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Inferring DNA Kinkability from Biased MD Simulations.

Arianna Fassino¹, Enrico Carlon¹, Aderik Voorspoels^1,2

¹Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, Leuven B-3001 Belgium.

Journal of Chemical Theory and Computation

|January 13, 2026

Summary

This summary is machine-generated.

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Mechanical stress causes DNA kinks, which are sequence-dependent. Two kink types, twist-bend and pure bend, arise from DNA deformation, impacting biological processes.

Area of Science:

Structural biology
Biophysics
Computational biology

Background:

DNA undergoes significant deformation in biological processes like looping and protein interactions.
While often modeled as smooth polymers, DNA can form localized kinks under mechanical stress.

Purpose of the Study:

To investigate the properties of highly deformed DNA using all-atom simulations.
To characterize sequence-dependent DNA kink formation and its energetic cost.

Main Methods:

Utilized the Rigid Base Biasing of Nucleic Acids (RBB-NA) algorithm.
Applied bias to bending (roll) and twist in short DNA dodecamers.
Employed umbrella sampling to construct free energy landscapes.

Main Results:

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Identified sequence-dependent effects in DNA kink formation.
Quantified the energetic cost associated with kinking.
Revealed anharmonic effects and asymmetries in roll deformation.
Characterized two distinct kink types: twist-bend and pure bend kinks.

Conclusions:

DNA kink formation is sequence-dependent and energetically quantifiable.
Two distinct kink types, twist-bend and pure bend, have different formation mechanisms and implications.
Twist-bend kinks are relevant to DNA-protein interactions and negatively supercoiled DNA, while pure bend kinks are favored in torsionally constrained DNA like minicircles.