Abstract: The present invention presents methods for gene expression monitoring that utilize microelectronic arrays to drive the transport and hybridization of nucleic acids. Procedures are described for generating mRNA expression samples for use in these methods from populations of cells, tissues, or other biological source materials, that may differ in their physiological and/or pathological state. Provided in the invention are methods for generating a reusable nucleic acid transcript library from mRNA in a sample of biological material. In order to improve gene expression monitoring on the microelectronic arrays, the transcripts are amplified to produce sample nucleic acid amplicons of a defined length. Because multiple sample amplicons may be selectively hybridized to controlled sites in the electronic array, the gene expression profiles of the polynucleotide populations from different sources can be directly compared in an array format using electronic hybridization methodologies.

Abstract: Methods, apparatus, and applications for use of a stacked, reconfigurable system for electrophoretic transport are provided. In one embodiment, a system having a first chamber including at least a bottom support and an intermediate support, and a second chamber, said second chamber including a bottom support and a top member, the first and second chambers being coupled through a via. Electrophoretic, and optional electro-osmotic and thermal, transport is effected. In another aspect of this invention, three or more chambers are coupled by an electrophoretic buss. The electrophoretic buss includes driving electrodes and is adapted to receive fluid containing materials for transport. The chambers are coupled to the electrophoretic buss and serve as a tap from the buss for delivery of charged materials. In one embodiment, certain functions are performed in different chambers.

Abstract: A biologic electrode array assembly is formed on an integrated circuit chip that includes an array of electrodes. At least one metal oxide semiconductor (MOS) switch is coupled to at least one of the electrodes within the array. A voltage line is provided that is selectively connected to the at least one electrode via the MOS switch. A voltage source is coupled to the voltage line. In one preferred aspect of the invention, the MOS switch is a CMOS switch. In another aspect of the invention, an addressable memory is associated with the at least one electrode located within the array.

Abstract: Methods of manufacture and devices for performing active biological operations utilize various structures to advantageously collect and provide charged biological materials to an array of microlocations. In one embodiment, a device includes focusing electrodes to aid in the direction and transport of materials from a collection electrode to an array. Preferably, one or more intermediate transportation electrodes are utilized, most preferably of monotonically decreasing size between the collection electrode and the array, so as to reduce current density mismatches. In another aspect, a flow cell is utilized over devices to provide containment of solution containing materials to be analyzed. Preferably, the volume of the flow cell is more advantageously interrogated through use of relatively large collection and return electrodes, such as where the area of those electrodes relative to the footprint of the flowcell is at least 40%.

Abstract: An optical detection system is adapted particularly for detection of biological reactions, especially fluorescent or chemilluminescent reactions. An excitation source, preferably a laser, illuminates a portion of an object to be examined, the portion preferably comprising one microlocation out of an array of microlocations. An intervening optical detection platform serves to direct the excitation radiation, preferably through use of a scanning system, most preferably through use of an x-y mirror-based scanning system to the portion of the object to be illuminated. A detector, preferably a photomultiplier tube, receives the emitted radiation from the objects to be examined, the detector being characterized in that the diameter of the region examined by the detector is the same as or smaller than the diameter of the illuminated region, and comprises less than the entire surface of the object to be examined, and most preferably images a whole or a part of a single microlocation.

Abstract: Devices for performing active biological operations utilize various structures to advantageously collect and provide charged biological materials to an array of microlocations. An active biological matrix device includes an array of unit cells, each unit cell including a variable current control element, a select switch, and a return electrode. The output of the select switch is preferably adapted to contact a conductive solution including charged biological materials. The return electrode is preferably connected to a second potential and adapted to contact the conductive solution. In the presence of the conductive solution, current is provided between the return electrode and the output of the select switch. The variable current control element includes a control element that is adapted to receive a first control signal via, preferably, a first column line. The select switch includes a control element that is adapted to receive a second control signal via, preferably, a first row line.

