Abstract: The apparatus and method of the present invention disclose a system in which multiple injections may be made into a capillary array. The injections are spaced in time with each injection followed by an interval of electrophoresis. Once all samples are loaded into the capillaries, continuous electrophoresis and detection is used to separate and detect target compounds within the sample. The interval between injections is matched to the target compound migration rate to be sufficient to allow the target compounds to be detectably separated when the compounds reach the detector.

Abstract: Methods for preparing nanoscale reactions using nucleic acids are presented. Nucleic acids are captured saturably, yet reversibly, on the internal surface of the reaction chamber, typically a capillary. Excess nucleic acid is removed and the reaction is performed directly within the capillary. Alternatively, the saturably bound nucleic acid is eluted, dispensing a metered amount of nucleic acid for subsequent reaction in a separate chamber. Devices for effecting the methods of the invention and a system designed advantageously to utilize the methods for high throughput nucleic acid sequencing reactions are also provided.

Abstract: Methods for preparing nanoscale reactions using nucleic acids are presented. Nucleic acids are captured saturably, yet reversibly, on the internal surface of the reaction chamber, typically a capillary. Excess nucleic acid is removed and the reaction is performed directly within the capillary. Alternatively, the saturably bound nucleic acid is eluted, dispensing a metered amount of nucleic acid for subsequent reaction in a separate chamber. Devices for effecting the methods of the invention and a system designed advantageously to utilize the methods for high throughput nucleic acid sequencing reactions are also provided.

Abstract: The present invention provides for the selective covalent modification of nucleic acids with redox active moieties such as transition metal complexes. Electron donor and electron acceptor moieties are covalently bound to the ribose-phosphate backbone of a nucleic acid at predetermined positions. The resulting complexes represent a series of new derivatives that are bimolecular templates capable of transferring electrons over very large distances at extremely fast rates. These complexes possess unique structural features which enable the use of an entirely new class of bioconductors and photoactive probes.

Abstract: A method and device for preparing nanoscale reactions. An automated system utilizes an array of reaction chambers. The ends of the chambers are temporarily sealed with deformable membranes and reactions effected by incubation or temperature cycling. Reaction mixtures may be assembled by using the reaction containers to meter reaction components. After the reaction is finished, the reaction containers may be dispensed onto a substrate and the reaction products analyzed. An automated transfer device may be used for automated transport of the reaction container array or other transportable elements.

Abstract: Method and reagents for analysis of nucleic acid sequences is disclosed. In this method a plurality of padlock probes is provided. Each padlock probe may hybridize to a locus on a target nucleic acid under hybridization conditions. If a targeted variant is present at the locus, the padlock probe may be ligated to form an amplification target circle. The amplification target circle acts as a template for production of tandem-sequence DNA. The tandem-sequence DNA may then be digested into non-tandem detection fragments which are subsequently separated and detected. The plurality of padlock probes are designed such that ligation of the probes, amplification of the target circle, and digestion of the tandem-sequence DNA subsequently produced, and detection may all be effected with the same set of reagents.

Abstract: A capillary valve, connector and router where one or more cylindrical fibers, which may be capillaries, plugged capillaries, optical fibers, or the like, including at least one capillary tube are contained in a first cylindrical bundle of fibers that terminates at a first face. A second cylindrical bundle of fibers also containing one or more fibers including at least one capillary tube terminates in a second face abutting the first face. A fastener or adapter holds the members together with faces in mutually biased alignment, allowing relative rotation of the two cylindrical bundles which terminate in rotatable ferrules. Various functions achieved by rotation include a zero dead volume slide valve, a fluid router and a manifold. The fibers in each sleeve are preferably of uniform size for close symmetrical packing, but could be of disparate sizes, allowing connection of macroscale tubes to capillary tubes.

