Christine P. Tan

Single Molecule Epigenetic Analysis in a Nanofluidic Channel

Epigenetic states are governed by DNA methylation and a host of modifications to histones bound with DNA. These states are essential for proper developmentally regulated gene expression and are perturbed in many diseases. There is great interest in identifying epigenetic mark placement genome wide and understanding how these marks vary among cell types, with changes in environment or according to health and disease status. Current epigenomic analyses employ bisulfite sequencing and chromatin immunoprecipitation, but query only one type of epigenetic mark at a time, DNA methylation, or histone modifications and often require substantial input material. To overcome these limitations, we established a method using nanofluidics and multicolor fluorescence microscopy to detect DNA and histones in individual chromatin fragments at about 10 Mbp/min. We demonstrated its utility for epigenetic analysis by identifying DNA methylation on individual molecules. This technique will provide the unprecedented opportunity for genome wide, simultaneous analysis of multiple epigenetic states on single molecules.

Surface Engineering and Patterning Using Parylene for Biological Applications

Parylene is a family of chemically vapour deposited polymer with material properties that are attractive for biomedicine and nanobiotechnology. Chemically inert parylene “peel-off” stencils have been demonstrated for micropatterning biomolecular arrays with high uniformity, precise spatial control down to nanoscale resolution. Such micropatterned surfaces are beneficial in engineering biosensors and biological microenvironments. A variety of substituted precursors enables direct coating of functionalised parylenes onto biomedical implants and microfluidics, providing a convenient method for designing biocompatible and bioactive surfaces. This article will review the emerging role and applications of parylene as a biomaterial for surface chemical modification and provide a future outlook.

Prion protein detection using nanomechanical resonator arrays and secondary mass labeling

Nanomechanical resonators have shown potential application for mass sensing and have been used to detect a variety of biomolecules. In this study, a dynamic resonance-based technique was used to detect prion proteins (PrP), which in conformationally altered forms are known to cause neurodegenerative diseases in animals as well as humans. Antibodies and nanoparticles were used as mass labels to increase the mass shift and thus amplify the frequency shift signal used in PrP detection. A sandwich assay was used to immobilize PrP between two monoclonal antibodies, one of which was conjugated to the resonators surface while the other was either used alone or linked to the nanoparticles as a mass label. Without additional mass labeling, PrP was not detected at concentrations below 20 microg/mL. In the presence of secondary antibodies the analytical sensitivity was improved to 2 microg/mL. With the use of functionalized nanoparticles, the sensitivity improved an additional 3 orders of magnitude to 2 ng/mL.

Parylene peel-off arrays to probe the role of cell–cell interactions in tumour angiogenesis

Microenvironmental conditions impact tumour angiogenesis, but the role of cell-cell interactions in modulating the angiogenic capability of tumour cells is not well understood. We have microfabricated a peel-off cell-culture array (PeelArray) chip to spatiotemporally control interactions between tumour cells in a large array format and to analyse angiogenic factor secretion in response to these conditions. The PeelArray chip consists of a polyethylene glycol (PEG) treated glass coverslip coated with a parylene-C template that can be easily peeled off to selectively micropattern biomolecules and cells. We have designed the PeelArray chip to reproducibly deposit large uniform arrays of isolated single cells or isolated cell clusters on fibronectin features of defined surface areas. We have utilised this microfabricated culture system to study the secretion of angiogenic factors by tumour cells, in the presence or absence of cell-cell contact as controlled by micropatterning. Our results indicate that cell-cell interactions play a synergistic role in regulating the expression of angiogenic factors (i.e., vascular endothelial growth factor [VEGF] and interleukin-8 [IL-8]) in various cancer cell lines, independent of other more complex microenvironmental cues (e.g. hypoxia). Our PeelArray chip is a simple and adaptable micropatterning method that enables quantitative profiling of protein secretions and hence, a better understanding of the mechanisms by which cell-cell interactions regulate tumour cell behaviour and angiogenesis.

Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel.

Epigenetic modifications, such as DNA and histone methylation, are responsible for regulatory pathways that affect disease. Current epigenetic analyses use bisulfite conversion to identify DNA methylation and chromatin immunoprecipitation to collect molecules bearing a specific histone modification. In this work, we present a proof-of-principle demonstration for a new method using a nanofluidic device that combines real-time detection and automated sorting of individual molecules based on their epigenetic state. This device evaluates the fluorescence from labeled epigenetic modifications to actuate sorting. This technology has demonstrated up to 98% accuracy in molecule sorting and has achieved postsorting sample recovery on femtogram quantities of genetic material. We have applied it to sort methylated DNA molecules using simultaneous, multicolor fluorescence to identify methyl binding domain protein-1 (MBD1) bound to full-duplex DNA. The functionality enabled by this nanofluidic platform now provides a workflow for color-multiplexed detection, sorting, and recovery of single molecules toward subsequent DNA sequencing.

High-Q, in-plane modes of nanomechanical resonators operated in air

Nanomechanical resonators have traditionally been limited to use in vacuum due to low quality factors that come as a result of viscous damping effects in air or liquid. We have fabricated arrays of 90 nm thick trampoline-shaped resonators, studied their resonant frequency spectrum as a function of pressure, and found that some high frequency modes exhibit quality factors over 2000 at atmospheric pressure. We have excited the in-plane resonances of these devices, verified their identities both experimentally and with finite element modeling, and demonstrated their advantageous characteristics for ambient sensing. Even after deposition of a relatively thick polymer layer, the in-plane resonant modes still boast quality factors on the order of 2000. These results show promise for the use of nanomechanical resonant sensors in real-time atmospheric sensing applications.

Atomic layer deposited silicon dioxide films on nanomechanical silicon nitride resonators

Thin silicon dioxide films are deposited on nanomechanical resonators using atomic layer deposition (ALD), and their effect on the resonant properties of silicon nitride devices is studied as a function of thickness. We present experimental data and an analytical model for the effect of ALD growth and corroborate the model by studying resonators coated with atomic layer deposited aluminum nitride as well. As thicker films are deposited, device frequency shifts, become nonlinear with thickness, and quality factors drop significantly. Thin silicon dioxide coatings can be deposited on virtually any device surface to support surface chemistries commonly used in biochemical functionalization on glass surfaces. We also demonstrate that the efficiency of silane functionalization improves by 35% when low stress silicon nitride surfaces are coated with only 2.1 nm of atomic layer deposited silicon dioxide. This ALD modification technique should be particularly useful for nanomechanical resonant sensors since a thi...