Journal article
Coarse-grained modeling of DNA oligomer hybridization: length, sequence, and salt effects
The Journal of chemical physics, v 141(3), pp 035102-035102
21 Jul 2014
PMID: 25053341
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
A recently published coarse-grained DNA model [D. M. Hinckley, G. S. Freeman, J. K. Whitmer, and J. J. de Pablo, J. Chem. Phys. 139, 144903 (2013)] is used to study the hybridization mechanism of DNA oligomers. Forward flux sampling is used to construct ensembles of reactive trajectories from which the effects of sequence, length, and ionic strength are revealed. Heterogeneous sequences are observed to hybridize via the canonical zippering mechanism. In contrast, homogeneous sequences hybridize through a slithering mechanism, while more complex base pair displacement processes are observed for repetitive sequences. In all cases, the formation of non-native base pairs leads to an increase in the observed hybridization rate constants beyond those observed in sequences where only native base pairs are permitted. The scaling of rate constants with length is captured by extending existing hybridization theories to account for the formation of non-native base pairs. Furthermore, that scaling is found to be similar for oligomeric and polymeric systems, suggesting that similar physics is involved.
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Details
- Title
- Coarse-grained modeling of DNA oligomer hybridization: length, sequence, and salt effects
- Creators
- Daniel M Hinckley - University of Wisconsin–MadisonJoshua P Lequieu - University of ChicagoJuan J de Pablo - University of ChicagoArgonne National Lab. (ANL), Argonne, IL (United States)
- Publication Details
- The Journal of chemical physics, v 141(3), pp 035102-035102
- Publisher
- American Institute of Physics (AIP)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemical and Biological Engineering
- Web of Science ID
- WOS:000340711300048
- Scopus ID
- 2-s2.0-84904663330
- Other Identifier
- 991020950339604721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Chemistry, Physical
- Physics, Atomic, Molecular & Chemical