Atomistic Molecular Dynamics Simulations of DNA in Complex 3D Arrangements for Comparison with Lower Resolution Structural Experiments

TY - JOUR

T1 - Atomistic Molecular Dynamics Simulations of DNA in Complex 3D Arrangements for Comparison with Lower Resolution Structural Experiments

AU - Watson, George

AU - Velasco-Berrelleza, Victor

AU - Noy, Agnes

PY - 2022/5/31

Y1 - 2022/5/31

N2 - Atomic-level computer simulations are a very useful tool for describing the structure and dynamics of complex biomolecules such as DNA and for providing detail at a resolution where experimental techniques cannot arrive. Molecular dynamics (MD) simulations of mechanically distorted DNA caused by agents like supercoiling and protein binding are computationally challenging due to the large size of the associated systems and timescales. However, nowadays they are achievable thanks to the efficient usage of GPU and to the improvements of continuum solvation models. This together with the concurrent improvements in the resolution of single-molecule experiments, such as atomic force microscopy (AFM), makes possible the convergence between the two. Here we present detailed protocols for doing so: for performing molecular dynamics (MD) simulations of DNA adopting complex three-dimensional arrangements and for comparing the outcome of the calculations with single-molecule experimental data with a lower resolution than atomic.

AB - Atomic-level computer simulations are a very useful tool for describing the structure and dynamics of complex biomolecules such as DNA and for providing detail at a resolution where experimental techniques cannot arrive. Molecular dynamics (MD) simulations of mechanically distorted DNA caused by agents like supercoiling and protein binding are computationally challenging due to the large size of the associated systems and timescales. However, nowadays they are achievable thanks to the efficient usage of GPU and to the improvements of continuum solvation models. This together with the concurrent improvements in the resolution of single-molecule experiments, such as atomic force microscopy (AFM), makes possible the convergence between the two. Here we present detailed protocols for doing so: for performing molecular dynamics (MD) simulations of DNA adopting complex three-dimensional arrangements and for comparing the outcome of the calculations with single-molecule experimental data with a lower resolution than atomic.

KW - DNA/chemistry

KW - Microscopy, Atomic Force

KW - Molecular Dynamics Simulation

KW - Protein Binding

U2 - 10.1007/978-1-0716-2221-6_8

DO - 10.1007/978-1-0716-2221-6_8

M3 - Article

C2 - 35635699

SN - 1064-3745

VL - 2476

SP - 95

EP - 109

JO - Methods in Molecular Biology

JF - Methods in Molecular Biology

ER -