Abstract: A sample substrate for use in a fluorescence imaging system includes a rigid base with a specularly reflective surface, typically metal, on which is deposited a transparent coating layer. The coating layer has a thickness selected so that a particular fluorescence excitation wavelength, corresponding to a specified fluorescent constituent to be sought in sample material, has an optical path from the top of the coating layer to the reflecting surface in the base of substantially an odd multiple of one-quarter wavelength, so that the standing wave of the fluorescence excitation wavelength of light incident on the substrate has an antinode located at or near where sample material would be disposed on top of the coating layer. This maximizes fluorescence excitation of the sample on the reflective substrate. The transparent coating layer may be a dielectric material (e.g. silica) or may be a multilayer structure with a top layer of biologically active material for binding a specified sample constituent.

Abstract: The apparatus and method of the present invention disclose a system in which multiple injections may be made into a capillary array. The injections are spaced in time with each injection followed by an interval of electrophoresis. Once all samples are loaded into the capillaries, continuous electrophoresis and detection is used to separate and detect target compounds within the sample. The interval between injections is matched to the target compound migration rate to be sufficient to allow the target compounds to be detectably separated when the compounds reach the detector.

Abstract: A method for performing separation assays of biochemical samples includes computing a quality metric based on peak data produced during the separation run. The quality metric is the basis for selecting a subsequent step in the assay, including whether to re-run the separation when the quality metric indicates a low quality separation run. In a preferred embodiment, the quality metric is computed based on a peak resolution metric indicative of the peak resolution of the sample peaks in the data and a signal-to-noise ratio of the data. When a co-migrating standard is included in the separation run, the quality metric is further based on the degree of migration linearity of the reference peaks produced by the standard. The method was reduced to practice in separations to size and sort DNA fragments in high-throughput capillary array electrophoresis separations.

Abstract: A sample substrate for use in a fluorescence imaging system includes a rigid base with a specularly reflective surface, typically metal, on which is deposited a transparent coating layer. The coating layer has a thickness selected so that a particular fluorescence excitation wavelength, corresponding to a specified fluorescent constituent to be sought in sample material, has an optical path from the top of the coating layer to the reflecting surface in the base of substantially an odd multiple of one-quarter wavelength, so that the standing wave of the fluorescence excitation wavelength of light incident on the substrate has an antinode located at or near where sample material would be disposed on top of the coating layer. This maximizes fluorescence excitation of the sample on the reflective substrate. The transparent coating layer may be a dielectric material (e.g. silica) or may be a multilayer structure with a top layer of biologically active material for binding a specified sample constituent.

Abstract: A coaxial illumination and collection laser scanning system designed to provide increased sensitivity by reducing auto-fluorescence while having a substantially uniform detection sensitivity across the field of view of an objective lens by reducing lateral chromatic aberrations at the expense of amplifying axial chromatic aberrations. Axial chromatic aberrations in the system are removed in the path of a retro-beam. A laser is in optical communication with the objective lens. The laser produces a collimated beam of coherent light that is directed by a scanner through the objective lens to illuminate a raster of spots on the sample's surface, thereby stimulating a series of small regions of the sample to emit light. The system may be used as a confocal or non-confocal imaging system.

Abstract: A microspot deposition system featuring a hollow cylindrical wall extending from a closed end, terminating in an open end and including a longitudinal gap extending from the open end toward the closed end to allow the rapid exhaustion of the atmosphere and efficient cleaning within the cylindrical wall. The cylindrical wall defines a lumen with both the lumen and the gap adapted to facilitate capillary action of liquid in fluid communication therewith to form a meniscus proximate to the open end. To facilitate deposition of liquid contained within the lumen, the gap may be tapered so that it is narrowest proximate to the open end. The narrowed portion of the gap results in a meniscus having a reduced area to ensure preferential fluid flow toward the open end, which facilitates deposition via capillary action between the liquid in the lumen and a working surface on which the liquid is to be deposited.

Abstract: A method for coupling DNA to a glass substrate by aminating the glass substrate with an aminosilane, reacting DNA with a carbodiimide/imidazole solution to create a 5'-phosphorimidazolide, and reacting the aminated glass substrate and phosphorimidazolide to couple the DNA to the substrate.