Abstract: A method of improving amplification of nucleic acids using a nucleic acid sequence-based amplification (“NASBA”) method is provided wherein target nucleic acids and NASBA primers are electronically addressed to electronically addressable capture sites of a microchip. This improvement uses electronically induced hybridization of the target nucleic acids to the primers. The primers may be solution-based or immobilized on the capture sites of the microchip.

Abstract: The present invention comprises devices and methods for performing channel-less separation of cell particles by dielectrophoresis, DC high voltage-pulsed electronic lysis of separated cells, separation of desired components from crude mixtures such as cell lysates, and/or enzymatic reaction of such lysates, all of which can be conducted on a single bioelectronic chip. A preferred embodiment of the present invention comprises a cartridge (10) including a microfabricated silicon chip (12) on a printed circuit board (14) and a flow cell (16) mounted to the chip (12) to form a flow chamber. The cartridge (10) also includes output pins (22) for electronically connecting the cartridge (10) to an electronic controller. The chip (12) includes a plurality of circular microelectrodes (24) which are preferably coated with a protective permeation layer. Specific cells from various cell mixtures were separated, lysed, and enzymatically digested on the chip.

Abstract: Methods, apparatus, and applications for use of a stacked, reconfigurable system for electrophoretic transport are provided. In one embodiment, a system having a first chamber including at least a bottom support and an intermediate support, and a second chamber, said second chamber including a bottom support and a top member, the first and second chambers being coupled through a via. Electrophoretic, and optional electro-osmotic and thermal, transport is effected. In another aspect of this invention, three or more chambers are coupled by an electrophoretic buss. The electrophoretic buss includes driving electrodes and is adapted to receive fluid containing materials for transport. The chambers are coupled to the electrophoretic buss and serve as a tap from the buss for delivery of charged materials. In one embodiment, certain functions are performed in different chambers.

Abstract: An electronic device for performing active biological operations includes a support substrate, a second substrate, a source of illumination, and an edge illumination layer. The support substrate includes first and second surfaces and a via between the first and second surfaces to permit fluid flow through the substrate. The second substrate includes a first surface that is adapted to be disposed in facing arrangement with the second surface of the first substrate. The second substrate includes an array of microlocations wherein the array is adapted to receive the fluid. A sealant is disposed between the second face of the support substrate and the first face of the second substrate. The device includes a source of illumination and an edge illumination layer having an input adapted to receive the illumination from the source, and an output adapted to direct the illumination to the array. The edge illumination layer is disposed adjacent to and between the support substrate and the second substrate.

Abstract: Methods, apparatus, and applications for use of a stacked, reconfigurable system for electrophoretic transport are provided. In one embodiment, a system having a first chamber including at least a bottom support and an intermediate support, and a second chamber, said second chamber including a bottom support and a top member, the first and second chambers being coupled through a via. Electrophoretic, and optional electro-osmotic and thermal, transport is effected. In another aspect of this invention, three or more chambers are coupled by an electrophoretic buss. The electrophoretic buss includes driving electrodes and is adapted to receive fluid containing materials for transport. The chambers are coupled to the electrophoretic buss and serve as a tap from the buss for delivery of charged materials. In one embodiment, certain functions are performed in different chambers.

Abstract: An optical detection system is adapted for detection of biological reactions. An excitation source illuminates a portion of an object to be examined, the portion preferably comprising one microlocation out of an array of microlocations. An intervening optical detection platform serves to direct the excitation radiation to the portion of the object to be illuminated. A detector receives the emitted radiation from the object to be examined, the detector being characterized in that the diameter of the region examined by the detector is the same as or smaller than the diameter of the illuminated region, and comprises less than the entire surface of the object to be examined, and most preferably images a whole or a part of a single microlocation. In operation, a microscopy system is formed in which the excitation radiation is substantially in focus at the surface of the object to be examined.

