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Theory on the Mechanism of DNA Renaturation: Stochastic Nucleation and Zipping
Gnanapragasam Niranjani,
Published in Public Library of Science
2016
PMID: 27074030
Volume: 11
   
Issue: 4
Abstract
Renaturation of the complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA renaturation. According to our model there are at least three steps in the renaturation process viz. nonspecific-contact formation, correct-contact formation and nucleation, and zipping. Most of the earlier two-state models combined nucleation with nonspecific-contact formation step. In our model we suggest that it is considerably meaningful when we combine the nucleation with the zipping since nucleation is the initial step of zipping and nucleated and zipping molecules are indistinguishable. Nonspecific contact formation step is a pure three-dimensional diffusion controlled collision process. Whereas nucleation involves several rounds of one-dimensional slithering and internal displacement dynamics of one single strand of DNA on the other complementary strand in the process of searching for the correct-contact and then initiate nucleation. Upon nucleation, the stochastic zipping follows to generate a fully renatured double stranded DNA. It seems that the square-root dependency of the overall renaturation rate constant on the length of reacting single strands originates mainly from the geometric constraints in the diffusion controlled nonspecific-contact formation step. Further the inverse scaling of the renaturation rate on the viscosity of reaction medium also originates from nonspecific contact formation step. On the other hand the inverse scaling of the renaturation rate with the sequence complexity originates from the stochastic zipping which involves several rounds of crossing over the free-energy barrier at microscopic levels. When the sequence of renaturing single strands of DNA is repetitive with less complexity then the cooperative effects will not be noticeable since the parallel zipping will be a dominant enhancing factor. However for DNA strands with high sequence complexity and length one needs to consider the underlying cooperative effects both at microscopic and macroscopic levels to explain various scaling behaviours of the overall renaturation rate. © 2016 Niranjani, Murugan. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in anymedium, provided the original author and source are credited.
About the journal
JournalPLoS ONE
PublisherPublic Library of Science
ISSN19326203
Open AccessNo
Concepts (24)
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    Double stranded dna
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    Single stranded dna
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    Article
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    Complex formation
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    Diffusion
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    Dna conformation
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    DNA RENATURATION
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    Dna sequence
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    Geometry
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    Mathematical computing
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    Microscopy
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    Process development
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    Protein dna interaction
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    RENATURATION
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    Sequence analysis
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    Static electricity
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    Stochastic model
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    Viscosity
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    Biological model
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    Conformation
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    Metabolism
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    Dna, single-stranded
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    Models, genetic
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    Nucleic acid conformation