Ionic Effects on the Equilibrium Dynamics of DNA Confined in Nanoslits

Abstract

The ionic effects on the dynamics and conformation of DNA in silt-like confinement are investigated. Confined λ-DNA is considered as a model polyelectrolyte, and its longest relaxation time, diffusivity, and size are measured at a physiological ionic strength between 1.7-170 mM. DNA properties change drastically in response to the varying ionic environment, and these changes can be explained by blob theory with an electrostatically mediated effective diameter and persistence length. In the ionic range we investigate, the effective diameter of DNA that represents the electrostatic repulsion between remote segments is found to be the main driving force for the observed change in DNA properties. Our results are useful for understanding the manipulation of biomolecules in nanofluidic devices.With the advance of nanotechnology, new devices have been created to manipulate biomolecules. Many such applications, including DNA separation 1 and gene mapping, 2 rely on the confinement-induced change in molecular properties. Several studies have been devoted to the investigation of those confinement effects on DNA and have had fruitful progress.3-6 On the other hand, the ionic environment is also known to have a strong influence on biomolecule properties and can be readily manipulated in experiments. However, the compound effects of confinement and ionic environment, critical for many applications, are yet to be fully understood.Several studies have investigated the ionic effects on confined DNA conformation in rectangular channels (height (h) ≈ width (d)).2,7,8 DNA extension was found to increase with decreasing ionic strength. This observation was explained either by de Gennes' blob theory (h and d > p (persistence length)) 9,10 or by Odijk's deflection chain theory (h and d < p). 11Although the finding is promising, we find that the buffer ionic strengths reported in these studies are somewhat inaccurate especially at low salt concentration due to neglect of the ionic contribution of antiphotobleaching agents. Furthermore, it is not clear how ionic environment will influence DNA dynamics and whether the above theories can be applied. In the current study, we investigate the ionic effects on both conformation and dynamics of DNA confined in nanoslits with better control on buffer ionic strength. We show that our analysis can be used to explain the ionic effects on both confined and unconfined DNA, providing a consistent picture for this highly debated issue of DNA/polyelectrolytes.To understand the physical origin of the ionic effects on polyelectrolytes, we first consider the conformation of neutral polymers. From the Flory theory, 12 the equilibrium size (R bulk ) of an unconfined, semiflexible polymer in good solvents can be expressed as:

Wall depletion length of a channel-confined polymer

“…For these calculations, we considered TBE buffer, which is commonly used in experiments, and determined the ionic concentration of the system through an iterative procedure of solving the system chemical equilibria [66]. We have also included in our calculation the presence of 0.5% (v/v) β-mercaptoethanol (BME) which is commonly present in DNA confinement experiments to delay the onset of photobleaching [6]. To model the zeta potential of the channel walls, which are typically fused silica or PDMS, we used the phenomenological approximations proposed by Kirby and Hasselbrink [67],…”

“…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].…”

Mixed confinement regimes during equilibrium confinement spectroscopy of DNA

“…To this end, we use Pruned-Enriched Rosenbluth Method (PERM) simulations 25,26 of an off-lattice, discrete wormlike chain model of confined DNA, following our recent work in this area. 14,27,28 We first simulated the mean extension and its variance for the rectangular channels used in our experiments, using the ionic strength of the buffer to compute the effective width 29 and persistence length 30,31 of the DNA. The increase of the backbone length due to the intercalating dye is thus the only free parameter.…”

DNA-based highly tunable particle focuser

“…The structural characteristics of DNA result in both larger coiled size at equilibrium, which is represented by radius of gyration (R g ), and longer relaxation time (l DNA ) than those of common synthetic flexible polymers [2][3][4] . For instance, the values of R g ¼ 0.53 mm and l DNA ¼ 140 ms, which were estimated in a 2.1 cP solvent for unstained double-stranded l-DNA 5,6 , are much larger than the respective values of 0.065 mm and 0.7 ms for a representative water-soluble synthetic polymer: poly(ethylene oxide) (PEO) (molecular weight (Mw) ¼ 2 Â 10 6 g mol À 1 ) of a similar contour length (see Methods for theoretical background) 6,7 .…”