Abstract: A method for amplifying nucleic acids is provided wherein detection of amplified species is enhanced by the use of asymmetric amplification. Such amplification is made asymmetric by using divergent ratios of amplification primers or by using non-extending and/or non-cleavable amplification primers. Detection of the amplicons is improved because maintenance of single stranded species of amplicons during amplification facilitates their direct capture by immobilized probes without having to include denaturing steps.

Abstract: The present invention pertains to a method of, and a device created by, depositing an inorganic permeation layer on a micro-electronic device for molecular biological reactions. The permeation layer is preferably sol-gel. The sol-gel permeation layer can be created with pre-defined porosity, pore size distribution, pore morphology, and surface area. The sol-gel permeation layer may also function as the attachment layer of the micro-electric device.

Abstract: Electronically addressable microchips having covalently bound permeation layers and methods of making such covalently bonded permeation layers to microchips are provided. The covalent bonding is derived from combining the use of electrodes with silane derivatives. Such chemistry provides the ability to apply an electronic bias to the electrodes of the microchip while preventing permeation layer delaminating from the electrode surface.

Abstract: A circuit for control of an output current in a multiple unit cell array includes an array of unit cells arranged in rows and columns. Each unit cell includes a column select transistor being adapted for control by a column selector and a row select transistor being adapted for control by a row selector. The column select transistor and the row select transistor are connected together in series to each other and between an output node and a first supply. A return electrode is provided to complete the circuit.

Abstract: A system useful in performing active biological reactions includes an array of unit cells arranged in rows and columns. Row lines are coupled to row contacts of unit cells of the array. A row selector is coupled to the row lines to provide a row select voltage. Column lines are coupled to column contacts of the array. A column selector is coupled to the column lines to provide more than two column voltage states on the column lines. The unit cells are coupled to a supply and to an electrode, the row select and column select voltage states provides variable current output from the electrode of the unit cell. A return electrode is coupled to a potential and adapted to contact conductive solution including charged biological materials, wherein in the presence of the conductive solution, current is provided between various unit cells and the return electrode.

Abstract: Methods of manufacture and devices for performing active biological operations utilize laminated structures. In the preferred embodiment, a first planar sample support includes at least one sample through hole, a planar electrode is disposed adjacent the first planar sample support, and includes an electrode through region, a second planar support includes a vent through hole, the planar electrode being in a laminated relationship between the first planar sample support and the second planar support, further characterized in that the sample through hole, electrode through hole and vent through hole are in overlapping arrangement. Preferably, some or all of the through holes, through regions and vent through holes are aligned. In one embodiment, the lateral dimension of the vent through hole is larger than the lateral dimension of the electrode through hole. In an alternative embodiment, the lateral dimension of the sample through hole is larger than the lateral dimension of the vent through hole.

Abstract: This invention provides an apparatus and method for desalting a low volume solution for use in connection with an electronically addressable microarray. The apparatus comprises a tubular molecular weight cut-off membrane embedded within a ion exchange resin filled chamber. The apparatus provides a very high surface to volume ratio of membrane pore surface to exchange resin capacity for absorbing charged molecules. The design facilitates the speedy removal of charged molecules from test solutions with the resultant desalted solution having a very low ionic strength suitable for use in the electronic transport of nucleic acids, proteins, and cells.

Abstract: The present invention comprises devices and methods for performing channel-less separation of cell particles by dielectrophoresis, DC high voltage-pulsed electronic lysis of separated cells, separation of desired components from crude mixtures such as cell lysates, and/or enzymatic reaction of such lysates, all of which can be conducted on a single bioelectronic chip. A preferred embodiment of the present invention comprises a cartridge (10) including a microfabricated silicon chip (12) on a printed circuit board (14) and a flow cell (16) mounted to the chip (12) to form a flow chamber. The cartridge (10) also includes output pins (22) for electronically connecting the cartridge (10) to an electronic controller. The chip (12) includes a plurality of circular microelectrodes (24) which are preferably coated with a protective permeation layer which prevents direct contact between any electrode and a sample introduced into the flow chamber.