Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides
Open Access
- 16 February 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Communications
- Vol. 12 (1), 1-12
- https://doi.org/10.1038/s41467-021-21243-y
Abstract
In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition, that may have broader implications for DNA interactions with other molecular species.Keywords
This publication has 81 references indexed in Scilit:
- Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNAProceedings of the National Academy of Sciences, 2012
- Transfection of shRNA-encoding Minivector DNA of a few hundred base pairs to regulate gene expression in lymphoma cellsGene Therapy, 2010
- Cellular Strategies for Regulating DNA Supercoiling: A Single-Molecule PerspectiveCell, 2010
- Theoretical Analysis of Disruptions in DNA MinicirclesBiophysical Journal, 2009
- GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular SimulationJournal of Chemical Theory and Computation, 2008
- A common topology for bacterial and eukaryotic transcription initiation?EMBO Reports, 2007
- Exploring writhe in supercoiled minicircle DNAJournal of Physics: Condensed Matter, 2006
- UCSF Chimera?A visualization system for exploratory research and analysisJournal of Computational Chemistry, 2004
- VMD: Visual molecular dynamicsJournal of Molecular Graphics, 1996
- Computer Visualization of Three-Dimensional Image Data Using IMODJournal of Structural Biology, 1996