Showing papers by "Stephen R. Quake published in 2004"

A nanoliter-scale nucleic acid processor with parallel architecture.

Abstract: The purification of nucleic acids from microbial and mammalian cells is a crucial step in many biological and medical applications1. We have developed microfluidic chips for automated nucleic acid purification from small numbers of bacterial or mammalian cells. All processes, such as cell isolation, cell lysis, DNA or mRNA purification, and recovery, were carried out on a single microfluidic chip in nanoliter volumes without any pre- or postsample treatment. Measurable amounts of mRNA were extracted in an automated fashion from as little as a single mammalian cell and recovered from the chip. These microfluidic chips are capable of processing different samples in parallel, thereby illustrating how highly parallel microfluidic architectures can be constructed to perform integrated batch-processing functionalities for biological and medical applications.

Solvent-Resistant Photocurable “Liquid Teflon” for Microfluidic Device Fabrication

Abstract: We report the first fabrication of a solvent-compatible microfluidic device based on photocurable “Liquid Teflon” materials The materials are highly fluorinated functionalized perfluoropolyethers (PFPEs) that have liquidlike viscosities that can be cured into tough, highly durable elastomers that exhibit the remarkable chemical resistance of fluoropolymers such as Teflon Poly(dimethylsiloxane) (PDMS) elastomers have rapidly become the material of choice for many recent microfluidic device applications Despite the advantages of PDMS in relation to microfluidics technology, the material suffers from a serious drawback in that it swells in most organic solvents The swelling of PDMS-based devices in organic solvents greatly disrupts the micrometer-sized features and makes it impossible for fluids to flow inside the channels Our approach to this problem has been to replace PDMS with photocurable perfluoropolyethers Device fabrication and valve actuation were accomplished using established procedures for

Scaling properties of a low-actuation pressure microfluidic valve

Abstract: Using basic physical arguments, we present a design and method for the fabrication of microfluidic valves using multilayer soft lithography. These on-off valves have extremely low actuation pressures and can be used to fabricate active functions, such as pumps and mixers in integrated microfluidic chips. We characterized the performance of the valves by measuring both the actuation pressure and flow resistance over a wide range of design parameters, and compared them to both finite element simulations and alternative valve geometries.

Tip-enhanced fluorescence microscopy at 10 nanometer resolution.

Abstract: We demonstrate unambiguously that the field enhancement near the apex of a laser-illuminated silicon tip decays according to a power law that is moderated by a single parameter characterizing the tip sharpness. Oscillating the probe in intermittent contact with a semiconductor nanocrystal strongly modulates the fluorescence excitation rate, providing robust optical contrast and enabling excellent background rejection. Laterally encoded demodulation yields images with <10 nm spatial resolution, consistent with independent measurements of tip sharpness.

Systematic investigation of protein phase behavior with a microfluidic formulator

Abstract: We demonstrated a microfluidic device for rapidly generating complex mixtures of 32 stock reagents in a 5-nl reactor. This "formulation chip" is fully automated and allows thousands of experiments to be performed in a single day with minimal reagent consumption. It was applied to systematically study the phase behavior of the protein xylanase over a large and complex chemical space. For each chemical formulation that demonstrated a pronounced effect on solubility, the protein phase behavior was completely mapped in the chip, generating a set of empirical phase diagrams. This ab initio phase information was used to devise a rational crystallization screen that resulted in 72-fold improvement in successful crystallization hits compared with conventional sparse matrix screens. This formulations tool allows a physics-based approach to protein crystallization that may prove useful in structural genomics efforts.

A microfluidic rectifier: Anisotropic flow resistance at low Reynolds numbers

Abstract: It is one of the basic concepts of Newtonian fluid dynamics that at low Reynolds number (Re) the Navier-Stokes equation is linear and flows are reversible. In microfluidic devices, where Re is essentially always low, this implies that flow resistance in microchannels is isotropic. Here we present a microfluidic rectifier: a microscopic channel of a special shape whose flow resistance is strongly anisotropic, differing by up to a factor of 2 for opposite flow directions. Its nonlinear operation at arbitrary small Re is due to non-Newtonian elastic properties of the working fluid, which is a 0.01% aqueous solution of a high molecular weight polymer. The rectifier works as a dynamic valve and may find applications in microfluidic pumps and other integrated devices.

