Nanoconfinement-Enhanced Conformational Response of Single DNA Molecules to Changes in Ionic Environment

We show that the ionic environment plays a critical role in determining the configurational properties of DNA confined in silica nanochannels. The extension of DNA in the nanochannels increases as the ionic strength is reduced, almost tripling over two decades in ionic strength for channels around $100\times 100\mathrm{nm}$ in dimension. Surprisingly, we find that the variation of the persistence length alone with ionic strength is not enough to explain our results. The effect is due mainly to increasing self-avoidance created by the reduced screening of electrostatic interactions at low ionic strength. To quantify the increase in self-avoidance, we introduce a new parameter into the de Gennes theory: an effective DNA width that gives the increase in the excluded volume due to electrostatic repulsion.

Figure 1

Log-log plot of $\lambda$-DNA extension as a function of ionic strength for the three channel widths used (Filled diamonds, circles, and squares TBE series measurements in the 200, 100, and 50 nm channels respectively; open diamonds NaCl series measurements in the 200 nm channel). (a) Fits of the de Gennes scaling to extension measurements using the known ionic strength dependence of the effective width and persistence length. (b) The subpersistence length Odijk theory plotted against extension measurements (bold curve prediction for 50 nm channel, dashed curve prediction for 100 nm channel, and dot-dashed curve prediction for 200 nm channel).The de Gennes theory gives the better agreement for all three curves. The error bars given on the extension are the reported standard deviations from the extension of all molecules measured in the channel at a given ionic strength, between 5 and 20 molecules for the 100 and 200 nm channels and between 2 and 5 molecules for the 50 nm channel.

Figure 2

SEM images of nanochannels. High magnification image of 200 nm (a), 100 nm (c), and 50 nm (e) channels with tapping mode AFM scan (inset). Low magnification SEM of 200 nm (b), 100 nm (d), and 50 nm (f) channels The channel dimensions can be estimated from these images with a 10% uncertainty.

Figure 3

A montage of individual fluorescently stained $\lambda$-DNA molecules measured at differing TBE dilutions (left to right, $0.05\times$, $0.2\times$, $0.5\times$, $2\times$, $5\times \mathrm{TBE}$) in (a) 200 nm channels, (b) 100 nm channels, and (c) 50 nm channels.