Simulations of DNA denaturation dynamics under constrained conditions

Amal Al Qanobi; Davide Marenduzzo; Issam Ali

doi:10.1088/1361-648x/ac6d39

Simulations of DNA denaturation dynamics under constrained conditions

Amal Al Qanobi, Davide Marenduzzo, Issam Ali^*

^*Corresponding author for this work

Physics

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

Abstract

We study the dynamics of double-stranded DNA (dsDNA) denaturation using Brownian dynamics simulations. We use a coarse-grained single nucleotide model for dsDNA which considers the helix structure. We compare the melting dynamics for free DNA of length 300 base pairs with that of a DNA of the same length but fixed from one end - mimicking DNA tethered to a substrate. We find that free DNA melts at faster rate because the entropic gain associated with denaturation is larger. Additionally, we insert the DNA in nanochannels of different widths to study the influence of the confinement on the melting dynamics.

Original language	English
Article number	295101
Pages (from-to)	295101
Number of pages	8
Journal	Journal of Physics: Condensed Matter
Volume	34
Issue number	29
DOIs	https://doi.org/10.1088/1361-648x/ac6d39
Publication status	Published - May 5 2022

Keywords

confined DNA
constrained DNA
DNA melting
molecular dynamics simulations
Nucleic Acid Denaturation
DNA/chemistry
Base Pairing
Entropy
Nucleic Acid Conformation
Molecular Dynamics Simulation

ASJC Scopus subject areas

General Materials Science
Condensed Matter Physics

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10.1088/1361-648x/ac6d39

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title = "Simulations of DNA denaturation dynamics under constrained conditions",

abstract = "We study the dynamics of double-stranded DNA (dsDNA) denaturation using Brownian dynamics simulations. We use a coarse-grained single nucleotide model for dsDNA which considers the helix structure. We compare the melting dynamics for free DNA of length 300 base pairs with that of a DNA of the same length but fixed from one end - mimicking DNA tethered to a substrate. We find that free DNA melts at faster rate because the entropic gain associated with denaturation is larger. Additionally, we insert the DNA in nanochannels of different widths to study the influence of the confinement on the melting dynamics.",

keywords = "confined DNA, constrained DNA, DNA melting, molecular dynamics simulations, Nucleic Acid Denaturation, DNA/chemistry, Base Pairing, Entropy, Nucleic Acid Conformation, Molecular Dynamics Simulation",

author = "{Al Qanobi}, Amal and Davide Marenduzzo and Issam Ali",

note = "Publisher Copyright: {\textcopyright}3/4Rg/2, where R g is the radius of gyration of DNA. Instead, at channel width of R g/4 we only see partial denaturation at the free DNA melting temperature. Surprisingly, this trend is reversed at higher temperature, and we find that at 110 °C tight confinement results in faster melting. This is due to the fact that confinement promotes segregation of the single-stranded segment, thereby acting as an effective entropic force aiding denaturation.",

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doi = "10.1088/1361-648x/ac6d39",

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AU - Al Qanobi, Amal

AU - Marenduzzo, Davide

AU - Ali, Issam

N1 - Publisher Copyright: ©3/4Rg/2, where R g is the radius of gyration of DNA. Instead, at channel width of R g/4 we only see partial denaturation at the free DNA melting temperature. Surprisingly, this trend is reversed at higher temperature, and we find that at 110 °C tight confinement results in faster melting. This is due to the fact that confinement promotes segregation of the single-stranded segment, thereby acting as an effective entropic force aiding denaturation.

PY - 2022/5/5

Y1 - 2022/5/5

N2 - We study the dynamics of double-stranded DNA (dsDNA) denaturation using Brownian dynamics simulations. We use a coarse-grained single nucleotide model for dsDNA which considers the helix structure. We compare the melting dynamics for free DNA of length 300 base pairs with that of a DNA of the same length but fixed from one end - mimicking DNA tethered to a substrate. We find that free DNA melts at faster rate because the entropic gain associated with denaturation is larger. Additionally, we insert the DNA in nanochannels of different widths to study the influence of the confinement on the melting dynamics.

AB - We study the dynamics of double-stranded DNA (dsDNA) denaturation using Brownian dynamics simulations. We use a coarse-grained single nucleotide model for dsDNA which considers the helix structure. We compare the melting dynamics for free DNA of length 300 base pairs with that of a DNA of the same length but fixed from one end - mimicking DNA tethered to a substrate. We find that free DNA melts at faster rate because the entropic gain associated with denaturation is larger. Additionally, we insert the DNA in nanochannels of different widths to study the influence of the confinement on the melting dynamics.

KW - confined DNA

KW - constrained DNA

KW - DNA melting

KW - molecular dynamics simulations

KW - Nucleic Acid Denaturation

KW - DNA/chemistry

KW - Base Pairing

KW - Entropy

KW - Nucleic Acid Conformation

KW - Molecular Dynamics Simulation

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Simulations of DNA denaturation dynamics under constrained conditions

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