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Alpha/gamma transitions in the B-DNA backbone.
Péter Várnai1, Dragana Djuranovic, Richard Lavery
1Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, Paris 75005, France. varnai@ibpc.fr
Nucleic Acids Research
|December 20, 2002
Summary
Non-canonical DNA backbone conformations (alpha/gamma torsion angles) are rare in free DNA but emerge during protein binding. These unusual structures facilitate protein-DNA interactions by enabling fine-tuning of DNA geometry.
Area of Science:
- Molecular Biology
- Structural Biology
- Computational Chemistry
Background:
- Protein-DNA complexes often display non-canonical alpha and gamma DNA backbone torsion angles in crystal structures.
- The accessibility and functional role of these alternative conformations in solution remain unclear.
Purpose of the Study:
- To investigate the accessibility of non-canonical alpha/gamma torsion angle conformations in solution.
- To determine if these conformations contribute to specific DNA recognition by proteins.
Main Methods:
- Computer simulations were used to analyze coupled alpha/gamma torsion angle transitions in a B-DNA dodecamer.
- Analysis of high-resolution crystallographic structures of protein-DNA complexes.
Main Results:
- Five stable or metastable non-canonical alpha/gamma sub-states were identified.
- Spontaneous transitions to unusual conformations are energetically improbable in free B-DNA.
- Non-canonical backbones were exclusively observed in protein-bound DNA structures.
- These transitions influence DNA roll and twist, reducing structural parameter dispersion.
Conclusions:
- Unusual alpha/gamma backbone conformations are likely induced during protein-DNA complexation.
- These conformations aid in structural adjustments between proteins and DNA.
- They play a role in the overall free energy of protein-DNA complexation.