Abstract: Methods and apparatus are provided for miniaturized DNA sequencing using four-color detection. The method employs a multichannel chip where the channels are simultaneously irradiated to excite fluorophores in the channels. The emitted light is divided into four different wavelength beams and read by CCDs. The results are multiplexed for rapid sequencing of a large number of samples, with high fidelity of the sequences.

Abstract: Devices and methods are provided using microfluidic devices for manipulating small volumes and determining a variety of chemical and physical events. The devices rely upon an opening to the atmosphere of a small volume in a zone, where a sample is placed in the zone where evaporation can occur. The zone is maintained in contact with a liquid medium that serves to replenish the liquid in the zone and maintain the composition of the mixture in the zone substantially constant. The diffusion of components in the zone is restricted during the course of the determination by the liquid flux into the zone.

Abstract: A method and apparatus for performing a plurality of small-volume reactions simultaneously with components in a bulk-phase medium are disclosed. The apparatus includes a device having an elongate or planar channel providing a plurality of discrete small-volume reaction regions within the channel, each communicating with supply and hold reservoirs from which material can be introduced into the regions, and to which material can be transferred from the reaction regions. A reaction-specific reagent is carried on a wall portion of each reaction region, or in a reservoir associated with a reaction region, for reacting in solution with one or more components in the bulk-phase medium, to effect a selected solution-phase reaction in each region or in a region-specific reservoir associated therewith.

Abstract: Methods and compositions are provided for detecting target molecules, e.g. DNA sequences, particularly single nucleotide polymorphisms, using a pair of nucleotide sequences, a primer and a snp detection sequence, where the snp detection sequence binds downstream from the primer to the target DNA in the direction of primer extension, or ligands and receptors. The methods employ e-tags comprising a mobility-identifying region joined to a detectable label and a target-binding region. The result of the binding of the target-binding region to the target is to have a bond cleaved in the starting material with the production of a detectable product with a different mobility from the starting material, where the different e-tags can be separated and detected.

Abstract: The present invention provides for methods and apparatus for locating a capillary channel that is disposed within a lab chip. The method provides for scanning the channel with a light source, monitoring the resulting light at the edges of the lab chip, and interpreting this information whereby the light detected at the edges of the lab chip can be used as a means for characterizing the location of the side walls of the channel within the lab chip. The apparatus provides for a carriage system to which a light source and the lab chip are attached. It also provides for one or more scatter detectors directed towards the edges of the chip and connected to a computer processor for purposes of analysis.

Abstract: Methods and compositions are provided for nucleic acid analysis. The method employs a primer and a probe that bind to a target nucleic acid sequence, where the primer has an effector agent, which causes cleavage of a bond when the primer and the probe are bound to the same target molecule. The primer and probe have arms that do not bind to the target, hybridize with each other and comprise the effector and cleavable bond, where the probe has a tag defining the probe that is released upon bond cleavage.

Abstract: A microchannel apparatus and method for processing a sample are disclosed. The apparatus include a multisite reaction channel, one or more sample-preparation stations upstream of the reaction channel, for carrying out one or more selected sample-preparation steps effective to convert a sample to the bulk-phase medium, and one or more product-processing stations downstream of the reaction channel, for processing products generated in one or more of the reaction regions. Also included is structure for transferring solvent or solvent components between one of the sample-preparation stations and one or more selected reaction regions in the reaction channel, and between one or more selected reaction regions in the reaction channel and one of said product-processing stations, under the control of a control unit.

Abstract: Multiplexed determinations of large numbers of events are achieved in an accurate and simple manner by using a multitude of primer reagents in combination with different capture reagents that serve for sequestering all the reagents at a single site, followed by independent release of subsets of the primer reagents using differential release conditions. Also included as part of the primer reagents may be identifiers, which serve to identify a particular characteristic. The method is illustrated using primers with sequences for initiation of chain extension that are joined to or serve as a capture sequence, and where the extended primer has an identifier. After extending the primer, the extended primers are sequestered via the capture sequence onto a sequestering agent, sequentially released and the released extended primers analyzed to provide multiplexed determinations.

Abstract: Methods of sample loading and separation in a microfluidics device are described. The methods provide high resolution and high signal intensity, using, in a preferred embodiment, a simple two-electrode injection scheme with isotachophoretic (ITP) stacking, followed by ZE separation in the same channel.

Abstract: Devices and methods are provided using microfluidic devices for manipulating small volumes and determining a variety of chemical and physical events. The devices rely upon an opening to the atmosphere of a small volume in a zone, where a sample is placed in the zone where evaporation can occur. The zone is maintained in contact with a liquid medium that serves to replenish the liquid in the zone and maintain the composition of the mixture in the zone substantially constant. The diffusion of components in the zone is restricted during the course of the determination by the liquid flux into the zone.

