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Molecular Simulation Volume 39, 2013 - Issue 9
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Original Articles

Molecular simulation study of the assembly of DNA-functionalised nanoparticles: Effect of DNA strand sequence and composition

Arezou SeifpourDepartment of Chemical and Biological Engineering, University of Colorado, Jennie Smoly Caruthers Biotechnology Building, 596 UCB, Boulder, CO80309-0596, USA
,
Steven R. DahlDepartment of Chemical and Biological Engineering, University of Colorado, Jennie Smoly Caruthers Biotechnology Building, 596 UCB, Boulder, CO80309-0596, USA
,
Brandon LinDepartment of Chemical and Biological Engineering, University of Colorado, Jennie Smoly Caruthers Biotechnology Building, 596 UCB, Boulder, CO80309-0596, USA
&
Arthi JayaramanDepartment of Chemical and Biological Engineering, University of Colorado, Jennie Smoly Caruthers Biotechnology Building, 596 UCB, Boulder, CO80309-0596, USACorrespondence[email protected]
Pages 741-753 | Received 16 Sep 2012, Accepted 07 Jan 2013, Published online: 14 Mar 2013

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Evan Pretti, Runfang Mao & Jeetain Mittal. (2019) Modelling and simulation of DNA-mediated self-assembly for superlattice design. Molecular Simulation 45:14-15, pages 1203-1210.
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Arezou Seifpour, Steven R. Dahl & Arthi Jayaraman. (2014) Molecular simulation study of assembly of DNA-grafted nanoparticles: effect of bidispersity in DNA strand length. Molecular Simulation 40:14, pages 1085-1098.
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Articles from other publishers (18)

Timothy Cholko & Chia-en A. Chang. (2021) Modeling Effects of Surface Properties and Probe Density for Nanoscale Biosensor Design: A Case Study of DNA Hybridization near Surfaces. The Journal of Physical Chemistry B 125:7, pages 1746-1754.
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Arthi Jayaraman, Arjita Kulshreshtha, Phillip Taylor & Ammu Prhashanna. 2021. Foundations of Molecular Modeling and Simulation. Foundations of Molecular Modeling and Simulation 37 74 .
Runfang Mao & Jeetain Mittal. (2020) Self-Assembly of DNA-Functionalized Nanoparticles Guided by Binding Kinetics. The Journal of Physical Chemistry B 124:51, pages 11593-11599.
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Arthi Jayaraman. (2020) 100th Anniversary of Macromolecular Science Viewpoint: Modeling and Simulation of Macromolecules with Hydrogen Bonds: Challenges, Successes, and Opportunities. ACS Macro Letters 9:5, pages 656-665.
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Ammu Prhashanna & Arthi Jayaraman. (2019) Melting thermodynamics of oligonucleic acids conjugated with relatively solvophobic linear polymers: A coarse‐grained molecular simulation study. Journal of Polymer Science Part B: Polymer Physics 57:18, pages 1196-1208.
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Timothy Cholko, Shivansh Kaushik & Chia-en A. Chang. (2019) Dynamics and molecular interactions of single-stranded DNA in nucleic acid biosensors with varied surface properties. Physical Chemistry Chemical Physics 21:29, pages 16367-16380.
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Sai Li, Zhiyu Zhang, Guanyi Hou, Jun Liu, Yangyang Gao, Phil Coates & Liqun Zhang. (2019) Self-assembly and structural manipulation of diblock-copolymer grafted nanoparticles in a homopolymer matrix. Physical Chemistry Chemical Physics 21:22, pages 11785-11796.
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Caroline Desgranges & Jerome Delhommelle. (2018) Modeling antigen-antibody nanoparticle bioconjugates and their polymorphs. The Journal of Chemical Physics 148:12.
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Chunyan Qiao, Jia Wu, Zhenrong Huang, Xuan Cao, Jiayu Liu, Bin Xiong, Yan He & Edward S. Yeung. (2017) Sequence-Modulated Interactions between Single Multivalent DNA-Conjugated Gold Nanoparticles. Analytical Chemistry 89:10, pages 5592-5597.
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Joshua E. Condon & Arthi Jayaraman. (2017) Effect of oligonucleic acid (ONA) backbone features on assembly of ONA–star polymer conjugates: a coarse-grained molecular simulation study. Soft Matter 13:38, pages 6770-6783.
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Mukta Tripathy. (2017) Self-assembly of polymer-linked nanoparticles and scaling behavior in the assembled phase. Soft Matter 13:13, pages 2475-2482.
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Théo Calais, Vincent Baijot, Mehdi Djafari Rouhani, David Gauchard, Yves J. Chabal, Carole Rossi & Alain Estève. (2016) General Strategy for the Design of DNA Coding Sequences Applied to Nanoparticle Assembly. Langmuir 32:37, pages 9676-9686.
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Ahmadreza F. Ghobadi & Arthi Jayaraman. (2016) Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study. Soft Matter 12:8, pages 2276-2287.
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Robert M. Elder, Jim Pfaendtner & Arthi Jayaraman. (2015) Effect of Hydrophobic and Hydrophilic Surfaces on the Stability of Double-Stranded DNA. Biomacromolecules 16:6, pages 1862-1869.
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Ruhong ZhouRuhong Zhou. 2015. Modeling of Nanotoxicity. Modeling of Nanotoxicity 101 113 .
Yajun Ding & Jeetain Mittal. (2014) Insights into DNA-mediated interparticle interactions from a coarse-grained model. The Journal of Chemical Physics 141:18.
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Robert M. Elder & Arthi Jayaraman. (2014) Simulation study of the effects of surface chemistry and temperature on the conformations of ssDNA oligomers near hydrophilic and hydrophobic surfaces. The Journal of Chemical Physics 140:15.
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Carla E. Estridge & Arthi Jayaraman. (2014) Assembly of diblock copolymer functionalized spherical nanoparticles as a function of copolymer composition. The Journal of Chemical Physics 140:14.
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