Microfluidic device reads up to four consecutive base pairs in DNA sequencing‐by‐synthesis

Abstract: We have developed the first fully integrated microfluidic system for DNA sequencing-by-synthesis. Using this chip and fluorescence detection, we have reliably sequenced up to 4 consecutive bps. The described sequencer can be integrated with other microfluidic components on the same chip to produce true lab-on-a-chip technology. The surface chemistry that was designed to anchor the DNA to elastomeric microchannels is useful in a broad range of studies and applications.

Microfluidic rotary flow reactor matrix

Abstract: A microfluidic device comprises a matrix (6000) of rotary flow reactors (6002). The microfluidic matrix device offers a solution to the 'world-to-chip' interface problem by accomplishing two important goals simultaneously: an economy of scale in reagent consumption is achieved, while simultaneously minimizing pipetting steps. N2 independent assays can be performed with only 2N+1 pipetting steps, using a single aliquot of enzyme amortized over all reactors. The chip reduces labor relative to conventional fluid handling techniques by using an order of magnitude less pipetting steps, and reduces cost by consuming two to three orders of magnitude less reagents per reaction. A PCR format has immediate applications in medical diagnosis and gene testing. Beyond PCR, the microfluidic matrix chip provides a universal and flexible platform for biological and chemical assays requiring parsimonious use of precious reagents and highly automated processing.

Correlating AFM Probe Morphology to Image Resolution for Single-Wall Carbon Nanotube Tips

Abstract: Scanning and transmission electron microscopy were used to image hundreds of single-wall carbon nanotube probes and to correlate probe morphology with AFM image resolution. Several methods for fabricating such probes were evaluated, resulting in a procedure that produces image-quality single-wall nanotube probes at a rate compatible with their routine use. Surprisingly, about one-third of the tips image with resolution better than the nanotube probe diameter and, in exceptional cases, with resolution better than 1 nm. This represents the highest lateral resolution reported to date for a SWNT probe.

Photocurable perfluoropolyethers for use as novel materials in microfluidic devices

Abstract: A solvent-resistant microfluidio device (MD) is fabricated from a functionalized, photo-curable perfluoropolyether (PFPE). In one embodiment, a polymeric precursor (PP), comprising PFPE, is disposed on a patterned surface (PS) of a substrate (S), having raised protrusions (P). Ultraviolet light (UV) is applied to yield a patterned layer (PL) of photo-cured PFPE having recesses (R) comprising at least one channel (CH). Patterned layer (PL) is removed from patterned surface (PS) of substrate (S) to yield microfluidic device (MD).

Microfabricated rubber microscope using soft solid immersion lenses

Abstract: Soft lithography with surface tension control is used to microfabricate extremely efficient solid immersion lenses (SILs; 102, 104) out of rubber elastomeric material for use in microscope (100) type applications. In order to counteract the surface tension of the mold material in a negative mold that causes creep on a positive mold, material such as RTV is partially cured before use in order to allow the reticulation of polymer chains to change the viscosity of the uncured material in a controllable manner. In a specific embodiment, the techniques of soft lithography with surface tension control are used to make molded SILs out of the elastomer polydimethylsiloxane. The lenses achieve an NA in the range of 1.25. The principle of compound lens design is used to make the first compound solid immersion lens (102), which is corrected for higher light gathering ability and has a calculated NA=1.32. An important application of these lenses is integrated optics for microfluidic devices, specifically in a handheld rubber microscope (100) for microfluidic flow cytometry.

Nanometer-scale Fluorescence Resonance Optical Waveguides

Abstract: The telecommunications revolution has created a strong motivation to build photonic devices of ever smaller size and higher density. Using photosynthetic structures found in nature as an inspiration, we synthesized artificial structures that act like diffusive waveguides. These waveguides use FRET to transport energy, and we demonstrated the idea with 3- and 5-fluorophore structures which utilize DNA as a scaffold. A quantitative model that explains the results and provides the mechanism behind the energy transfer is also presented.

Device for immobilizing chemical and biochemical species and methods of using same

Abstract: A substrate is provided that facilitates immobilization of nucleic acid molecules, including DNA molecules and RNA molecules Also provided is a device that includes the substrate, which, for example, can be a chip In addition, methods of using the substrate are provided, including, for example, methods of sequencing a DNA molecule anchored to the substrate, and methods for conducting the process of sequencing using such devices

Microfluidic protein crystallography techniques

Abstract: The present invention relates to microfluidic devices and methods facilitating the growth and analysis of crystallized materials such as proteins. In accordance with one embodiment, a crystal growth architecture is separated by a permeable membrane from an adjacent well having a much larger volume. The well may be configured to contain a fluid having an identity and concentration similar to the solvent and crystallizing agent employed in crystal growth, with diffusion across the membrane stabilizing that process. Alternatively, the well may be configured to contain a fluid having an identity calculated to affect the crystallization process. In accordance with the still other embodiment, the well may be configured to contain a material such as a cryo-protectant, which is useful in protecting the crystalline material once formed.

Fluorescently labeled nucleoside triphosphates and analogs thereof for sequencing nucleic acids

Abstract: The invention provides methods for sequencing a nucleic acid, and particularly methods for synthesizing fluorescently labeled nucleoside triphosphates and related analogs for sequencing nucleic acids.

Functional perfluoropolyethers as novel materials for microfluidics and soft lithography

Abstract: 1 Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA 2 Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695, USA 3 Department of Applied Physics, California Institute of Technology, Pasadena, CA, 91125, USA 4 IBM Almaden Research Center, Center for Polymeric Interfaces and Macromolecular Assemblies, 650 Harry Road, San Jose, CA, 95120-6099, USA

Monolithic Integration of Microfluidics and Optoelectronics for Biological Analysis

Abstract: : We have integrated microfluidic structures with optoelectronic lasers in the same device. Very sensitive and ultra-small laser sensors could be connected to fluidic systems by using microfluidic multiplexing technology and replication molded microfluidic chips. The basis of our sensor is a two-dimensional photonic crystal laser with an unusual cavity geometry that permits the introduction of analyte into the highest optical field region. This photonic crystal laser sensor can measure parts per million changes in the refractive index in volumes of several femtoliters, and is the home run" we were looking for. We have used our microfluidic systems to perform a large number of analytical tasks, such as cell sorting, protein synthesis and even polymerase chain reaction (PCR) amplification of DNA. The photonc crystal laser sensors were also tested in different solutions, and their performance was calibrated by using standard index matching fluids, showing a linear response of the lasing frequency with changes in the refractive index. The fluidic delivery system together with the napo-spectroscopy tools developed in this program led to the possibility of interrogating and testing of picoliter volumes of solution with femtoliter sensitivity on compact and robust micro-chips.

Chemical sensors based on photonic crystal nanolasers

Abstract: Photonic crystal nano-lasers that permit introduction of analyte within the peak of the optical field of the lasing mode are realized, and they are used to perform spectroscopic tests on femtoliter volumes of analyte.

Perfluoropolyethers photopolymerisables destines a etre utilises comme nouveaux materiaux dans des dispositifs microfluidiques

Abstract: L'invention concerne un perfluoropolyether photopolymerisable fonctionnalise utilise comme materiau pour fabriquer un dispositif microfluidique resistant aux solvants. De tels dispositifs microfluidiques resistant aux solvants peuvent etre utilises pour reguler l'ecoulement de petites quantites d'un fluide, tel qu'un solvant organique, et pour realiser des reactions chimiques a petite echelle ne pouvant pas etre mises en oeuvre avec d'autres dispositifs microfluidiques a base de materiaux polymeres.