Diffusive dynamics of DNA unzipping in a nanopore

Stachiewicz, Anna; Molski, Andrzej

doi:10.1002/jcc.24236

Cited by 5 publications

(9 citation statements)

References 44 publications

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“…Four hairpin sequences compared in the present work are denoted as H10, H7, H12, and H10m: H10: 5′-GCTCTGTTGCTCTCTCGCAACAGAGCA 30 -3′ H7: 5′-TGAATGATCTCTCTCATTCAA 30 -3′ H12: 5′-GCGCGCGGCCGCTCTCTCGCGGCCGCGC-GCA 30 -3′ H10m: 5′-GCTATGTTGCTCTCTCGCAACAGAGCA 30 -3′ H10 (Figure 1a) is a hairpin consisting of 10 base pairs and 60% ratio of cytosine/guanine to thymine/adenine. Diffusive dynamics of H10 were studied by Stachiewicz et al, 35 where we demonstrated that CG simulations combined with BD can unravel the mechanism of unzipping. Here, we extend our work by comparing H10 to three new sequences.…”

Section: ■ Introductionmentioning

confidence: 68%

“…The KN (C1′) superatom of the leading edge (base from the helical part connected directly with the coil) was chosen as the characteristic point used for measuring translocation progress and estimation of PMF, D, and q eff . The model and unzipping protocol validation can be found in paper by Stachiewicz et al 35 PMF(z). For each system, a number of unzipping simulations at different voltages were performed.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Therefore, for the sake of presentation, we recall the relevant characteristics of its unzipping dynamics. 35 On the force curve for H10 unzipping, four extrema (two maxima and two minima) can be distinguished (Figure 5a).…”

Section: ■ Introductionmentioning

confidence: 99%

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Sequence-Dependent Unzipping Dynamics of DNA Hairpins in a Nanopore

Stachiewicz

Molski

2019

J. Phys. Chem. B

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By applying an electric field to an insulating membrane, movement of charged particles through a nanopore can be induced. The measured ionic current reports on biomolecules passing through the nanopore. In this paper, we explore the sequence-dependent dynamics of DNA unzipping using our recently developed coarse-grained model. We estimated three molecular profiles (the potential of mean force, position-dependent diffusion coefficient, and positiondependent effective charge) for the DNA unzipping of four hairpins with different sequences. We found that the molecular profiles are correlated with the ionic current and molecular events. We also explored the unzipping kinetics using Brownian dynamics. We found that the effect of hairpin structure on the unzipping/translocation times is not only energetic (weaker hairpins unzip more quickly) but also kinetic (different unzipping and translocation pathways play an important role).

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Section: ■ Introductionmentioning

confidence: 68%

Section: ■ Introductionmentioning

confidence: 99%

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Sequence-Dependent Unzipping Dynamics of DNA Hairpins in a Nanopore

Stachiewicz

Molski

2019

J. Phys. Chem. B

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“…The dependence of unzipping kinetics on pore diameter and threshold voltage have been studied for a wide range of voltages and lengths of hairpins. 25–30 These studies find that the unfolding process dominates the total translocation time.…”

Section: Introductionmentioning

confidence: 99%

Unfolding of RNA via Translocation Through a Nanopore

Muthukumar

Chalise

2021

Preprint

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RNA unfolding and refolding are important biological phenomena, which occur during the transfer of genetic information from DNA to RNA to proteins. During these processes, RNA is found in single stranded, secondary and tertiary structures, including secondary conformations like hairpins and pseudoknots. Understanding the diverse conformations of RNA and how these influence the dynamics of unfolding and refolding is crucial to gain insight to fundamental biological processes. In this work, we employ coarse-grained Langevin dynamics simulations of a simple model of different RNA hairpins passing through a geometric nanopore to find the influence of structural changes on the translocation dynamics. The threshold voltage of unfolding depends on the length of the hairpin attached to the tail. The lag time to unfold is longer for smaller applied voltages and for the architectures containing a longer hairpin attached to the tail. Chain translocation dynamics for different architectures are largely collapsed by the threshold. A distinct signature for the base unfolding time was observed for the bases around the unpaired bases in all the RNA hairpin models. These results can motivate future technologies or experiments that use translocation to predict secondary structures of polynucleotides.

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“…Since the blockade signal depends on the DNA properties, it can be used to evaluate the purity and phosphorylation state of nucleic acid preparations, 168 for analysing unzipping kinetics of double-stranded DNA and hairpins, [169][170][171] DNA polymerase activity, 30,172 or DNA-protein interactions. 173 The most prominent application of threading the DNA through a nanopore, is though DNA sequencing.…”

Section: Physics Of Confined Dna: From the Odijk To The De Gennes Regimementioning

confidence: 99%

Flow of DNA in micro/nanofluidics: From fundamentals to applications

et al. 2016

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Thanks to direct observation and manipulation of DNA in micro/nanofluidic devices, we are now able to elucidate the relationship between the polymer microstructure and its rheological properties, as well as to design new single-molecule platforms for biophysics and biomedicine. This allows exploration of many new mechanisms and phenomena, which were previously unachievable with conventional methods such as bulk rheometry tests. For instance, the field of polymer rheology is at a turning point to relate the complex molecular conformations to the nonlinear viscoelasticity of polymeric fluids (such as coil–stretch transition, shear thinning, and stress overshoot in startup shear). In addition, nanofluidic devices provided a starting point for manipulating single DNA molecules by applying basic principles of polymer physics, which is highly relevant to numerous processes in biosciences. In this article, we review recent progress regarding the flow and deformation of DNA in micro/nanofluidic systems from both fundamental and application perspectives. We particularly focus on advances in the understanding of polymer rheology and identify the emerging research trends and challenges, especially with respect to future applications of nanofluidics in the biomedical field.

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Diffusive dynamics of DNA unzipping in a nanopore

Cited by 5 publications

References 44 publications

Sequence-Dependent Unzipping Dynamics of DNA Hairpins in a Nanopore

Sequence-Dependent Unzipping Dynamics of DNA Hairpins in a Nanopore

Unfolding of RNA via Translocation Through a Nanopore

Flow of DNA in micro/nanofluidics: From fundamentals to applications

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