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A structural snapshot of base-pair opening in DNA
D M van Aalten1, D A Erlanson, G L Verdine
1W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
Summary
DNA torsional stress response revealed through crystal structures. Engineered crosslinks show two states: one stabilized by calcium, the other with a base pair rupture and cytosine extrusion.
Area of Science:
- Biochemistry
- Structural Biology
- Molecular Biology
Background:
- Double-helical DNA (deoxyribonucleic acid) undergoes torsional stress during various biological processes.
- Understanding DNA's structural response to stress is crucial for deciphering DNA-related mechanisms.
Purpose of the Study:
- To elucidate the structural mechanisms by which DNA accommodates torsional stress.
- To investigate the conformational flexibility of DNA in response to engineered crosslinks.
Main Methods:
- X-ray crystallography at 1.55-A resolution to determine DNA structures.
- Engineering a minor groove crosslink in a DNA oligonucleotide d(CCAGGCCTGG)(2).
- Molecular dynamics simulations to analyze nucleotide mobility.
Main Results:
- Two distinct DNA conformational states were observed in the crystal structure.
- One state showed a strained crosslink stabilized by calcium ion binding in the major groove.
- The other state featured relieved crosslink strain via base pair rupture, cytosine extrusion, and helix bending.
Conclusions:
- DNA can adopt diverse conformations to manage torsional stress.
- The observed cytosine extrusion mimics a mechanism targeted by the HaeIII methylase enzyme.
- Molecular dynamics confirmed increased mobility of the extruded cytosine, suggesting its dynamic role.