An A-type double helix of DNA having B-type puckering of the deoxyribose rings
Language English Country Netherlands Media print
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
10736226
DOI
10.1006/jmbi.2000.3592
PII: S0022283600935927
Knihovny.cz E-resources
- MeSH
- Circular Dichroism MeSH
- Cytosine metabolism MeSH
- Nucleic Acid Denaturation MeSH
- Deoxyribose chemistry genetics metabolism MeSH
- DNA chemistry genetics metabolism MeSH
- Guanine metabolism MeSH
- Nucleic Acid Conformation * drug effects MeSH
- Models, Molecular MeSH
- Nuclear Magnetic Resonance, Biomolecular MeSH
- Oligodeoxyribonucleotides chemistry genetics metabolism MeSH
- Base Pairing drug effects genetics MeSH
- Computer Simulation MeSH
- Rotation MeSH
- Solutions MeSH
- Base Sequence MeSH
- Temperature MeSH
- Thermodynamics MeSH
- Trifluoroethanol metabolism pharmacology MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Cytosine MeSH
- Deoxyribose MeSH
- DNA MeSH
- Guanine MeSH
- Oligodeoxyribonucleotides MeSH
- Solutions MeSH
- Trifluoroethanol MeSH
DNA usually adopts structure B in aqueous solution, while structure A is preferred in mixtures of trifluoroethanol (TFE) with water. However, the octamer d(CCCCGGGG) and other d(C(n)G(n)) fragments of DNA provide CD spectra that suggest that the base-pairs are stacked in an A-like fashion even in aqueous solution. Yet, d(CCCCGGGG) undergoes a cooperative TFE-induced transition into structure A, indicating that an important part of the aqueous duplex retains structure B. NMR spectroscopy shows that puckering of the deoxyribose rings is of the B-type. Hence, combination of the information provided by CD spectroscopy and NMR spectroscopy suggests an unprecedented double helix of DNA in which A-like base stacking is combined with B-type puckering of the deoxyribose rings. In order to determine whether this combination is possible, we used molecular dynamics to simulate the duplex of d(CCCCGGGG). Remarkably, the simulations, completely unrestrained by the experimental data, provided a very stable double helix of DNA, exhibiting just the intermediate B/A features described above. The double helix contained well-stacked guanine bases but almost unstacked cytosine bases. This generated a hole in the double helix center, which is a property characteristic for A-DNA, but absent from B-DNA. The minor groove was narrow at the double helix ends but wide at the central CG step where the Watson-Crick base-pairs were buckled in opposite directions. The base-pairs stacked tightly at the ends but stacking was loose in the duplex center. The present double helix, in which A-like base stacking is combined with B-type sugar puckering, is relevant to replication and transcription because both of these phenomena involve a local B-to-A transition.
References provided by Crossref.org
Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field
A sodium/potassium switch for G4-prone G/C-rich sequences
Non-canonical DNA structures in the human ribosomal DNA
Circular dichroism and conformational polymorphism of DNA
Mapping the B-A conformational transition along plasmid DNA
Program MULDER -- a tool for extracting torsion angles from NMR data
Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine