Polymer-based dense fluidic networks for high throughput screening with ultrasensitive fluorescence detection

Rapid, single-molecule assays in nano/micro-fluidic chips with arrays of closely spaced parallel channels fabricated by femtosecond laser machining

Cost-effective pharmaceutical drug discovery depends on increasing assay throughput while reducing reagent needs. To this end, we are developing an ultrasensitive, fluorescence-based platform that incorporates a nano/micro-fluidic chip with an array of closely spaced channels for parallelized optical readout of single-molecule assays. Here we describe the use of direct femtosecond laser machining to fabricate several hundred closely spaced channels on the surfaces of fused silica substrates. The channels are sealed by bonding to a microscope cover slip spin-coated with a thin film of poly(dimethylsiloxane). Single-molecule detection experiments are conducted using a custom-built, wide-field microscope. The array of channels is epi-illuminated by a line-generating red diode laser, resulting in a line focus just a few microns thick across a 500 micron field of view. A dilute aqueous solution of fluorescently labeled biomolecules is loaded into the device and fluorescence is detected with an electron-multiplying CCD camera, allowing acquisition rates up to 7 kHz for each microchannel. Matched digital filtering based on experimental parameters is used to perform an initial, rapid assessment of detected fluorescence. More detailed analysis is obtained through fluorescence correlation spectroscopy. Simulated fluorescence data is shown to agree well with experimental values.

Study of double-side ultrasonic embossing for fabrication of microstructures on thermoplastic polymer substrates

Double-side replication of polymer substrates is beneficial to the design and the fabrication of 3-demensional devices. The ultrasonic embossing method is a promising, high efficiency and low cost replication method for thermoplastic substrates. It is convenient to apply silicon molds in ultrasonic embossing, because microstructures can be easily fabricated on silicon wafers with etching techniques. To reduce the risk of damaging to silicon molds and to improve the replication uniformity on both sides of the polymer substrates, thermal assisted ultrasonic embossing method was proposed and tested. The processing parameters for the replication of polymethyl methacrylate (PMMA), including ultrasonic amplitude, ultrasonic force, ultrasonic time, and thermal assisted temperature were studied using orthogonal array experiments. The influences of the substrate thickness, pattern style and density were also investigated. The experiment results show that the principal parameters for the upper and lower surface replication are ultrasonic amplitude and thermal assisted temperature, respectively. As to the replication uniformity on both sides, the ultrasonic force has the maximal influence. Using the optimized parameters, the replication rate reached 97.5% on both sides of the PMMA substrate, and the cycle time was less than 50 s.

Purification and specific assays for measuring APE-1 endonuclease activity

Human apurinic/apyrimidinic endonuclease-1 (APE-1) is essential for base excision repair and plays a major role in DNA repair and maintaining genomic stability. Cancer cells treated with conventional DNA-damaging agents develop resistance due in part to upregulation of enzymes involved in DNA repair. It is hypothesized that inhibiting DNA repair machinery should sensitize the cells to DNA-damaging agents. Previously, it has been shown that APE-1 is implicated in drug resistance and cancer progression. Therefore, APE-1 inhibitors are being sought after for their synergistic properties with various chemotherapeutics agents. Screening of several compound libraries and optimization of known inhibitors of APE-1 endonuclease activity have been accelerated by the use of high-throughput screening. Nevertheless, potential inhibitors must be tested in other counterscreens to validate their selectivity for APE-1. Here, we describe in-depth protocols for APE-1 purification and development of assays specific for APE-1 endonuclease activity.

Unbiased binding assays for discovering small-molecule probes and drugs

2011 marks the 10-year anniversary of milestone manuscripts describing drafts of the human genome sequence. Over the past decade, a number of new proteins have been linked to disease-many of which fall into classes that have been historically considered challenging from the perspective of drug discovery. Several of these newly associated proteins lack structural information or strong annotation with regard to function, making development of conventional in vitro functional assays difficult. A recent resurgence in the popularity of simple small molecule binding assays has led to new approaches that do not require knowledge of protein structure or function in advance. Here we briefly review selected methods for executing binding assays that have been used successfully to discover small-molecule probes or drug candidates.