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Related Experiment Video

Updated: May 5, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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Published on: March 1, 2022

Hidden Conformation Events in DNA Base Extrusions: A Generalized Ensemble Path Optimization and Equilibrium

Liaoran Cao¹, Chao Lv, Wei Yang

¹Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306.

Journal of Chemical Theory and Computation

|November 20, 2013

Summary

DNA base extrusion involves base-plane elongation, not just flipping, driven by base pair stretching and surrounding DNA dynamics. New methods reveal key in-plane rotations influencing selectivity.

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Published on: July 14, 2015

Area of Science:

Biophysics
Computational Biology
Molecular Dynamics

Background:

DNA base extrusion is vital for numerous biological processes.
Understanding base extrusion mechanisms is key to comprehending DNA conformational changes.

Purpose of the Study:

To elucidate the minimum free energy path (MFEP) and free energy profile of B-DNA major-groove base extrusion.
To characterize intermediate and transition states in base extrusion pathways.
To identify key molecular motions and reaction coordinates governing base extrusion.

Main Methods:

Improved on-the-path random walk (OTPRW) method for finite-temperature string path optimizations.
Obtained MFEP and free energy profile for B-DNA major-groove base extrusion.
Performed equilibrium generalized ensemble simulations along the optimized path.

Main Results:

Identified base-plane elongation as dominant in transition state formation, with base pair stretching as the main energetic penalty.
Characterized intermediate and transition states along the MFEP.
Found that common base-flipping angles alone do not adequately represent the extrusion pathway; in-plane rotations of the base-pairing partner are crucial.

Conclusions:

Base extrusion is facilitated by base-plane elongation, requiring intimate involvement of the surrounding DNA environment.
In-plane rotations of the base-pairing partner are critical for base-plane elongation and may determine extrusion selectivity.
A base-plane rotation angle is proposed as a potential reaction coordinate for these motions.