Abstract: The present invention relates to systems, compositions, and methods for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. The present invention relates to methods for attaching nucleic acids to solid supports and modifying nucleic acids. For example, in some embodiments, the 5? nuclease activity of a cleavage agent is used to cleave a cleavage structure formed on the solid support, the occurrence of the cleavage event indicating the presence of specific nucleic acid sequences.

Abstract: The invention provides devices, device configurations and methods for improved sensitivity, resolution and efficiency in mass spectrometry, particularly as applied to biological molecules, including biological polymers, such as proteins and nucleic acids. More particularly, the invention provides methods and devices for analyzing and detecting electrically charged particles, especially suitable for gas phase ions generated from high molecular weight compounds. In one aspect, the invention provides devices and methods for determining the velocity, charged state or both of electrically charged particles and packets of electrically charged particles. In another aspect, the invention provides methods and devices for the time-of-flight analysis of electrically charged particles comprising spatially collimated sources. In another aspect, the invention relates to multiple detection using inductive detectors, improved methods of signal averaging and charged particle detection in coincidence.

Abstract: The present invention relates to compositions and methods for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. The present invention relates to methods for forming a nucleic acid cleavage structure on a solid support and cleaving the nucleic acid cleavage structure in a site-specific manner. For example, in some embodiments, a 5′ nuclease activity from any of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Abstract: The invention provides devices, device configurations and methods for improved sensitivity, resolution and efficiency in mass spectrometry, particularly as applied to biological molecules, including biological polymers, such as proteins and nucleic acids. More particularly, the invention provides methods and devices for analyzing and detecting electrically charged particles, especially suitable for gas phase ions generated from high molecular weight compounds. In one aspect, the invention provides devices and methods for determining the velocity, charged state or both of electrically charged particles and packets of electrically charged particles. In another aspect, the invention provides methods and devices for the time-of-flight analysis of electrically charged particles comprising spatially collimated sources. In another aspect, the invention relates to multiple detection using inductive detectors, improved methods of signal averaging and charged particle detection in coincidence.

Abstract: The charge state of ions produced by electrospray ionization is reduced in a controlled manner to yield predominantly singly charged ions through reactions with bipolar ions generated using a 210Po alpha particle source or equivalent. The multiply charged ions generated by the electrospray undergo charge reduction in a charge reduction chamber. The charge-reduced ions are then detected using a commercial orthogonal electrospray TOF mass spectrometer, although the charge reduction chamber can be adapted to virtually any mass analyzer. The results obtained exhibit a signal intensity drop-off with increased oligonucleotide size similar to that observed with MALDI mass spectrometry, yet with the softness of ESI and without the off-line sample purification and pre-separation required by MALDI.

Abstract: Disclosed are methods of using structure-specific, invasive nucleic acid cleavage reactions, in an addressed array format, to detect polymorphisms in general, and single nucleotide polymorphisms in particular. In the preferred embodiment of the invention, the addressed array format utilizes surface plasmon resonance imaging as a means for detecting the products of the invasive cleavage reaction and hence the presence of polymorphisms in the target nucleic acid. Sensitivity of the SPR detection is further enhanced by rolling circle amplification of the bound cleavage products.

Abstract: The present invention relates to compositions and methods for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. The present invention relates to methods for forming a nucleic acid cleavage structure on dendrimers and cleaving the nucleic acid cleavage structure in a site-specific manner. For example, in some embodiments, a 5′ nuclease activity from any of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Abstract: Chemically-modified surfaces on unoxidized, bromine- or iodine-terminated carbon, silicon, and germanium substrates are disclosed. Visible light mediates the reaction of protected &ohgr;-modified, &agr;-unsaturated aminoalkenes (preferred) with bromine- or iodine-terminated carbon, silicon, or germanium surfaces. Removal of the protecting group yields an aminoalkane-modified silicon surface. These amino groups can be coupled to terminal-modified oligonucleotides using a bifunctional crosslinker, thereby permitting the preparation of modified surfaces and arrays. Methods for controlling the surface density of molecules attached to the substrate are also disclosed.

Abstract: Methods and devices for use in mass spectral analysis of samples. In particular, methods and devices for generating ions from liquid samples containing chemical species with high molecular masses. These methods and devices provide a continuous or pulsed stream of gas phase analyte ions of either positive polarity, negative polarity or both possessing either a selected fixed charge-state distribution or one that may be selectively varied with time. More specifically, ion sources with adjustable control of the charge-state distribution of the gas phase analyte ions generated are provided in which charged droplets and/or gas phase analyte ions are exposed to electrons and/or gas phase reagent ions generated by a reagent ion source to provide desired control. A corona discharge exemplifies the reagent ion source employed in charge-state distribution control.

Abstract: The present invention relates to systems, compositions, and methods for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. The present invention relates to methods for attaching nucleic acids to solid supports and modifying nucleic acids. For example, in some embodiments, the 5′ nuclease activity of a cleavage agent is used to cleave a cleavage structure formed on the solid support, the occurrence of the cleavage event indicating the presence of specific nucleic acid sequences.

