Mechanism of DNA assembly as revealed by energy barriers

Niu, Lin; Yang, Xuyan; Zhou, Jihan; Mao, Chengde; Liang, Haojun; Liang, Dehai

doi:10.1039/c5cc00783f

Cited by 9 publications

(19 citation statements)

References 33 publications

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“…At macroscopic level the rate of change in the number of mol-bases in ssDNA form in the process of zipping will be directly proportional to the number of mol-bases in ssDNA form as well as number of mol-bases in dsDNA form which results in a cooperative sigmoidal type time evolution of the renaturation process [ 16 – 17 , 28 ] where the macroscopic kinetic rate equation will be written as dn DS / dt ∝ n cc ( n 0 − n DS ) n DS . Here n 0 is the initial concentration of mol-bases of c-ssDNA molecules in the system and n cc is the total number of cc-ssDNA molecules in the system.…”

Section: Resultsmentioning

confidence: 99%

“…Here one should note that we are dealing with the cooperative effects at a mesoscopic level within an independent and single renaturing cc-ssDNA molecule rather than at macroscopic level where the descriptive parameter of the renaturation process will be the number of mol-bases in ssDNA (nSS) or dsDNA (nDS) form rather than the number of correct-contacts in cc-ssDNA (u) as in the current context. At macroscopic level the rate of change in the number of mol-bases in ssDNA form in the process of zipping will be directly proportional to the number of molbases in ssDNA form as well as number of mol-bases in dsDNA form which results in a cooperative sigmoidal type time evolution of the renaturation process (16)(17)28) where the macroscopic kinetic rate equation will be written as ( )…”

Section: Role Of Cooperativity In Renaturation Kineticsmentioning

confidence: 99%

“…Here one should note that the two-step model of Wetmur-Davidson will be inconsistent whenever the complexity has same magnitude as that of the length of c-ssDNA. Subsequent experimental studies on renaturation phenomenon were mainly focussed (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28) on unravelling the molecular mechanisms and the underlying thermodynamics and kinetics aspects. In line of these experimental studies, several theoretical and computational models (6, 7, 14-17, 23-27) were also developed to explain the observed scaling behaviours of the overall second order renaturation rate constant on the size of reacting c-ssDNAs, temperature, ionic strength and viscosity of the reaction medium.…”

Section: Introductionmentioning

confidence: 99%

“…According to the current theoretical understandings over experimental and computational observations (23)(24)(25)(26)(27)(28)(29), the renaturation process should have at least three distinct steps namely (a) incorrect contact formation (b) nucleation or correct contact formation and (c) zipping. In the first step, the reacting c-ssDNAs collide with each other via three-dimensional (3D) diffusion controlled routes.…”

Section: Introductionmentioning

confidence: 99%

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Theory on the Mechanism of DNA Renaturation: Stochastic Nucleation and Zipping

Niranjani

Murugan

2016

PLoS ONE

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Role Of Cooperativity In Renaturation Kineticsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Theory on the Mechanism of DNA Renaturation: Stochastic Nucleation and Zipping

Niranjani

Murugan

2016

PLoS ONE

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“…33 As indicated in Scheme 1, the DNA strands can assemble together. Some DNA strands cannot perfectly hybridize with each other because of the geometrical constraint, especially at high concentration (2.0 mM), which is several orders of magnitude higher than the DNA concentration normally used for DNA assembly.…”

Section: View Article Onlinementioning

confidence: 99%

Effects of chain flexibility on the properties of DNA hydrogels

et al. 2016

Self Cite

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The effect of chain rigidity on the mechanic properties of DNA hydrogels was studied. Counterintuitively, the hydrogel formed by mainly flexible chains exhibited better stability, stretchability, and much mechanical properties than the hydrogel containing only rigid chains. Calculations showed that the crosslinking ratio in the hydrogel formed by flexible chains was about twice that of the hydrogel formed by rigid chains under the same conditions. We attributed this to the ease of conformational adjustment of flexible chains. Incorporation of 25% rigid chains further improved the performance of DNA hydrogel by shrinking the pore size and tuning its distribution.

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Rational Design of DNA Hydrogels Based on Molecular Dynamics of Polymers

Li,

Chen,

Zhou

et al. 2023

Advanced Materials

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In recent years, DNA has emerged as a fascinating building material to engineer hydrogels due to its excellent programmability, which has gained considerable attention in biomedical applications. Understanding the structure‐property relationship and underlying molecular determinants of DNA hydrogel is essential to precisely tailor its macroscopic properties at molecular level. In this review, we highlight the rational design principles of DNA molecular networks based on molecular dynamics of polymers on the temporal scale, which can be engineered via the backbone rigidity and crosslinking kinetics. By elucidating the underlying molecular mechanisms and theories, we aim to provide a comprehensive overview of how the tunable DNA backbone rigidity and the crosslinking kinetics lead to desirable macroscopic properties of DNA hydrogels, including mechanical properties, diffusive permeability, swelling behaviors, and dynamic features. Furthermore, we also discuss how the tunable macroscopic properties make DNA hydrogels promising candidates for biomedical applications, such as cell culture, tissue engineering, bio‐sensing, and drug delivery.This article is protected by copyright. All rights reserved

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Mechanism of DNA assembly as revealed by energy barriers

Cited by 9 publications

References 33 publications

Theory on the Mechanism of DNA Renaturation: Stochastic Nucleation and Zipping

Theory on the Mechanism of DNA Renaturation: Stochastic Nucleation and Zipping

Effects of chain flexibility on the properties of DNA hydrogels

Rational Design of DNA Hydrogels Based on Molecular Dynamics of Polymers

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