| Analysis of a DNA simulation model through hairpin melting experiments. | |
| | |
MedLine Citation:
|
PMID: 20886965 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
|
We compare the predictions of a two-bead Brownian dynamics simulation model to melting experiments of DNA hairpins with complementary AT or GC stems and noninteracting loops in buffer A. This system emphasizes the role of stacking and hydrogen bonding energies, which are characteristics of DNA, rather than backbone bending, stiffness, and excluded volume interactions, which are generic characteristics of semiflexible polymers. By comparing high throughput data on the open-close transition of various DNA hairpins to the corresponding simulation data, we (1) establish a suitable metric to compare the simulations to experiments, (2) find a conversion between the simulation and experimental temperatures, and (3) point out several limitations of the model, including the lack of G-quartets and cross stacking effects. Our approach and experimental data can be used to validate similar coarse-grained simulation models. |
| | |
Authors:
|
Margaret C Linak; Kevin D Dorfman |
Related Documents
:
|
19905345 - Adsorption of a hydrophobic-polar-model heteropolymer in an attractive nanotube. 21161795 - Optimal length of smooth muscle assessed by a microstructurally and statistically based... 21531075 - Modeling uranium transport in acidic contaminated groundwater with base addition. 21186905 - Numerical modeling of stress in stenotic arteries with microcalcifications: a parameter... 20628555 - Algorithmic estimation of pauses in extended speech samples of dysarthric and typical s... 20413965 - Vascular calcification in animal models of ckd: a review. |
Publication Detail:
|
Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't |
Journal Detail:
|
Title: The Journal of chemical physics Volume: 133 ISSN: 1089-7690 ISO Abbreviation: J Chem Phys Publication Date: 2010 Sep |
Date Detail:
|
Created Date: 2010-10-04 Completed Date: 2011-02-09 Revised Date: 2012-05-07 |
Medline Journal Info:
|
Nlm Unique ID: 0375360 Medline TA: J Chem Phys Country: United States |
Other Details:
|
Languages: eng Pagination: 125101 Citation Subset: IM |
Affiliation:
|
Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
DNA
/
chemistry* Hot Temperature Hydrogen Bonding Models, Chemical* Nucleic Acid Conformation Nucleic Acid Denaturation* Phase Transition Thermodynamics |
| Grant Support | |
ID/Acronym/Agency:
|
5T32GM008347-20/GM/NIGMS NIH HHS |
| Chemical | |
Reg. No./Substance:
|
9007-49-2/DNA |
| Comments/Corrections | |
Erratum In:
|
J Chem Phys. 2011 Jul 14;135(2):029901 |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: Atomic structure and formation mechanism of identically sized Au clusters grown on Si(111)-(7×7) su...
Next Document: The protein folding transition state: insights from kinetics and thermodynamics.