Abstract: Chemically-modified surfaces on unoxidized carbon, silicon, and germanium substrates are disclosed. Ultraviolet radiation mediates the reaction of protected &ohgr;-modified, &agr;-unsaturated aminoalkenes (preferred) with hydrogen-terminated carbon, silicon, or germanium surfaces. Removal of the protecting group yields an aminoalkane-modified silicon surface These amino groups can be coupled to terminal-modified oligonucleotides using a bifunctional crosslinker, thereby permitting the preparation of modified surfaces and arrays. Methods for controlling the surface density of molecules attached to the substrate are also disclosed.

Abstract: The present invention relates to a molecular computer used to perform mathematical calculations and logical operations. In particular, the molecular computer disclosed herein simulates circuit-SAT mathematical models, and is thus a generalized computer. The present invention further relates to compositions and methods for performing biochemical reactions on a solid support.

Abstract: Chemically-modified surfaces on unoxidized carbon, silicon, and germanium substrates are disclosed. Ultraviolet radiation mediates the reaction of protected &ohgr;-modified, &agr;-unsaturated aminoalkenes (preferred) with hydrogen-terminated carbon, silicon, or germanium surfaces. Removal of the protecting group yields an aminoalkane-modified silicon surface. These amino groups can be coupled to terminal-modified oligonucleotides using a bifunctional crosslinker, thereby permitting the preparation of modified surfaces and arrays. Methods for controlling the surface density of molecules attached to the substrate are also disclosed.

Abstract: The present invention relates to compositions and methods for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. The present invention relates to methods for forming a nucleic acid cleavage structure on dendrimers and cleaving the nucleic acid cleavage structure in a site-specific manner. For example, in some embodiments, a 5′ nuclease activity from any of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Abstract: Chemically-modified surfaces on unoxidized, bromine- or iodine-terminated carbon, silicon, and germanium substrates are disclosed. Visible light mediates the reaction of protected &ohgr;-modified, &agr;-unsaturated aminoalkenes (preferred) with bromine- or iodine-terminated carbon, silicon, or germanium surfaces. Removal of the protecting group yields an aminoalkane-modified silicon surface. These amino groups can be coupled to terminal-modified oligonucleotides using a bifunctional crosslinker, thereby permitting the preparation of modified surfaces and arrays. Methods for controlling the surface density of molecules attached to the substrate are also disclosed.

Abstract: Methods and devices for use in mass spectral analysis of samples. In particular, methods and devices for generating ions from liquid samples containing chemical species with high molecular masses. These methods and devices provide a continuous or pulsed stream of gas phase analyte ions of either positive polarity, negative polarity or both possessing either a selected fixed charge-state distribution or one that may be selectively varied with time. More specifically, ion sources with adjustable control of the charge-state distribution of the gas phase analyte ions generated are provided in which charged droplets and/or gas phase analyte ions are exposed to electrons and/or gas phase reagent ions generated by a reagent ion source to provide desired control. A corona discharge exemplifies the reagent ion source employed in charge-state distribution control.

Abstract: A process for the electrophoretic analysis of DNA fragments produced in DNA sequencing operations wherein chromophores or fluorophores are used to tag the DNA fragments produced by the sequencing chemistry and permit the detection and characterization of the fragments as they are resolved by electrophoresis through a gel. Preferably four different fragment sets are tagged with the fluorophores fluorescein, Texas Red, tetramethyl rhodamine, and 7-nitro-benzofurazan.

Abstract: The charge state of ions produced by electrospray ionization is reduced in a controlled manner to yield predominantly singly charged ions through reactions with bipolar ions generated using a 210Po alpha particle source or equivalent. The multiply charged ions generated by the electrospray undergo charge reduction in a charge reduction chamber. The charge-reduced ions are then detected using a commercial orthogonal electrospray TOF mass spectrometer, although the charge reduction chamber can be adapted to virtually any mass analyzer. The results obtained exhibit a signal intensity drop-off with increased oligonucleotide size similar to that observed with MALDI mass spectrometry, yet with the softness of ESI and without the off-line sample purification and pre-separation required by MALDI.

Abstract: This invention provides a duplex comprising an oligonucleotide primer and a template, wherein the primer is coupled chemically to a chromophore or fluorophore so as to allow chain extension by a polymerase. In one embodiment, the primer is extended by a polymerase to generate the complement of the template. In a further embodiment, the extended primer is separated from the template for use in a number of methods, including sequencing reactions. Methods of generating these compositions of matter are further provided.

Abstract: A process for the electrophoretic analysis of DNA fragments produced in DNA sequencing operations wherein chromophores or fluorophores are used to tag the DNA fragments produced by the sequencing chemistry and permit the detection and characterization of the fragments as they are resolved by electrophoresis through a gel. Preferably four different fragment sets are tagged with the fluorophores fluorescein, Texas Red, tetramethyl rhodamine, and 7-nitrobenzofurazan. A system for the electrophoretic analysis of DNA fragments produced in DNA sequencing operations comprising: a source of chromophore or fluorescent tagged DNA fragments; a zone for contacting an electrophoresis gel; means for introducing said tagged DNA fragments to said zone; and photometric means for monitoring said tagged DNA fragments as they move through said gel.