Abstract: A process for purifying DNA comprising binding the DNA to a silicate compound in the presence of water, low salt buffer, or physiological buffer and eluting in the bound DNA by heating in a low salt buffer, a physiological buffer, or water. The silicate compound is prepared by reacting SiCl.sub.4 with a molar percentage of BCl.sub.3 of about 33.5%, 55.6%, or 83.3%, with a molar percentage of PCl.sub.3 of about 50.0%-83.3%, or with a molar percentage of AlCl.sub.3 of about 9.1%; cooling the reaction mixture; adding water until the evolution of gas is complete; and recovering the compound.

Abstract: A process for preparing borosilicate, aluminosilicate, or phosphosilicate comprising preparing a mixture of SiCl.sub.4 with a specific molar ratio of BCl.sub.3, AlCl.sub.3, or PCl.sub.3 ; cooling said mixture to zero degrees; and adding water to the reaction mixture until the evolution of gas is complete. These silicates are useful for purifying DNA wherein the DNA is bound in water or low salt buffers (i.e., in the absence of a chaotropic agent or alcohol).

Abstract: Oligonucleotide probes and primers which exhibit M. kansasii-specificity in nucleic acid hybridization assays and in nucleic acid amplification reactions are provided. The full-length M. kansasii-specific sequence, identified herein as clone MK7, is 493 base pairs in length and has a GC content of 63%. Several M. kansasii-specific subsequences of MK7 are also provided. The probes and primers are useful in assays for species-specific detection and identification of M. kansasii.

Abstract: Chromogenic and fluorogenic substrates for .beta.-lactamase, methods for synthesis thereof and methods for detecting .beta.-lactamase in a sample are provided. The substrates are substantially colorless or substantially nonfluorescent .beta.-lactam compounds which include an electronegative leaving group. The leaving group comprises a carbamate, carbonate, thiocarbamate or thiocarbonate linkage and a fluorescent moiety or a moiety capable of producing a visually detectable colored product. Upon cleavage of the lactam ring by .beta.-lactamase, the leaving group is liberated and fluorescence or a colored product is produced.

Abstract: Chromogenic and fluorogenic substrates for .beta.-lactamase, methods for synthesis thereof and methods for detecting .beta.-lactamase in a sample are provided. The substrates are substantially colorless or substantially nonfluorescent .beta.-lactam compounds which include an electronegative leaving group. The leaving group comprises a carbamate, carbonate, thiocarbamate or thiocarbonate linkage and a fluorescent moiety or a moiety capable of producing a visually detectable colored product. Upon cleavage of the lactam ring by .beta.-lactamase, the leaving group is liberated and fluorescence or a colored product is produced.

Abstract: M. kansasii-specific oligonucleotide amplification primers and methods for detecting and identifying M. kansasii nucleic acids using the amplification primers. One hundred percent of the clinical and environmental M. kanasii isolates tested were positive in amplification assays using the inventive amplification primers, with no cross-reactivity in other species of mycobacteria or closely related non-mycobacteria.

Abstract: Genus- and species-specific oligonucleotide probes derived from the M. paratuberculosis 70 kD heat shock protein gene sequence. The probes are useful for detecting Mycobacteria and for identifying specific species of Mycobacteria.

Abstract: Antibodies which recognize and bind to histidine rich protein II of Plasmodium falciparum. These antibodies exhibit improved specificity and affinity for the antigen which provides enhanced sensitivity in immunoassays. Peptides useful for generation of the antibodies are also provided.

Abstract: Mycobacteriophage DS6A has been characterized and found to specifically infect all species of the TB complex, without any detectable infection of mycobacteria species other than those of the TB complex. DNA sequence analysis revealed several potential open reading frames, including one encoding a protein analogous to gp37 of mycobacteriophage L5 and a second encoding a protein with significant homology to the S. coelicolor DNA polymerase .beta. subunit. Based on the DNA sequence analysis, cloning sites can be identified for insertion of reporter genes, making DS6A useful as a reporter phage for specific detection and identification of species of the TB complex.

Abstract: Primers and methods for adapter-mediated multiplex amplification of the IS6110 insertion element of Mycobacterium tuberculosis (M.tb) and the 16S ribosomal gene of Mycobacterium tuberculosis, useful for simultaneously detecting and/or identifying species of the M. tuberculosis complex and other clinically relevant Mycobacterium species. Multiplex Strand Displacement Amplification (SDA) is used in a single amplification reaction which is capable of simultaneously identifying M. tuberculosis and providing a screen for substantially all of the clinically relevant species of Mycobacteria. Also disclosed are methods for adapter-mediated multiplex amplification of multiple target sequences and a single internal control sequence for determination of sample efficacy or quantitation of the targets.

