Super-resolution imaging of PDMS nanochannels by single-molecule micelle-assisted blink microscopy

Toward a better modulus at shallow indentations-Enhanced tip and sample characterization for quantitative atomic force microscopy

Approximations of the geometry of indenting probes, particularly when using shallow indentations on soft materials, can lead to the erroneous reporting of mechanical data in atomic force microscopy (AFM). Scanning electron microscopy (SEM) identified a marked change in geometry toward the tip apex where the conical probe assumes a near linear flat-punch geometry. Polydimethylsiloxane (PDMS) is a ubiquitous elastomer within the materials and biological sciences. Its elastic modulus is widely characterized but the data are dispersed and can display orders of magnitude disparity. Herein, we compare the moduli gathered from a range of analytical techniques and relate these to the molecular architecture identified with AFM. We present a simple method that considers sub-100 nm indentations of PDMS using the Hertz and Sneddon contact mechanics models, and how this could be used to improve the output of shallow indentations on similarly soft materials, such as polymers or cells.

Dynamic simulations show repeated narrowing maximizes DNA linearization in elastomeric nanochannels

This paper uses computer simulations to reveal unprecedented details about linearization of deoxyribonucleic acid (DNA) inside dynamic nanochannels that can be repeatedly widened and narrowed. We first analyze the effect of rate of channel narrowing on DNA linearization dynamics. Quick (∼0.1 s) narrowing of nanoscale channels results in rapid overstretching of the semi-flexible chain followed by a slower (∼0.1-10 s) relaxation to an equilibrium extension. Two phenomena that induce linearization during channel narrowing, namely, elongational-flow and confinement, occur simultaneously, regardless of narrowing speed. Interestingly, although elongational flow is a minimum at the mid-point of the channel and increases towards the two ends, neither the linearization dynamics nor the degree of DNA extension varies significantly with the center-of-mass of the polymer projected on the channel axis. We also noticed that there was a significant difference in time to reach the equilibrium length, as well as the degree of DNA linearization at short times, depending on the initial conformation of the biopolymer. Based on these observations, we tested a novel linearization protocol where the channels are narrowed and widened repeatedly, allowing DNA to explore multiple conformations. Repeated narrowing and widening, something uniquely enabled by the elastomeric nanochannels, significantly decrease the time to reach the equilibrium-level of stretch when performed within periods comparable to the chain relaxation time and more effectively untangle chains into more linearized biopolymers.

Nanoscopic Cellular Imaging: Confinement Broadens Understanding

In recent years, single-molecule fluorescence imaging has been reconciling a fundamental mismatch between optical microscopy and subcellular biophysics. However, the next step in nanoscale imaging in living cells can be accessed only by optical excitation confinement geometries. Here, we review three methods of confinement that can enable nanoscale imaging in living cells: excitation confinement by laser illumination with beam shaping; physical confinement by micron-scale geometries in bacterial cells; and nanoscale confinement by nanophotonics.

Highly stretchable conductive polypyrrole film on a three dimensional porous polydimethylsiloxane surface fabricated by a simple soft lithography process

We create an elastic porous polydimethylsiloxane highly stretchable conductive substrate. The surface is fabricated by a simple soft lithography process that replicates the 3D corrugated porous microstructures from a low-cost commercially available abrasive paper.

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

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.

Characterization of Porous Materials by Fluorescence Correlation Spectroscopy Super-resolution Optical Fluctuation Imaging

Porous materials such as cellular cytosol, hydrogels, and block copolymers have nanoscale features that determine macroscale properties. Characterizing the structure of nanopores is difficult with current techniques due to imaging, sample preparation, and computational challenges. We produce a super-resolution optical image that simultaneously characterizes the nanometer dimensions of and diffusion dynamics within porous structures by correlating stochastic fluctuations from diffusing fluorescent probes in the pores of the sample, dubbed here as "fluorescence correlation spectroscopy super-resolution optical fluctuation imaging" or "fcsSOFI". Simulations demonstrate that structural features and diffusion properties can be accurately obtained at sub-diffraction-limited resolution. We apply our technique to image agarose hydrogels and aqueous lyotropic liquid crystal gels. The heterogeneous pore resolution is improved by up to a factor of 2, and diffusion coefficients are accurately obtained through our method compared to diffraction-limited fluorescence imaging and single-particle tracking. Moreover, fcsSOFI allows for rapid and high-throughput characterization of porous materials. fcsSOFI could be applied to soft porous environments such hydrogels, polymers, and membranes in addition to hard materials such as zeolites and mesoporous silica.

Fracture-based fabrication of normally closed, adjustable, and fully reversible microscale fluidic channels

Adjustable fluidic structures play an important role in microfluidic systems. Fracture of multilayered materials under applied tension has been previously demonstrated as a convenient, simple, and inexpensive approach to fabricate nanoscale adjustable structures; here, it is demonstrated how to extend this concept to the microscale. This is achieved by a novel pairing of materials that leverages fracture mechanics to limit crack formation to a specified region, allowing to create size-controllable and adjustable microfluidic structures. This technique can be used to fabricate "normally closed" microfluidic channels that are completely reversible, a feature that is challenging to achieve in conventional systems without careful engineering controls. The adjustable microfluidic channels are then applied to mechanically lyse single cells, and subsequently manipulate the released nuclear chromatin, creating new possibilities for epigenetic analysis of single cells. This simple, versatile, and robust technology provides an easily accessible pathway to construct adjustable microfluidic structures, which will be useful in developing complex assays and experiments even in resource-limited settings.

Fracture-based micro- and nanofabrication for biological applications

While fracture is generally considered to be undesirable in various manufacturing processes, delicate control of fracture can be successfully implemented to generate structures at micro/nano length scales. Fracture-based fabrication techniques can serve as a template-free manufacturing method, and enables highly-ordered patterns or fluidic channels to be formed over large areas in a simple and cost-effective manner. Such technologies can be leveraged to address biologically-relevant problems, such as in the analysis of biomolecules or in the design of culture systems that imitate the cellular or molecular environment. This mini review provides an overview of current fracture-guided fabrication techniques and their biological applications. We first survey the mechanical principles of fracture-based approaches. Then we describe biological applications at the cellular and molecular levels. Finally, we discuss unique advantages of the different system for biological studies.

Super-resolution mbPAINT for optical localization of single-stranded DNA

We demonstrate the application of superlocalization microscopy to identify sequence-specific portions of single-stranded DNA (ssDNA) with sequence resolution of 50 nucleotides, corresponding to a spatial resolution of 30 nm. Super-resolution imaging was achieved using a variation of a single-molecule localization method, termed as "motion blur" point accumulation for imaging in nanoscale topography (mbPAINT). The target ssDNA molecules were immobilized on the substrate. Short, dye-labeled, and complementary ssDNA molecules stochastically bound to the target ssDNA, with repeated binding events allowing super-resolution. Sequence specificity was demonstrated via the use of a control, noncomplementary probe. The results support the possibility of employing relatively inexpensive short ssDNAs to identify gene sequence specificity with improved resolution in comparison to the existing methods.

Micro- and nanofluidic technologies for epigenetic profiling

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.