A coarse‐grained MARTINI‐like force field for DNA unzipping in nanopores

Stachiewicz, Anna; Molski, Andrzej

doi:10.1002/jcc.23874

Cited by 10 publications

(25 citation statements)

References 64 publications

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“…The unzipping, observed for the 2.5-nm pore and high voltages, 4 V and more, is probably the consequence of the abnormally large current reported for our CG model at this voltage range. [30] The unzipping starts earlier than in other cases, and the increased base pair separation can be observed before the leading edge crosses the pore constriction. Like in the study by Comer et al, [31] there is a correlation between applied voltage and the translocation mode.…”

Section: Voltage and Pore Geometrymentioning

confidence: 96%

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Diffusive dynamics of DNA unzipping in a nanopore

Stachiewicz

Molski

2015

J Comput Chem

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When an electric field is applied to an insulating membrane, movement of charged particles through a nanopore is induced. The measured ionic current reports on biomolecules passing through the nanopore. In this work, we explored the kinetics of DNA unzipping in a nanopore using our coarse-grained model (Stachiewicz and Molski, J. Comput. Chem. 2015, 36, 947). Coarse graining allowed a more detailed analysis for a wider range of parameters than all-atom simulations. Dependence of the translocation mode (unzipping or distortion) on the pore diameter was examined, and the threshold voltages were estimated. We determined the potential of mean force, position-dependent diffusion coefficient, and position-dependent effective charge for the DNA unzipping. The three molecular profiles were correlated with the ionic current and molecular events. On the unzipping/translocation force profile, two energy maxima were found, one of them corresponding to the unzipping, and the other to the translocation barriers. The unzipping kinetics were further explored using Brownian dynamics.

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Section: Voltage and Pore Geometrymentioning

confidence: 96%

“…[30] To examine the influence of the pore geometry on unzipping pathway, a number of pores was prepared, by removing FULL PAPER WWW.C-CHEM.ORG the atoms, whose xyz coordinates of the centers satisfied the following equation [34] :…”

Section: Cg Modelmentioning

confidence: 99%

Diffusive dynamics of DNA unzipping in a nanopore

Stachiewicz

Molski

2015

J Comput Chem

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“…Previous work on nucleotides using the Martini force field include an ad hoc version of a small piece of Martini DNA, parameterized by Khalid and coworkers 31 and used to study complexes of DNA and lipids 31,32 . A modified version of the SIRAH DNA model has also been adapted to work with Martini solvent to simulate DNA hairpin translocation and unzipping in nanopores 33 . A preliminary version has also been used in a model of a lipid nanoparticle containing RNA 34,35 .…”

Section: Introductionmentioning

confidence: 99%

Martini Coarse-Grained Force Field: Extension to DNA

López¹,

Rzepiela²,

Vries³

et al. 2015

J. Chem. Theory Comput.

273

310

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We systematically parameterized a coarse-grained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nucleobases between polar and nonpolar solvents as well as base-base potential of mean force calculations. The bonded interactions are fit to single-stranded DNA (ssDNA) atomistic simulations and an elastic network is used to retain double-stranded DNA (dsDNA) and other specific DNA conformations. We present the implementation of the Martini DNA model and demonstrate the properties of individual bases, ssDNA as well as dsDNA, and DNA-protein complexes. The model opens up large-scale simulations of DNA interacting with a wide range of other (bio)molecules that are available within the Martini framework.

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“…Larger-scale assemblies can be simulated on limited time-scales of tens to hundreds of nanoseconds using high performance computing resources that are not broadly available (34). In contrast, coarse-grained models use united atom representations to model clusters of atoms and their interactions, thereby reducing the total number of degrees of freedom (DOF) and associated computational cost (37–49) at the expense of all-atom resolution.…”

Section: Introductionmentioning

confidence: 99%

Structure and conformational dynamics of scaffolded DNA origami nanoparticles

Pan

Bricker

Ratanalert

et al. 2017

Nucleic Acids Research

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Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fully determined by underlying Watson–Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5–100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost. We apply all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanoparticles to elucidate their fine-scale and global conformational structure and dynamics. We use our coarse-grained model with a set of secondary structural motifs to predict the equilibrium solution structures of 45 DX-based DNA origami nanoparticles including a tetrahedron, octahedron, icosahedron, cuboctahedron and reinforced cube. Coarse-grained models are compared with 3D cryo-electron microscopy density maps for these five DNA nanoparticles and with all-atom molecular dynamics simulations for the tetrahedron and octahedron. Our results elucidate non-intuitive atomic-level structural details of DX-based DNA nanoparticles, and offer a general framework for efficient computational prediction of global and local structural and mechanical properties of DX-based assemblies that are inaccessible to all-atom based models alone.

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A coarse‐grained MARTINI‐like force field for DNA unzipping in nanopores

Cited by 10 publications

References 64 publications

Diffusive dynamics of DNA unzipping in a nanopore

Diffusive dynamics of DNA unzipping in a nanopore

Martini Coarse-Grained Force Field: Extension to DNA

Structure and conformational dynamics of scaffolded DNA origami nanoparticles

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