Conformations of DNA in Triangular Nanochannels (original) (raw)
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Nanochannel confinement: DNA stretch approaching full contour length
Lab Chip, 2011
Fully stretched DNA molecules are becoming a fundamental component of new systems for comprehensive genome analysis. Among a number of approaches for elongating DNA molecules, nanofluidic molecular confinement has received enormous attentions from physical and biological communities for the last several years. Here we demonstrate a well-optimized condition that a DNA molecule can stretch almost its full contour length: the average stretch is 19.1 μm ± 1.1 μm for YOYO-1 stained λ DNA (21.8 μm contour length) in 250 nm × 400 nm channel, which is the longest stretch value ever reported in any nanochannels or nanoslits. In addition, based on Odijk's polymer physics theory, we interpret our experimental findings as a function of channel dimensions and ionic strengths. Furthermore, we develop a Monte Carlo simulation approach using a primitive model for the rigorous understandings of DNA confinement effects. Collectively, we present more complete understanding of nanochannel confined DNA stretching via the comparisons to computer simulation results and Odijk's polymer physics theory.
Statics and Dynamics of Single DNA Molecules Confined in Nanochannels
Physical Review Letters, 2005
The successful design of nanofluidic devices for the manipulation of biopolymers requires an understanding of how the predictions of soft condensed matter physics scale with device dimensions. Here we present measurements of DNA extended in nanochannels and show that below a critical width roughly twice the persistence length there is a crossover in the polymer physics.
Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range of 150-300 nm casted in a poly͑dimethylsiloxane͒ nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with the scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.
Conformation and Dynamics of DNA Confined in Slitlike Nanofluidic Channels
Physical Review Letters, 2008
Using laser fluorescence microscopy, we study the shape and dynamics of individual DNA molecules in slitlike nanochannels confined to a fraction of their bulk radius of gyration. With a confinement size spanning 2 orders of magnitude, we observe a transition from the de Gennes regime to the Odijk regime in the scaling of both the radius of gyration and the relaxation time. The radius of gyration and the relaxation time follow the predicted scaling in the de Gennes regime, while, unexpectedly, the relaxation time shows a sharp decrease in the Odijk regime. The radius of gyration remains constant in the Odijk regime. Additionally, we report the first measurements of the effect of confinement on the shape anisotropy.
Comparison of linear and ring DNA macromolecules moderately and strongly confined in nanochannels
Biochemical Society Transactions, 2013
Understanding the mechanism of DNA extension in nanochannels is necessary for interpretation of experiments in nanofluidic channel devices that have been conducted recently with both linear and ring chains. The present article reviews the situation with linear chains and analyses the experimental results and simulations for channel-induced extension (linearization) of ring chains. Results for confined rings indicate a transition between moderate and strong confinement similar to that of linear chains. Owing to stronger self-avoidance in confined rings, the transition and chain extension is shifted relative to linear DNA. We suggest that a relationship similar to that used for the extension of linear chains may also be used for circular DNA.
Detection of chain backfolding in simulation of DNA in nanofluidic channels
Soft Matter, 2012
The DNA extension in cylindrical nanochannels under moderately strong confinements in the ''transition'' region, where experiments are conducted, is examined by Monte Carlo simulations. The focal point is estimation of the amount of backfolding structures such as hairpins and loops in extended (linearized) DNA molecules. At the chain-ends of DNA an extensive folding (mainly as the J-type hairpins) is detected under all confinements, covering the Odijk and de Gennes regimes and the transition region between them. In contrast, in the DNA chain interior, the backfolding into Z-type hairpins is abundant in the de Gennes regime, significantly reduced in the transition region, and practically absent in the Odijk regime. The linear relationship between the DNA extension and its contour length is validated also in the transition region where explicit theories are absent.
Conformational Manipulation of DNA in Nanochannels Using Hydrodynamics
Macromolecules, 2013
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics, although the physics of soft matter in nanoscale flows has raised considerable interest over the last decade. In this report the migration of DNA is studied in nanochannels of lateral dimension spanning 100 to 500 nm using both actuation principles. We show that the relaxation kinetics are 3-fold slowed down and the extension increases up to 3-folds using hydrodynamics. We propose a
Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
Macromolecules, 2015
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.