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

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.

Supercoiling and looping promote DNA base accessibility and coordination among distant sites

“…Molecular dynamics simulations help to provide a mechanistic framework for the nucleation and subsequent expansion of denaturation sites 62,65,92,120 . There is an energetic barrier to the initial nucleation event of a base flipping from the helix 62,65 .…”

Twisting DNA by Salt

“…MD simulations are highly complementary to MT measurements, as they provide detailed, microscopic insights by resolving ionnucleic acid interactions and the resulting conformational changes with atomistic resolution. 9,12,13,[31][32][33][34][35] The resolution afforded by MD simulations [36][37][38][39] allows us to disentangle the contributions of backbone, nucleobases, ions, and water, which, in turn, provide a comprehensive view of the origin of ion specificity in DNA twist. Conversely, high-resolution twist measurements provide a useful test for current MD simulations.…”

“…Using external magnets, MT directly control the linking number of DNA at the single-molecule level 5,[29][30][31] and enable precise determination of DNA twist, 12,23,24 in solution, with high resolution, and without requiring enzymatic reactions or staining (Figure 1a,b). MD simulations are highly complementary to MT measurements, as they provide detailed, microscopic insights by resolving ion-nucleic acid interactions and the resulting conformational changes with atomistic resolution 12,[32][33][34][35][36][37] (Figure 1c,d). The resolution afforded by MD simulations [38][39][40][41][42][43] allows us to disentangle the contributions of backbone, nucleobases, ions, and water, which, in turn, provide a comprehensive view of the origin of ion specificity in DNA twist.…”

Homologous BHLH transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism

“…(Weintraub, Cheng, and Conrad 1986; Dunaway and Ostrander 1993) Furthermore, the torsional strain might be necessary for the initiation of transcription,(Dunaway and Ostrander 1993; Mizutani et al 1991; Schultz et al 1992; Tabuchi and Hirose 1988; Mizutani, Ura, and Hirose 1991) as DNA underwinding appears essential for the melting of the TATA-box sequence near transcription start sites. (Liebl and Zacharias 2020) To complete the picture of how torsional strain contributes to eukaryotic transcriptional control, we must also understand how torsional strain impacts DNA specific binding by transcription factor proteins. (Noy, Sutthibutpong, and A. Harris 2016; Pyne et al 2021; J.…”

“…Locally DNA responds to torsional strain in a highly sequence-specific manner. Certain dinucleotide steps, depending on their flanking environment,(Liebl and Zacharias 2020; Kannan, Kohlhoff, and Zacharias 2006; Liebl and Zacharias 2017; Reymer, Zakrzewska, and Lavery 2018; Johanna Hörberg and Reymer 2018) can effectively absorb both negative and positive torsional strain by switching their twist. These conformational transitions allow the rest of the DNA molecule to preserve a B-like conformation.…”