Coarse-Grained Simulation Study of Sequence Effects on DNA Hybridization in a Concentrated Environment

Markegard, Cade B.; Fu, Iris W.; Reddy, K. Anki; Nguyen, Hung D.

doi:10.1021/jp509857k

Cited by 23 publications

(47 citation statements)

References 76 publications

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“…Most of the successful CG models use from 2 (oxDNA [135][136][137][138], and Aksim nti v's m d l [148]), or 3 (3SPN [131][132][133]139,140], BioModi [149]), to eight beads per nucleotide (see Figure 2, and Table 1 for more details). However, coarser models with five beads per base-pair step (four nucleotides), or even a single bead per nucleotide have emerged [126,127].…”

Section: Coarse-grain Studiesmentioning

confidence: 99%

“…For example, the WT4 model, which condenses 11 water molecules in four beads, was meant to work in conjunction with the SIRAH force-field [142]. In the same way, the regular and polarized water models by The model developed by Nguyen and coworkers was thought to combine with ePRIME [152], and be delivered as BioModi [149], a unified CG force-field for DNA, proteins and general polymers. The DNA model from Scheraga's group [128] was derived with the same philosophy used to derive the UNRES [153] force-field for proteins, and is expected to be compatible.…”

Section: Coarse-grain Studiesmentioning

confidence: 99%

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Multiscale simulation of DNA

Dans¹,

Walther

Gómez

et al. 2016

Current Opinion in Structural Biology

144

131

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DNA is not only among the most important molecules in life, but a meeting point for biology, physics and chemistry, being studied by numerous techniques. Theoretical methods can help in gaining a detailed understanding of DNA structure and function, but their practical use is hampered by the multiscale nature of this molecule. In this regard, the study of DNA covers a broad range of different topics, from sub-Angstrom details of the electronic distributions of nucleobases, to the mechanical properties of millimeter-long chromatin fibers. Some of the biological processes involving DNA occur in femtoseconds, while others require years. In this review, we describe the most recent theoretical methods that have been considered to study DNA, from the electron to the chromosome, enriching our knowledge on this fascinating molecule.

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Section: Coarse-grain Studiesmentioning

confidence: 99%

Section: Coarse-grain Studiesmentioning

confidence: 99%

Multiscale simulation of DNA

Dans¹,

Walther

Gómez

et al. 2016

Current Opinion in Structural Biology

144

131

View full text Add to dashboard Cite

show abstract

“…The reported values of l p span a wide range, from 1.0 to 6.0 nm, and is often sensitive to the experimental setup. 54,55,57,71 To further validate the robustness of the TIS-DNA model in describing ssDNA, we compute l p using equation (19) for a homogeneous poly(dT), and a poly(dA) sequence, each of which is 40 nucleotide long.…”

Section: Sequence Dependent Stiffnessmentioning

confidence: 99%

Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

Chakraborty

Hori

Thirumalai

2018

Preprint

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We develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully reproduced. Without any further adjustments, the calculations based on the TIS model reproduces the experimentally measured salt and sequence dependence of the size of single stranded DNA (ssDNA), as well as the persistence lengths of poly(dA) and poly(dT) chains . Interestingly, upon application of mechanical force the extension of poly(dA) exhibits a plateau, which we trace to the formation of stacked helical domains. In contrast, the force-extension curve (FEC) of 1 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/256487 doi: bioRxiv preprint first posted online Jan. 29, 2018; poly(dT) is entropic in origin, and could be described by a standard polymer model.We also show that the persistence length of double stranded DNA, formed from two complementary ssDNAs with one hundred and thirty base pairs, is consistent with the prediction based on the worm-like chain. The persistence length, which decreases with increasing salt concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for stiff polyelectrolyte chains near the rod limit. The range of applications, which did not require adjusting any parameter after the initial construction based solely on PDB structures and melting profiles of dimers, attests to the transferability and robustness of the TIS model for ssDNA and dsDNA.

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“…Recently proposed CG models can accurately reproduce some of the properties observed in experiments (Freeman et al, 2014a; Hinckley and de Pablo, 2015; Markegard et al, 2015; Snodin et al, 2015; Singh and Granek, 2016) or all-atom models (Savelyev and Papoian, 2010; Setny and Zacharias, 2013; Naômé et al, 2014), which also depend on solution conditions. However, due to the large degrees of freedom, the computational cost of these models is still not low enough to be applicable to long DNA sequences containing more than 10 4 base pairs, corresponding to a 10-nm fiber with 100 nucleosomes or a mitochondrial nucleoid.…”

Section: Introductionmentioning

confidence: 99%

The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry

et al. 2017

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Coarse-grained models of DNA have made important contributions to the determination of the physical properties of genomic DNA, working as a molecular machine for gene regulation. In this study, to analyze the global dynamics of long DNA sequences with consideration of sequence-dependent geometry, we propose elastic network models of DNA where each particle represents k nucleotides (1-particle-per-k-nucleotides, 1PkN). The models were adjusted according to profiles of the anisotropic fluctuations obtained from our previous 1-particle-per-1-nucleotide (1P1N) model, which was proven to reproduce such profiles of all-atom models. We confirmed that the 1P3N and 1P4N models are suitable for the analysis of detailed dynamics such as local twisting motion. The models are intended for the analysis of large structures, e.g., 10-nm fibers in the nucleus, and nucleoids of mitochondrial or phage DNA at low computational costs. As an example, we surveyed the physical characteristics of the whole mitochondrial human and Plasmodium falciparum genomes.

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Coarse-Grained Simulation Study of Sequence Effects on DNA Hybridization in a Concentrated Environment

Cited by 23 publications

References 76 publications

Multiscale simulation of DNA

Multiscale simulation of DNA

Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry

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