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^*

^*المؤلف المقابل لهذا العمل

Physics

نتاج البحث: المساهمة في مجلة › Article › مراجعة النظراء

1 اقتباس (Scopus)

ملخص

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.

اللغة الأصلية	English
رقم المقال	295101
الصفحات (من إلى)	295101
عدد الصفحات	8
دورية	Journal of Physics: Condensed Matter
مستوى الصوت	34
رقم الإصدار	29
المعرِّفات الرقمية للأشياء	https://doi.org/10.1088/1361-648x/ac6d39
حالة النشر	Published - مايو 5 2022

ASJC Scopus subject areas

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???subjectarea.asjc.3100.3104???

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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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month = may,

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

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TY - JOUR

T1 - Simulations of DNA denaturation dynamics under constrained conditions

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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DO - 10.1088/1361-648x/ac6d39

M3 - Article

C2 - 35512678

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SN - 0953-8984

VL - 34

SP - 295101

JO - Journal of Physics: Condensed Matter

JF - Journal of Physics: Condensed Matter

IS - 29

M1 - 295101

ER -

Simulations of DNA denaturation dynamics under constrained conditions

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