van Aalten, D. M., Erlanson, D. A., Verdine, G. L., Joshua-Tor, L. (October 1999) A structural snapshot of base-pair opening in DNA. Proc Natl Acad Sci U S A, 96 (21). pp. 11809-14. ISSN 0027-8424 (Print) (Public Dataset)
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Abstract
The response of double-helical DNA to torsional stress may be a driving force for many processes acting on DNA. The 1.55-A crystal structure of a duplex DNA oligonucleotide d(CCAGGCCTGG)(2) with an engineered crosslink in the minor groove between the central guanine bases depicts how the duplex can accommodate such torsional stress. We have captured in the same crystal two rather different conformational states. One duplex contains a strained crosslink that is stabilized by calcium ion binding in the major groove, directly opposite the crosslink. For the other duplex, the strain in the crosslink is relieved through partial rupture of a base pair and partial extrusion of a cytosine accompanied by helix bending. The sequence used is the target sequence for the HaeIII methylase, and this partially flipped cytosine is the same nucleotide targeted for extrusion by the enzyme. Molecular dynamics simulations of these structures show an increased mobility for the partially flipped-out cytosine.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | Base Pairing Base Sequence Calcium metabolism Crystallography X-Ray DNA chemistry genetics Hydrogen Bonding Models Molecular Molecular Sequence Data Nucleic Acid Conformation Oligodeoxyribonucleotides chemistry |
| Subjects: | bioinformatics > genomics and proteomics > Mapping and Rendering > DNA Structure Rendering Investigative techniques and equipment > X-Ray Diffraction Investigative techniques and equipment > x ray crystallography |
| CSHL Authors: | |
| Communities: | CSHL labs > Joshua-Tor lab |
| Depositing User: | CSHL Librarian |
| Date: | 12 October 1999 |
| Date Deposited: | 20 Mar 2012 19:49 |
| Last Modified: | 09 Nov 2017 17:15 |
| PMCID: | PMC18368 |
| Related URLs: | |
| Dataset ID: | |
| URI: | https://repository.cshl.edu/id/eprint/25498 |
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