Abstract: Methods employing internal oligonucleotide standards in isothermal nucleic acid amplification reactions to determine the efficacy of the amplification reaction and to quantify pre-amplification target levels.

Abstract: This invention relates a nucleic acid target amplification and detection method which operates at a single temperature and makes use of a polymerase in conjunction with an endonuclease that will nick the polymerized strand such that the polymerase will displace the strand without digestion while generating a newly polymerized strand.

Abstract: Methods for multiplex amplification of target nucleic acid sequences using a single pair of primers. Defined sequences are appended to the ends of multiple target sequences as part of the amplification reaction so that no steps in addition to amplification are required. The target sequences with the appended defined sequences need not be isolated prior to amplification. In one embodiment for coamplification of two target sequences, a sequence corresponding to a terminal segment of the first target sequence is appended to one end of the second target sequence and a sequence corresponding to a terminal segment of the second target sequence is appended to one end of the first target sequence. Amplification of the two targets then requires only a single pair of primers. Alternatively, a single defined sequence may be appended to the 5' and 3' ends of any number of selected targets. All such modified target sequences may then be amplified using a single pair of primers which hybridize to the defined end-sequences.

Abstract: Fluorescent pH indicator compounds which exhibit an increase in fluorescence intensity with decreasing pH. The indicators are derivatives of rhodamine and sulforhodamine type dyes and are particularly useful for measuring pH in acidic environments such as carbon dioxide production by microorganisms and pH of certain acidic intracellular compartments.

Abstract: Stabilized microspherical particles having hydrophobic liquid cores prepared as oil-in-water microemulsions. The particles are stabilized by a surface layer comprising an amphiphilic compound and may be functionalized to allow covalent coupling of a ligand to the surface of the particle. When used as tracers in assays, a water insoluble dye may be incorporated in the core liquid of the microparticles.

Abstract: Fluorescent pH indicator compounds which exhibit an increase in fluorescence intensity with decreasing pH. The indicators are derivatives of rhodamine and sulforhodamine type dyes and are particularly useful for measuring pH in acidic environments such as carbon dioxide production by microorganisms and pH of certain acidic intracellular compartments.

Abstract: A method for detecting urea in a liquid sample in which urease is adsorbed on a solid support such as a membrane and contacted with a solution suspected of containing urea, a pH-dependent reducing agent and a tetrazolium salt. When urea is present in the solution, the adsorbed urease converts it to ammonia, thus raising the pH and causing the pH-dependent reducing agent to reduce the tetrazolium salt to an insoluble colored formazan. The formazan precipitates as a detectable spot on the solid support, indicating the presence of urea in the liquid sample.

Abstract: Oligonucleotide probes derived from Mycobacteria Kansasii capable of selectively hybridizing to Mycobacteria nucleic acid are disclosed. The oligonucleotide probe is selected from the group consisting of: (a) an oligonucleotide probe consisting essentially of the DNA sequence given herein as SEQ ID NO:1 (MK14); (b) oligonucleotide probes comprising fragments of MK14 which retain the capability of MK14 of selectively hybridizing to Mycobacteria nucleic acid; (c) oligonucleotide probes which hybridize to MK14 and are capable of selectively hybridizing to Mycobacteria nucleic acid; and (d) oligonucleotide probes which are complementary to any of the foregoing and are capable of selectively hybridizing to Mycobacteria nucleic acid. The probes are useful in nucleic acid amplification and hybridization assays for genus-specific detection of the mycobacteria, specific detection of M. kansasii and specific detection of the slow-growing mycobacteria.

Abstract: A process for purifying DNA comprising 1) binding the DNA to a hydrated silica in the presence of water or physiological buffers in which the hydrated silica is prepared by refluxing silicon dioxide in sodium hydroxide or potassium hydroxide at a molar ratio of about 2:1 to 10:1 for at least about 48 hours, 2) separating and washing hydrated silica and the DNA bound thereto, and eluting the DNA from the hydrated silica in a heated physiological buffer or in heated water.

Abstract: Chromogenic and fluorogenic substrates for .beta.-lactamase, methods for synthesis thereof and methods for detecting .beta.-lactamase in a sample are provided. The substrates are substantially colorless or substantially nonfluorescent .beta.-lactam compounds which include an electronegative leaving group. The leaving group comprises a carbamate, carbonate, thiocarbamate or thiocarbonate linkage and a fluorescent moiety or a moiety capable of producing a visually detectable colored product. Upon cleavage of the lactam ring by .beta.-lactamase, the leaving group is liberated and fluorescence or a colored product is produced.