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Helix morphology changes in B-DNA induced by spontaneous B(I)<==>B(II) substrate interconversion
R H Winger1, K R Liedl, A Pichler
1Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Austria.
Journal of Biomolecular Structure & Dynamics
|November 24, 1999
Summary
Molecular Dynamics Simulations reveal spontaneous B(I)<==>B(II) substates transitions in DNA. These transitions involve coordinated backbone and base changes, causing local distortions with similarities to X-ray structures.
Area of Science:
- Structural Biology
- Computational Biophysics
Background:
- DNA exists in various substates, including B(I) and B(II) forms.
- Understanding spontaneous transitions between these substates is crucial for DNA function.
Purpose of the Study:
- To investigate the spontaneous B(I)<==>B(II) substates transitions in the EcoRI dodecamer DNA sequence.
- To analyze the molecular dynamics of these transitions and their impact on DNA structure.
Main Methods:
- Molecular Dynamics (MD) Simulations were employed.
- Analysis focused on backbone angles (epsilon, zeta, beta, 5'-delta, 5'-chi, alpha) and base morphology parameters (buckle, propeller twist, shift, roll, twist, x-displacement, tip).
Main Results:
- Concerted changes in backbone angles and base morphology were observed during B(I)<==>B(II) transitions.
- Short-lived B(II) conformers were identified, involving specific base steps.
- Transitions primarily cause local distortions, with the preceding base being most affected.
- Simulated atomic positional fluctuations closely matched those from static X-ray structures.
Conclusions:
- Spontaneous B(I)<==>B(II) transitions in DNA involve coordinated structural rearrangements.
- These transitions lead to localized distortions, consistent with experimental findings.
- MD simulations provide valuable insights into DNA dynamics and substates.