Effects of Topology and Ionic Strength on Double-Stranded DNA Confined in Nanoslits

Lin, Po-Keng; Hsieh, Chia Chien; Chen, Yeng; Chou, Chia-Fu

doi:10.1021/ma202695e

Cited by 41 publications

(63 citation statements)

References 66 publications

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“…48 The interaction of Na + with dsDNA is similar to but weaker than that of the acidic form of Tris (Tris + ), 49 which was present in all of the experimental systems. Therefore, the presence of Na + in the experiments of Bonthuis et al 6 and Lin et al 13 probably did not significantly influence the dsDNA size. With regard to anions, however boric acid probably did significantly influence the dsDNA size.…”

Section: Solution Conditionsmentioning

confidence: 84%

“…1 summarizes single-molecule measurements of the in-plane radius of gyration R gJ of dsDNA obtained from references. 3,5,6,8,[11][12][13] The lower panel of Fig. 1 presents the in-plane size of the dsDNA normalized by an estimate of the most probable (mode) value in bulk solution R gJ (bulk).…”

Section: Brief Review Of Previous Studies Of Polymers Under Confinemementioning

confidence: 99%

“…50 In particular, Tang et al 8 found that the absence of boric acid in the experimental system of Bonthuis et al 6 resulted in moderate changes in dsDNA size relative to the other experimental systems. 8,[11][12][13] The various oxygen scavenging additives used to mitigate the photobleaching of YOYO-1 and the photodegradation of dsDNA are also a concern. In the presence of dissolved oxygen, the enzymatic oxygen scavenging system comprised of glucose, glucose oxidase, and catalase produced gluconic acid (pK a E 3.86).…”

Section: Solution Conditionsmentioning

confidence: 99%

“…Consequently, there have been many recent theoretical and experimental studies of this phenomenon. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15] In particular, it has been possible for two decades to image individual fluorescently labeled dsDNA under conditions of nanoscale confinement in nanofluidic devices with slit-like geometries. In this way, the in-plane radius of gyration of dsDNA as a function of slit height has been recently measured.…”

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Dimensional reduction of duplex DNA under confinement to nanofluidic slits

et al. 2015

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There has been much interest in the dimensional properties of double-stranded DNA (dsDNA) confined to nanoscale environments as a problem of fundamental importance in both biological and technological fields. This has led to a series of measurements by fluorescence microscopy of single dsDNA molecules under confinement to nanofluidic slits. Despite the efforts expended on such experiments and the corresponding theory and simulations of confined polymers, a consistent description of changes of the radius of gyration of dsDNA under strong confinement has not yet emerged. Here, we perform molecular dynamics (MD) simulations to identify relevant factors that might account for this inconsistency.Our simulations indicate a significant amplification of excluded volume interactions under confinement at the nanoscale due to the reduction of the effective dimensionality of the system. Thus, any factor influencing the excluded volume interaction of dsDNA, such as ionic strength, solution chemistry, and even fluorescent labels, can greatly influence the dsDNA size under strong confinement. These factors, which are normally less important in bulk solutions of dsDNA at moderate ionic strengths because of the relative weakness of the excluded volume interaction, must therefore be under tight control to achieve reproducible measurements of dsDNA under conditions of dimensional reduction. By simulating semi-flexible polymers over a range of parameter values relevant to the experimental systems and exploiting past theoretical treatments of the dimensional variation of swelling exponents and prefactors, we have developed a novel predictive relationship for the in-plane radius of gyration of long semi-flexible polymers under slit-like confinement. Importantly, these analytic expressions allow us to estimate the properties of dsDNA for the experimentally and biologically relevant range of contour lengths that is not currently accessible by state-of-the-art MD simulations.An understanding of the many factors influencing the size of dsDNA under nanoscale confinement is highly relevant to rationally designing measurement technologies for genomic sequencing and medical sensing and for accurately describing crowding effects on dsDNA organization in living systems. Consequently, there have been many recent theoretical and experimental studies of this phenomenon. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15] In particular, it has been possible for two decades to image individual fluorescently labeled dsDNA under conditions of nanoscale confinement in nanofluidic devices with slit-like geometries. In this way, the in-plane radius of gyration of dsDNA as a function of slit height has been recently measured. Fig. 1 summarizes the results of these experimental measurements, which exhibit a puzzling scatter under nominally similar experimental conditions. Scaling arguments and continuum chain models have dominated the majority of the recent theoretical treatments of this problem, which generally ignore polymer-surface interactions and hav...

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Section: Solution Conditionsmentioning

confidence: 84%

Section: Brief Review Of Previous Studies Of Polymers Under Confinemementioning

confidence: 99%

Section: Solution Conditionsmentioning

confidence: 99%

mentioning

confidence: 99%

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Dimensional reduction of duplex DNA under confinement to nanofluidic slits

et al. 2015

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“…DNA has played a key role in the experimental tests of theories of a polymer confined to a slit [1][2][3][4][5][6][7][8][9][10][11][12][13][14] or a channel [15][16][17][18][19][20][21][22][23][24][25][26][27], in particular the models by de Gennes and coworkers for weak confinement [28,29] and Odijk for strong confinement [30,31]. The key results of this body of work have been summarized in several recent reviews [32][33][34].…”

Section: Introductionmentioning

confidence: 99%

Wall depletion length of a channel-confined polymer

Cheong

Dorfman

2017

Phys. Rev. E

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Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte in a channel with charged walls) can be mapped to the theoretical model (a neutral polymer with hard walls). We test this assumption using pruned-enriched Rosenbluth method (PERM) simulations of a DNA-like semiflexible polymer confined in a tube. The polymer-wall interactions are modeled by augmenting a hard wall interaction with an exponentially decaying, repulsive soft potential. The free energy, mean span, and variance in the mean span obtained in the presence of a soft wall potential are compared to equivalent simulations in the absence of the soft wall potential to determine the depletion length. We find that the mean span and variance about the mean span have the same depletion length for all soft potentials we tested. In contrast, the depletion length for the confinement free energy approaches that for the mean span only when depletion length no longer depends on channel size. The results have implications for the interpretation of DNA confinement experiments under low ionic strengths. * dorfman@umn.edu

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Manipulation of DNA by Complex Confinement Using Nanofluidic Slits

Strychalski

Stavis

2015

Micro‐ and Nanomanipulation Tools

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Effects of Topology and Ionic Strength on Double-Stranded DNA Confined in Nanoslits

Cited by 41 publications

References 66 publications

Dimensional reduction of duplex DNA under confinement to nanofluidic slits

Dimensional reduction of duplex DNA under confinement to nanofluidic slits

Wall depletion length of a channel-confined polymer

Manipulation of DNA by Complex Confinement Using Nanofluidic Slits

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