Abstract: Electrophoretic probes comprising fluorescent compounds as detection groups and mobility modifiers are disclosed for the multiplexed detection of the binding of, or interaction between, one or more ligands and target antiligands are provided. In one embodiment, detection involves the release of identifying tags as a consequence of target recognition. Target antiligands are contacted with a set of e-tag probes and the contacted antiligands are treated with a selected cleaving agent resulting in a mixture of e-tag reporters. Typically, uncleaved or partially cleaved e-tag probes are removed and the mixture of e-tag reporters is separated by any technique that provides for separation by mass or mass to charge ratio and the like and detected to provide for target identification.

Abstract: Probe sets for the multiplexed detection of the binding of, or interaction between, one or more ligands and target antiligands are provided. Detection involves the release of identifying tags as a consequence of target recognition. The probe sets include electrophoretic tag probes or e-tag probes, comprising a detection region and a mobility-defining region called the mobility modifier, both linked to a target-binding moiety. Target antiligands are contacted with a set of e-tag probes and the contacted antiligands are treated with a selected cleaving agent resulting in a mixture of e-tag reporters and uncleaved and/or partially cleaved e-tag probes. The mixture is exposed to a capture agent effective to bind to uncleaved or partially cleaved e-tag probes, followed by electrophoretic separation. In a multiplexed assay, different released e-tag reporters may be separated and detected providing for target identification.

Abstract: Integrated microfluidic devices comprising at least an enrichment channel (10) and a main electrophoretic flowpath (12) are provided. In the subject integrated devices, the enrichment channel and the main electrophoretic flowpath are positioned so that waste fluid flows away from said main electrophoretic flowpath through a discharge outlet (6). The subject devices find use in a variety of electrophoretic applications, including clinical assays, high throughput screening for genomics and pharmaceutical applications, point-or-care in vitro diagnostics, molecular genetic analysis and nucleic acid diagnostics, cell separations, and bioresearch generally.

Abstract: Microfluidic unit arrays and their use are provided for performing in parallel a plurality of operations. The units are arrayed in a format comparable to microtiter well formats, so that transfer by a dispenser having a plurality of dispensing units can be performed with the same footprint, the format of the source and microfluidic unit receiving reservoirs are substantially the same. Operations are carried out simultaneously under comparable conditions, which permits more exact comparisons between the operations.

Abstract: An optical detection and orientation device is provided comprising housing having an excitation light source, an optical element for reflecting the excitation light to an aspherical lens and transmitting light emitted by a fluorophore excited by said excitation light, a focussing lens for focusing the emitted light onto the entry of an optical fiber, which serves as a confocal aperture, and means for accurately moving said housing over a small area in relation to a channel in a microfluidic device. The optical detection and orientation device finds use in identifying the center of the channel and detecting fluorophores in the channel during operations involving fluorescent signals.

Abstract: Methods are provided for the fabrication of polymeric microchannel structures having enclosed microchannels of capillary dimension. The microchannel structures are constructed of a base plate and a cover, sealed together. Microchannel structures having walls of a plastic material are formed in a generally planar surface of at least the base plate. The cover has at least one generally planar surface, and the microchannel structures are enclosed by bonding the planar surfaces of the cover and the base plate together. In some embodiments the surfaces of the cover and base plate are both of plastic material, and are directly thermally bonded. In some embodiments a bonding material is applied to one of the surface prior to bringing the surfaces together. Suitable bonding materials are disclosed.

Abstract: Compositions and methods are provided for performing capillary electrophoresis using a composition comprising in combination in an aqueous buffered medium a coating polymer and a sieving polymer, where the sieving polymer is more hydrophilic than the coating polymer and is present in greater amount. Of particular interest are uncrosslinked acrylamide polymer mixtures for coating plastic channels and providing sieving for performing DNA separations in microfluidic devices. Polyacrylamide or N,N-dimethyl acrylamide is used with a N,N-dialkyl acrylamide copolymer, either separately or together for sieving and coating, serving as the medium in capillary electrophoresis DNA separations.

Abstract: The present invention provides for methods and apparatus for locating a capillary channel that is disposed within a lab chip. The method provides for scanning the channel with a light source, monitoring the resulting light at the edges of the lab chip, and interpreting this information whereby the light detected at the edges of the lab chip can be used as a means for characterizing the location of the side walls of the channel within the lab chip. The apparatus provides for a carriage system to which a light source and the lab chip are attached. It also provides for one or more scatter detectors directed towards the edges of the chip and connected to a computer processor for purposes of analysis.

Abstract: Methods and compositions are provided for detecting single nucleotide polymorphisms using a pair of oligonucleotides, a primer and a snp detection sequence, where the snp detection sequence hybridizes to the target DNA downstream from the primer and in the direction of primer extension. The snp detection sequence is characterized by having a nucleotide complementary to the snp and adjacent nucleotide complementary to adjacent nucleotides in the target and an electophoretic tag bonded to the 5′-nucleotide. The pair of oligonucleotides is combined with the target DNA under primer extension conditions, where the polymerase has 5′-3′ exonuclease activity. When the snp is present, the electophoretic tag is released from the snp detection sequence, and can be detected by electrophoresis as indicative of the presence of the snp in the target DNA.