomly distributed A/T content and a near central TATA box sequence starting at base pair 17 (Table 1)
In terms of the helical parameters the system is described by a quadratic deformation energy surface

Summary

Introduction

In living cells DNA is under permanent torsional stress due to supercoiling and packing by proteins. The response to torsional stress is sequence-dependent and of high relevance for many biological processes. It can facilitate protein binding but can alter DNA’s global topology and influence properties at distant sites to induce protein association or damage recognition [1, 2, 3, 4, 5]. It is well established that the stability and flexibility of linear unrestrained duplex DNA is largely determined by local nearest neighbor effects. The stability or thermal melting of a double-stranded DNA oligonucleotide of any sequence can be estimated.

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Results

Conclusion