Site accessibility tailors DNA cleavage by restriction enzymes in DNA confined monolayers

Chiara Rotella; Giovanni Doni; Alessandro Bosco; Matteo Castronovo; Alessandro De Vita; Loredana Casalis; Giovanni M. Pavan; Pietro Parisse

doi:10.1039/C7NR00966F

Site accessibility tailors DNA cleavage by restriction enzymes in DNA confined monolayers

Chiara Rotella, Giovanni Doni, Alessandro Bosco, Matteo Castronovo, Alessandro De Vita, Loredana Casalis, Giovanni M. Pavan, Pietro Parisse

Physics

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3 Citations (Scopus)

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Abstract

Density-tunable nanografted monolayers (NAMs) of short oligonucleotide sequences on gold surfaces show novel properties that make them suitable for advanced biosensing applications, and in particular to study the effects of crowding and confinement on biomolecular interactions. Here, combining atomic force microscopy nanolithography, topography measurements and coarse-grained molecular dynamics simulations, we investigated restriction enzyme reaction mechanisms within confined DNA brushes highlighting the role played by the DNA sequence conformation and restriction site position along the chain, respectively, in determining the accessibility of the enzyme, and its consequent cleavage efficiency.

Original language	English
Pages (from-to)	6399-6405
Number of pages	7
Journal	Nanoscale
Volume	9
Issue number	19
Early online date	17 Apr 2017
DOIs	https://doi.org/10.1039/C7NR00966F
Publication status	Published - 21 May 2017

Keywords

molecular dynamics
DNA

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10.1039/C7NR00966F

Site accessibility tailors DNA _ROTELLA_Firstonline17April2017_GREEN AAMAccepted author manuscript, 1.02 MB

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title = "Site accessibility tailors DNA cleavage by restriction enzymes in DNA confined monolayers",

abstract = "Density-tunable nanografted monolayers (NAMs) of short oligonucleotide sequences on gold surfaces show novel properties that make them suitable for advanced biosensing applications, and in particular to study the effects of crowding and confinement on biomolecular interactions. Here, combining atomic force microscopy nanolithography, topography measurements and coarse-grained molecular dynamics simulations, we investigated restriction enzyme reaction mechanisms within confined DNA brushes highlighting the role played by the DNA sequence conformation and restriction site position along the chain, respectively, in determining the accessibility of the enzyme, and its consequent cleavage efficiency.",

keywords = "molecular dynamics , DNA",

author = "Chiara Rotella and Giovanni Doni and Alessandro Bosco and Matteo Castronovo and {De Vita}, Alessandro and Loredana Casalis and Pavan, {Giovanni M.} and Pietro Parisse",

year = "2017",

month = may,

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doi = "10.1039/C7NR00966F",

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T1 - Site accessibility tailors DNA cleavage by restriction enzymes in DNA confined monolayers

AU - Rotella, Chiara

AU - Doni, Giovanni

AU - Bosco, Alessandro

AU - Castronovo, Matteo

AU - De Vita, Alessandro

AU - Casalis, Loredana

AU - Pavan, Giovanni M.

AU - Parisse, Pietro

PY - 2017/5/21

Y1 - 2017/5/21

N2 - Density-tunable nanografted monolayers (NAMs) of short oligonucleotide sequences on gold surfaces show novel properties that make them suitable for advanced biosensing applications, and in particular to study the effects of crowding and confinement on biomolecular interactions. Here, combining atomic force microscopy nanolithography, topography measurements and coarse-grained molecular dynamics simulations, we investigated restriction enzyme reaction mechanisms within confined DNA brushes highlighting the role played by the DNA sequence conformation and restriction site position along the chain, respectively, in determining the accessibility of the enzyme, and its consequent cleavage efficiency.

AB - Density-tunable nanografted monolayers (NAMs) of short oligonucleotide sequences on gold surfaces show novel properties that make them suitable for advanced biosensing applications, and in particular to study the effects of crowding and confinement on biomolecular interactions. Here, combining atomic force microscopy nanolithography, topography measurements and coarse-grained molecular dynamics simulations, we investigated restriction enzyme reaction mechanisms within confined DNA brushes highlighting the role played by the DNA sequence conformation and restriction site position along the chain, respectively, in determining the accessibility of the enzyme, and its consequent cleavage efficiency.

KW - molecular dynamics

KW - DNA

U2 - 10.1039/C7NR00966F

DO - 10.1039/C7NR00966F

M3 - Article

SN - 2040-3364

VL - 9

SP - 6399

EP - 6405

JO - Nanoscale

JF - Nanoscale

IS - 19

ER -

Site accessibility tailors DNA cleavage by restriction enzymes in DNA confined monolayers

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Keywords

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