Abstract: The present invention features two flat-field, telecentric, infinite conjugate, achromatic objectives each of which has an external pupil lying in a common plane located equidistant from the two objectives, defining a mechanically accessible central pupil of an imaging system centered in the common plane. Each of the objectives are afocal in the common plane, with one of the lenses forming a focal plane proximate to a sample. The lenses are adapted to provide varying levels of magnification while keeping constant the number of resolvable points in the field of view. An array detector is positioned proximate to a focal plane formed of the remaining objective lens. The double objective lens assembly is described as being included in transillumination and epi-illumination systems.

Abstract: A fluorescence imaging system that includes an objective that is both achromatic and has an external entrance pupil. The objective also serves as a condenser for the system which substantially reduces the system's cost and footprint. With the objective positioned above a sample so that they are in close proximity to one another, a laser directs a collimated beam of light to a scan device located at the objective entrance pupil. The scan device reflects, refracts, or diffracts the light through the lens to illuminate a spot on the sample's surface. The scan device illuminates a line or an area on the sample surface by varying the angle of laser light, in one or two dimensions, into the objective. The sample emits fluorescent light in response to the illumination. The fluorescence light is collected by the objective and passes through the system along the path of the illumination light.

Abstract: A fluorescence imaging system that includes an objective that is both achromatic and has an external entrance pupil. The objective also serves as a condenser for the system which substantially reduces the system's cost and footprint. With the objective positioned above a sample so that they are in close proximity to one another, a laser directs a collimated beam of light to a scan device located at the objective entrance pupil. The scan device reflects, refracts, or diffracts the light through the lens to illuminate a spot on the sample's surface. The scan device illuminates a line or an area on the sample surface by varying the angle of laser light, in one or two dimensions, into the objective. The sample emits fluorescent light in response to the illumination. The fluorescence light is collected by the objective and passes through the system along the path of the illumination light.

Abstract: A coaxial illumination and collection laser scanning system provides substantially uniform detection sensitivity across the field of view of an objective lens by reducing lateral chromatic aberrations at the expense of amplifying axial chromatic aberrations. Axial chromatic aberrations in the system are removed in the path of a retro-beam. A laser is in optical communication with the objective lens. The laser produces a collimated beam of coherent light that is directed by a scanner through the objective lens to illuminate a raster of spots on the sample's surface, thereby stimulating a series of small regions of the sample to emit light. The system may be used as a confocal or non-confocal imaging system. Alternatively, the system may be employed for reflection imaging of the laser beam. In a second embodiment, a plurality of lasers are provided, each of which emits a wavelength different from the remaining lasers.

Abstract: A compact, movable scan head having multiple scanning modalities and capable of high speed, high resolution scanning of a variety of samples is disclosed. Stimulation and detection of storage phosphor screens and fluorescent samples are preferably achieved with a first and second channel in the optical path of the first side of the scan head. This first side preferably has a laser diode light source. Reading of reflective and transmissive signals is also possible. A third channel is available in the optical path of the second side of the scan head. This third channel preferably provides LED point scanning and reading of fluorescence, reflective, and transmissive signals received from the sample. The various modalities of the scan head of the present invention may or may not have coincident optical paths. Any two of the above channels, or additional channels similar to the above channels, may be incorporated into the scan head.

Abstract: A high-speed fluorescence scanner for scanning a sample at equal angles is disclosed. The scanner has most of its optical components, including a light beam source, a detector, and various filters, lenses, and reflectors, in a fixed position, removed from the scan head. The lightweight scan head contains a single reflector and lens combination which is reciprocated rapidly along one axis to lengthen and shorten a region of the path of a collimated excitation beam and to form a scan line on a sample. The fluorescence emission may be gathered by the lens of the scan head and directed back, generally along the optical path of the excitation beam, to a detector. Another embodiment of the scanner places the light source, in miniature form, directly on the scan head. The sample may be translated in an axis orthogonal to the scan line in order to stimulate fluorescent emission from a two-dimensional portion of the sample.