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DNA Topoisomerases

DNA Topoisomerases

Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. Type I...

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B-Z DNA Transitions under Z-DNA-Favoring Conditions: Benchmarking the OL21-vdW7 Force Field.

Hyeonjun Kim¹, Youngshang Pak¹

¹Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea.

Journal of Chemical Information and Modeling

|May 18, 2026

Summary

The OL21-vdW7 force field accurately models the B-Z DNA transition, a crucial test for DNA simulations. This validated force field correctly predicts DNA structural preferences under various conditions.

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Area of Science:

Computational Biology
Molecular Dynamics
Biophysics

Background:

The B-Z DNA transition is a critical benchmark for evaluating the accuracy of all-atom DNA force fields.
This transition involves complex interplay of conformational states, ion organization, and hydration patterns.

Purpose of the Study:

To rigorously assess the performance of the modified OL21-vdW7 force field in simulating the B-Z DNA transition.
To investigate the thermodynamic and structural mechanisms governing the B-Z DNA transition under various stabilizing conditions.

Main Methods:

Utilized enhanced-sampling molecular dynamics simulations in the NPT ensemble across a wide pressure range.
Analyzed two-dimensional free-energy landscapes to elucidate the transition pathway and associated responses.

Main Results:

The OL21-vdW7 force field accurately reproduces the thermodynamic preference for B-DNA and Z-DNA under Z-DNA stabilizing conditions (elevated pressure, high salt, polycations).
A cooperative nucleation-propagation mechanism for the B-Z transition was identified, initiated by a minimal Z-DNA segment.
The pressure dependence indicates a negative volume change, most pronounced under low-salt conditions.

Conclusions:

The OL21-vdW7 force field demonstrates excellent transferability for simulating duplex DNA.
B-Z DNA transitions serve as a stringent validation test for developing and refining molecular dynamics force fields.