Dimensional reduction of duplex DNA under confinement to nanofluidic slits

Abstract

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...

Persistent draining crossover in DNA and other semi-flexible polymers: Evidence from hydrodynamic models and extensive measurements on DNA solutions

“…This conclusion should not be extended to DNA under high confinement (scales on the order of the persistence length a) since the strength of the excluded volume interaction should be greatly amplified under these conditions. 51 Our conclusions also do not apply to low salt conditions where long-range electrostatic interactions must have an appreciable effect on the dimensions of DNA.…”

Universal interrelation between measures of particle and polymer size

“…For instance, ν eff is a function of the aspect ratio r for oblate and prolate ellipsoids, where r is the ratio between the largest to the smallest ellipsoid axis. 24 The same situation arises for dendrimers, 25,26 duplex DNA, 27 carbon nanotube domains, 8 nanoparticle with grafted layers of DNA chains, 28,29 etc. In each case, the molecular parameters describing the object must be prescribed over which the mass scaling relation is exhibited.…”

Evidence for the extended de Gennes regime of a semiflexible polymer in slit confinement

“…We found that the free energy converges more quickly than the chain size, which is convenient for our purposes. The predictions by de Gennes for both of the in-plane radius of gyration [17, 19, 28, 30, 31, 40, 42, 43, 46] and confinement free energy [29, 30], or equivalently the force of the confinement [31, 42], have been verified many times. There is one report [39] claiming that the de Gennes theory for the confinement free energy fails for long chains; our results correspond to very long chains simulated with a state-of-the-art methodology and the agreement of the data in Fig.…”