What do we know about DNA mechanics so far?

Aggarwal, Ankur; Naskar, Supriyo; Sahoo, Anindita; Mogurampelly, Santosh; Garai, Ashok; Maiti, Prabal K.

doi:10.1016/j.sbi.2020.05.010

Cited by 38 publications

(35 citation statements)

References 67 publications

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“…Mechanical properties of DNA strongly influence how the double helix performs its various tasks in the cell, where it is often bent and twisted [1]. Computer simulations have been playing an increasingly important role in understanding these properties.…”

Section: Introductionmentioning

confidence: 99%

Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models

et al. 2021

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We investigate the influence of non-local couplings on the torsional and bending elasticities of DNA. Such couplings have been observed in the past by several simulation studies. Here, we use a description of DNA conformations based on the variables tilt, roll and twist. Our analysis of both coarse-grained (oxDNA) and all-atom models indicates that these share strikingly similar features: there are strong off-site couplings for tilt-tilt and twist-twist, while they are much weaker in the roll-roll case. By developing an analytical framework to estimate bending and torsional persistence lengths in non-local DNA models, we show how off-site interactions generate a length scale dependent elasticity. Based on the simulation generated elasticity data the theory predicts a significant length scale dependent effect on torsional fluctuations, but only a modest effect on bending fluctuations. These results are in agreement with experiments probing DNA mechanics from single base pair to kilobase pair scales.

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Section: Introductionmentioning

confidence: 99%

Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models

et al. 2021

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“…DNA intercalators have been a subject of intense scientific research because of their various uses, such as in anticancer and antitumor drugs [1] and fluorescent tags in imaging [2]. The molecular mechanism of the ligand intercalation process, especially the kinetics and thermodynamics of ligand intercalation, have been well studied [3][4][5][6][7]. Recently, many experimental studies have focused on understanding how intercalators modify the mechanical properties of doublestranded DNA (dsDNA) [3,[8][9][10][11][12][13][14][15], inferring how intercalators could affect many active biological processes, such as DNA repair, replication, and transcription.…”

Section: Introductionmentioning

confidence: 99%

“…DNA charge transport also has relevance in various biological processes, such as redox switching of [4Fe4S] clusters found in all DNA processing enzymes, which in turn affects DNA repair and replication processes [43,44]. DNA structure is highly distorted in the process of ligand intercalation, in which the planar aromatic rings of a ligand intercalate between two successive DNA base pairs [7,45], significantly affecting the charge transport in DNA.…”

Section: Introductionmentioning

confidence: 99%

Fine-tuning the DNA conductance by intercalation of drug molecules

et al. 2021

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In this work we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modeling approach where extensive ab initio calculations are performed on numerous MD-simulated configurations of dsDNA and dsDNA intercalated with two different intercalators, ethidium and daunomycin. DNA conductance is found to increase by one order of magnitude upon drug intercalation due to the local unwinding of the DNA base pairs adjacent to the intercalated sites, which leads to modifications of the density of states in the near-Fermi-energy region of the ligand-DNA complex. Our study suggests that the intercalators can be used to enhance or tune the DNA conductance, which opens new possibilities for their potential applications in nanoelectronics.

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“…During the last few decades, with the advancement of single-molecule manipulation techniques, our understanding of DNA and DNA nanostructure's mechanics has expanded immensely [3,7,9,[42][43][44][45][46]. Utilizing experimental techniques such as optical trapping, magnetic tweezers, atomic force microscopy (AFM), it has now turn out to be feasible to externally pull DNA at different physiological conditions [9,43,45,47,48].…”

Section: Introductionmentioning

confidence: 99%

Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, martini and oxDNA

Naskar,

Maiti

2021

Preprint

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The flexibility and stiffness of small DNA play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) having length ranging from 12 base-pairs (bps) to 56 bps, paranemic crossover (PX) DNA, and hexagonal DNA nanotubes (DNTs) using two widely used coarse-grain models -Martini and oxDNA. To calculate the persistence length (L p ) and the stretch modulus (γ) of the dsDNA, we incorporate the worm-like chain and elastic rod model, while for DNT, we implement our previously developed theoretical framework. We compare and contrast all the results with previously reported all-atom molecular dynamics (MD) simulation and experimental results. The mechanical properties of dsDNA (L p ∼ 50nm, γ ∼ 800-1500 pN), PX DNA (γ ∼ 1600-2000 pN) and DNTs (L p ∼ 1-10 µm, γ ∼ 6000-8000 pN) estimated using Martini soft elastic network and oxDNA are in very good agreement with the all-atom MD and experimental values, while the stiff elastic network Martini reproduces order of magnitude higher values of L p and γ. The high flexibility of small dsDNA is also depicted in our calculations. However, Martini models proved inadequate to capture the salt concentration effects on the mechanical properties with increasing salt molarity. oxDNA captures the salt concentration effect on small dsDNA mechanics. But it is found to be ineffective to reproduce the salt-dependent mechanical properties of DNTs. Also, unlike Martini, the time evolved PX DNA and DNT structures from the oxDNA models are comparable to the all-atom MD simulated structures. Our findings provide a route to study the mechanical properties of DNA and DNA based nanostructures with increased time and length scales and has a remarkable implication in the context of DNA nanotechnology.

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What do we know about DNA mechanics so far?

Cited by 38 publications

References 67 publications

Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models

Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models

Fine-tuning the DNA conductance by intercalation of drug molecules

Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, martini and oxDNA

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