Resolution limit for DNA barcodes in the Odijk regime

Wang, Yanwei; Reinhart, Wes F; Tree, Douglas R.; Dorfman, Kevin D.

doi:10.1063/1.3672691

Cited by 24 publications

(42 citation statements)

References 41 publications

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“…While the normal-inverse Gaussian is a convenient description of the data (and superior to the other distributions that we tested for this purpose), one might question the basic premise of using the normal-inverse Gaussian distribution in the first place; it seems logical that the distances between labels should be described by a probability density with compact support, 36 since their distances are bounded from below by zero extension and above by the contour length of the DNA between labels. In response, we note that although the normal-inverse Gaussian distribution has semi-heavy tails, the decay of the probability density is sufficiently fast to make it a physically realistic model in practice.…”

Section: Resultsmentioning

confidence: 99%

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Reinhart

Reifenberger

Gupta

et al. 2015

The Journal of Chemical Physics

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We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension. C 2015 AIP Publishing LLC. [http://dx

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Section: Resultsmentioning

confidence: 99%

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Reinhart

Reifenberger

Gupta

et al. 2015

The Journal of Chemical Physics

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“…21 Briefly, the DNA backbone is represented by a series of touching beads of diameter w ¼ 4.6 nm, the Stigter effective width for DNA in TBE 5Â buffer, 15,20 and the commonly invoked persistence length l p ¼ 53 nm. 22 The chain has N ¼ 1024 beads, giving a contour length L ¼ 4.7 lm.…”

Section: Simulation Methodsmentioning

confidence: 99%

“…In what follows, we use Monte Carlo simulations of confined DNA 15,21 to show that entropic depletion indeed plays an important role in a triangular nanochannel, as seen in the simulation data in Fig. 1(b).…”

Section: Introductionmentioning

confidence: 99%

Entropic depletion of DNA in triangular nanochannels

2013

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Using Monte Carlo simulations of a touching-bead model of double-stranded DNA, we show that DNA extension is enhanced in isosceles triangular nanochannels (relative to a circular nanochannel of the same effective size) due to entropic depletion in the channel corners. The extent of the enhanced extension depends non-monotonically on both the accessible area of the nanochannel and the apex angle of the triangle. We also develop a metric to quantify the extent of entropic depletion, thereby collapsing the extension data for circular, square, and various triangular nanochannels onto a single master curve for channel sizes in the transition between the Odijk and de Gennes regimes. V C 2013 American Institute of Physics.

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“…We demonstrate that CLINT can efficiently load DNA into nanochannels less than 30 nm in size, imposing subpersistence length confinement at which stretching is high, polymer back-folding is energetically unfeasible, and thermal fluctuations are suppressed (i.e., the Odijk regime). The ability to operate devices in this regime is critical as the suppression of back-bending and thermal fluctuations leads to more efficient alignment of optically mapped DNA fragments to a reference genome (11). Finally, unlike enclosed classical nanofluidic devices, the CLINT device interior can be easily exposed, leading to greater reusability and ease of access.…”

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confidence: 99%

Convex lens-induced nanoscale templating

Berard

Michaud

Mahshid

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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We demonstrate a new platform, convex lens-induced nanoscale templating (CLINT), for dynamic manipulation and trapping of single DNA molecules. In the CLINT technique, the curved surface of a convex lens is used to deform a flexible coverslip above a substrate containing embedded nanotopography, creating a nanoscale gap that can be adjusted during an experiment to confine molecules within the embedded nanostructures. Critically, CLINT has the capability of transforming a macroscale flow cell into a nanofluidic device without the need for permanent direct bonding, thus simplifying sample loading, providing greater accessibility of the surface for functionalization, and enabling dynamic manipulation of confinement during device operation. Moreover, as DNA molecules present in the gap are driven into the embedded topography from above, CLINT eliminates the need for the high pressures or electric fields required to load DNA into direct-bonded nanofluidic devices. To demonstrate the versatility of CLINT, we confine DNA to nanogroove and nanopit structures, demonstrating DNA nanochannel-based stretching, denaturation mapping, and partitioning/trapping of single molecules in multiple embedded cavities. In particular, using ionic strengths that are in line with typical biological buffers, we have successfully extended DNA in sub-30-nm nanochannels, achieving high stretching (90%) that is in good agreement with Odijk deflection theory, and we have mapped genomic features using denaturation analysis.single-molecule manipulation | polymer confinement | genomic mapping | CLIC imaging | nanotechnology N anoconfinement-based manipulation is a powerful approach for controlling the conformation of single DNA molecules on chip. When single polymer chains are squeezed into environments confined at length scales below their diameter of gyration in free solution, the polymer equilibrium conformation will be molded by the surrounding nanoscale geometry. Nanochannel arrays can be used for massively parallel extension of DNA across an optical field, serving as the basis for a highthroughput optical mapping of genomes (1, 2). More varied manipulations can be performed based on the design of the surrounding nanotopology, such as using nanocavities embedded in a nanoslit to trap single DNA molecules (3). Nanoconfinementbased manipulation, compared with competing techniques for single-molecule manipulation such as tweezer technology and surface/hydrodynamic-based stretching, has three key advantages (4): (i) It is highly parallel, providing the high throughput essential for mapping gigabase-scale mammalian genomes (1); (ii) it can be efficiently integrated with microfluidics to rapidly cycle molecules through the channel arrays for upstream/downstream pre-and postprocessing of DNA; and (iii) it does not require applied flow or electric force to maintain the DNA extension.Nanoconfinement-based approaches have, however, a key difficulty inherent to the use of nanoscale dimensions: the need to bridge length scales differing by up to 5 orders...

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Resolution limit for DNA barcodes in the Odijk regime

Cited by 24 publications

References 41 publications

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Entropic depletion of DNA in triangular nanochannels

Convex lens-induced nanoscale templating

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