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      How Well Can DNA Rupture DNA? Shearing and Unzipping Forces inside DNA Nanostructures

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      ACS Omega
      American Chemical Society

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          Abstract

          A purely DNA nanomachine must support internal stresses across short DNA segments with finite rigidity, producing effects that can be qualitatively very different from experimental observations of isolated DNA in fixed-force ensembles. In this article, computational simulations are used to study how well the rigidity of a driving DNA duplex can rupture a double-stranded DNA target into single-stranded segments and how well this stress can discriminate between unzipping or shearing geometries. This discrimination is found to be maximized at an optimal length but deteriorates as the driving duplex is either lengthened or shortened. This differs markedly from a fixed-force ensemble and has implications for the design parameters and limitations of dynamic DNA nanomachines.

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          Most cited references55

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          A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.

          A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented. DNA NN DeltaG degrees 37 parameters from seven laboratories are presented in the same format so that careful comparisons can be made. The seven studies used data from natural polymers, synthetic polymers, oligonucleotide dumbbells, and oligonucleotide duplexes to derive NN parameters; used different methods of data analysis; used different salt concentrations; and presented the NN thermodynamics in different formats. As a result of these differences, there has been much confusion regarding the NN thermodynamics of DNA polymers and oligomers. Herein I show that six of the studies are actually in remarkable agreement with one another and explanations are provided in cases where discrepancies remain. Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics. Empirical salt dependencies are also derived for oligonucleotides and polymers.
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            Dynamic DNA nanotechnology using strand-displacement reactions.

            The specificity and predictability of Watson-Crick base pairing make DNA a powerful and versatile material for engineering at the nanoscale. This has enabled the construction of a diverse and rapidly growing set of DNA nanostructures and nanodevices through the programmed hybridization of complementary strands. Although it had initially focused on the self-assembly of static structures, DNA nanotechnology is now also becoming increasingly attractive for engineering systems with interesting dynamic properties. Various devices, including circuits, catalytic amplifiers, autonomous molecular motors and reconfigurable nanostructures, have recently been rationally designed to use DNA strand-displacement reactions, in which two strands with partial or full complementarity hybridize, displacing in the process one or more pre-hybridized strands. This mechanism allows for the kinetic control of reaction pathways. Here, we review DNA strand-displacement-based devices, and look at how this relatively simple mechanism can lead to a surprising diversity of dynamic behaviour.
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              A synthetic DNA walker for molecular transport.

              Inspired by kinesin movement along a microtubule, we demonstrate a processive bipedal DNA walker. Powered by externally controlled DNA fuel strands, the walker locomotes with a 5 nm stride by advancing the trailing foot to the lead at each step. Real-time monitoring of specific bidirectional walker movement is achieved via multiplexed fluorescence quenching.
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                Author and article information

                Journal
                ACS Omega
                ACS Omega
                ao
                acsodf
                ACS Omega
                American Chemical Society
                2470-1343
                10 January 2018
                31 January 2018
                : 3
                : 1
                : 292-301
                Affiliations
                [1]Department of Physics, National University of Singapore , 2 Science Drive 3, 117542 Singapore
                Author notes
                Article
                10.1021/acsomega.7b01692
                6044922
                30023776
                d8d4b27f-2383-4f8f-8359-4007f0afe695
                Copyright © 2018 American Chemical Society

                This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.

                History
                : 01 November 2017
                : 26 December 2017
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                ao7b01692
                ao-2017-01692a

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