Nanoscale Squeezing in Elastomeric Nanochannels for Single Chromatin Linearization

Matsuoka, Toshifumi; Kim, Byoung Choul; Huang, Jian; Douville, Nicholas J.; Thouless, M.D.; Takayama, Shuichi

doi:10.1021/nl304063f

Cited by 47 publications

(85 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…With fluorescent labeling using multiple antibodies against specific histone modification, positions of epigenetic markers can then be directly imaged. [81][82][83] To date, efforts to study DNA linearization in micro/nanofluidics have been oriented toward the visualization of single DNA molecules and the detection of target markers on DNA. [84][85][86] In this short review, we focus on fluidic approaches that linearize chromatin where DNA with its associated proteins is stretched intact.…”

Section: B Chromatin Linearizationmentioning

confidence: 99%

“…In this method, an array of nanochannels are fabricated based on cracking of a brittle PDMS surface layer. 83 The key to achieving chromatin linearization in these nanochannels is the ability to modulate the channel cross-sectional dimensions. This channel tuneability is useful not only for easily loading of chromatin into the channels using the channel-widened state but also for actively linearizing the chromatin structure by the application of elongational squeezing shear flows as the channels are narrowed (Fig.…”

Section: B Chromatin Linearizationmentioning

confidence: 99%

“…Computational modeling of chromatin states and dynamics in confined geometries has only just begun. 83,87 There are unique challenges and opportunities for performing such analyses. In addition to the interaction with boundaries, the hydrodynamic effects and polymer drift (such as in electrophoresis), must be properly addressed in the model.…”

Section: B Chromatin Linearizationmentioning

confidence: 99%

See 2 more Smart Citations

Micro- and nanofluidic technologies for epigenetic profiling

et al. 2013

Self Cite

View full text Add to dashboard Cite

This short review provides an overview of the impact micro- and nanotechnologies can make in studying epigenetic structures. The importance of mapping histone modifications on chromatin prompts us to highlight the complexities and challenges associated with histone mapping, as compared to DNA sequencing. First, the histone code comprised over 30 variations, compared to 4 nucleotides for DNA. Second, whereas DNA can be amplified using polymerase chain reaction, chromatin cannot be amplified, creating challenges in obtaining sufficient material for analysis. Third, while every person has only a single genome, there exist multiple epigenomes in cells of different types and origins. Finally, we summarize existing technologies for performing these types of analyses. Although there are still relatively few examples of micro- and nanofluidic technologies for chromatin analysis, the unique advantages of using such technologies to address inherent challenges in epigenetic studies, such as limited sample material, complex readouts, and the need for high-content screens, make this an area of significant growth and opportunity.

show abstract

Section: B Chromatin Linearizationmentioning

confidence: 99%

Section: B Chromatin Linearizationmentioning

confidence: 99%

Section: B Chromatin Linearizationmentioning

confidence: 99%

See 1 more Smart Citation

Micro- and nanofluidic technologies for epigenetic profiling

et al. 2013

Self Cite

View full text Add to dashboard Cite

show abstract

“…Nanofluidic channels fabricated by cracking a thin film supported on an elastic substrate are used for biological applications including DNA and chromatin analyses [1][2][3][4], cell patterning [5][6][7], and biomimetic systems [8]. The fabrication of this type of nanochannel is fairly easy and cost-effective: an array of parallel channels is created by applying tension to a layered structure.…”

Section: Introductionmentioning

confidence: 99%

“…In particular, opening the channels by applying a strain allows single strands of DNA and chromatin to be loaded into the channels. Subsequent narrowing of the channels by relaxing the strain provides the confinement that, accompanied by nanoscale squeezing flow, can linearize the DNA and chromatin [4]. The present work was motivated by the need to understand the interaction between a collapsing elastic channel and a fluid contained within it, so as to help develop the optimal design of such channels and the operation of them.…”

Section: Introductionmentioning

confidence: 99%

The Collapse and Expansion of Liquid-Filled Elastic Channels and Cracks

Meng

Huang

Thouless

2015

Journal of Applied Mechanics

Self Cite

View full text Add to dashboard Cite

The rate at which fluid drains from a collapsing channel or crack depends on the interaction between the elastic properties of the solid and the fluid flow. The same interaction controls the rate at which a pressurized fluid can flow into a crack. In this paper, we present an analysis for the interaction between the viscous flow and the elastic field associated with an expanding or collapsing fluid-filled channel. We first examine an axisymmetric problem for which a completely analytical solution can be developed. A thick-walled elastic cylinder is opened by external surface tractions, and its core is filled by a fluid. When the applied tractions are relaxed, a hydrostatic pressure gradient drives the fluid to the mouth of the cylinder. The relationship between the change in dimensions, time, and position along the cylinder is given by the diffusion equation, with the diffusion coefficient being dependent on the modulus of the substrate, the viscosity of the fluid, and the ratio of the core radius to the exterior radius of the cylinder. The second part of the paper examines the collapse of elliptical channels with arbitrary aspect ratios, so as to model the behavior of fluid-filled cracks. The channels are opened by a uniaxial tension parallel to their minor axes, filled with a fluid, and then allowed to collapse. The form of the analysis follows that of the axisymmetric calculations, but is complicated by the fact that the aspect ratio of the ellipse changes in response to the local pressure. Approximate analytical solutions in the form of the diffusion equation can be found for small aspect ratios. Numerical solutions are given for more extreme aspect ratios, such as those appropriate for cracks. Of particular note is that, for a given cross-sectional area, the rate of collapse is slower for larger aspect ratios. With minor modifications to the initial conditions and the boundary conditions, the analysis is also valid for cracks being opened by a pressurized fluid.

show abstract

Visualization of large elongated DNA molecules

et al. 2015

View full text Add to dashboard Cite

Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.

show abstract

Nanoscale Squeezing in Elastomeric Nanochannels for Single Chromatin Linearization

Cited by 47 publications

References 29 publications

Micro- and nanofluidic technologies for epigenetic profiling

Micro- and nanofluidic technologies for epigenetic profiling

The Collapse and Expansion of Liquid-Filled Elastic Channels and Cracks

Visualization of large elongated DNA molecules

Contact Info

Product

Resources

About