Abstract: The present invention describes methods of sequencing a nucleic acid in a sample, based on the use of terminal-phosphate-labeled nucleotides as substrates for nucleic acid polymerases. The methods provided by this invention utilize a nucleoside polyphosphate, dideoxynucleoside polyphosphate, or deoxynucleoside polyphosphate analogue which has a calorimetric dye, chemiluminescent, or fluorescent moiety, a mass tag or an electrochemical tag attached to the terminal-phosphate. When a nucleic acid polymerase uses this analogue as a substrate, an enzyme-activatable label would be present on the inorganic polyphosphate by-product of phosphoryl transfer. Cleavage of the polyphosphate product of phosphoryl transfer via phosphatase leads to a detectable change in the label attached thereon. In some instances the labeled polyphosphate may be detected directly via the label and provide information on the nucleic acid.

Abstract: The present invention describes terminal phosphate blocked nucleoside polyphosphates that are stable at high temperature and their use in nucleic acid amplification and analysis. Current invention further describes charge modified terminal phosphate blocked nucleoside polyphosphates for improved incorporation and direct loading of nucleic acid sequencing reactions onto separating media.

Abstract: A method of characterizing a nucleic acid sample is provided that includes the steps of: (a) conducting a DNA polymerase reaction that includes the reaction of a template, an allele specific primer, at least one terminal phosphate-labeled nucleotide, DNA polymerase, and optionally an enzyme having 3′→5′ exonuclease activity when the primer is non-hydrolyzable, which reaction results in the production of labeled polyphosphate; (b) permitting the labeled polyphosphate to react with a phosphatase to produce a detectable species; (c) detecting the detectable species; and (d) characterizing the nucleic acid sample based on such detection.

Abstract: Oligonucleotide tagged nucleoside triphosphates, OTNTPs, which are substrates for polymerases and or terminal nucleotidyl transferases are provided as well as methods of making these OTNTPs. Further provided are OTNTPs with fluorescent dyes including energy transfer dyes, attached to the oligonucleotide chain, OTNTPs with unnatural bases incorporated in the oligonucleotide sequence and methods for incorporating these OTNTPs in DNA or RNA. Also provided are methods for using the oligonucleotides on OTNTPs for amplifying the oligo sequence on the OTNTP using an amplification method described above. Further provided are reactive bifunctional amidites, methods of making these compounds and methods for detecting single nucleotide polymorphisms using the above OTNTPs. Methods for detecting differential gene expression using the OTNTPs and methods of separating specifically modified DNA or RNA using the OTNTPs are also provided.

Abstract: The present invention relates to improved methods of detecting a target using a labeled substrate or substrate analog. The methods comprise reacting the substrate or substrate analog in an enzyme-catalyzed reaction which produces a labeled moiety with independently detectable signal only when such substrate or substrate analog reacts. The present invention, in particular, describes methods of detecting a nucleic acid in a sample, based on the use of terminal-phosphate-labeled nucleotides as substrates for nucleic acid polymerases. The methods provided by this invention utilize a nucleoside polyphosphate, dideoxynucleoside polyphosphate, or deoxynucleoside polyphosphate analogue which has a colorimetric dye, chemiluminescent, or fluorescent moiety, a mass tag or an electrochemical tag attached to the terminal-phosphate. When a nucleic acid polymerase uses this analogue as a substrate, an enzyme-activatable label would be present on the inorganic polyphosphate by-product of phosphoryl transfer.

Abstract: The present invention describes new compositions of matter in the form of labeled nucleoside polyphosphates with four or more phosphates. In addition compositions of nucleoside polyphosphates with four or more phosphates that are substrates for nucleic acid polymerases with enhanced substrate properties and methods of using these nucleoside polyphosphates for nucleic acid detection, charcterization and quantification are described. The compositions provided by this invention include nucleoside polyphosphate, dideoxynucleoside polyphosphate, or deoxynucleoside polyphosphate analogues which have calorimetric, chemiluminescent, or fluorescent moieties, mass tags or an electrochemical tags attached to the terminal-phosphate. When a nucleic acid polymerase uses this analogue as a substrate, an enzyme-activatable label would be present on the inorganic polyphosphate by-product of phosphoryl transfer.

Abstract: A method of characterizing a nucleic acid sample is provided that includes the steps of: (a) conducting a DNA polymerase reaction that includes the reaction of a template, a non-hydrolyzable primer, at least one terminal phosphate-labeled nucleotide, DNA polymerase, and an enzyme having 3′→5′ exonuclease activity which reaction results in the production of labeled polyphosphate; (b) permitting the labeled polyphosphate to react with a phosphatase to produce a detectable species characteristic of the sample; (c) detecting the detectable species; and (d) characterizing the nucleic acid sample based on the detection.

Abstract: The present invention describes methods of detecting a nucleic acid in a sample, based on the use of terminal-phosphate-labeled nucleotides as substrates for nucleic acid polymerases. The methods provided by this invention utilize a nucleoside polyphosphate, dideoxynucleoside polyphosphate, or deoxynucleoside polyphosphate analogue which has a colorimetric dye, chemiluminescent, or fluorescent moiety, a mass tag or an electrochemical tag attached to the terminal-phosphate. When a nucleic acid polymerase uses this analogue as a substrate, an enzyme-activatable label would be present on the inorganic polyphosphate by-product of phosphoryl transfer. Cleavage of the polyphosphate product of phosphoryl transfer via phosphatase leads to a detectable change in the label attached thereon. When the polymerase assay is performed in the presence of a phosphatase, there is provided a convenient method for real-time monitoring of DNA or RNA synthesis and detection of a target nucleic acid.

Abstract: A novel class of pharmaceutically active boronated compounds are provided. The boronated compounds include boronated purine and pyrimidine bases and boronated nucleosides, as well as phosphate esters and oligomers thereof. The compounds are boronated at the ring nitrogen of the purine or pyrimidine base, or at a 2', 3' or 5' amino substituent of the nucleoside sugar.

Abstract: A method is disclosed for detecting boron labeled biopolymers, biooligomers, and other species that bind to the biopolymers, and biooligomers with specificity. The biopolymers include RNA, DNA and proteins. The biooligomers include RNA oligomers, DNA oligomers, and peptides. The biopolymers and biooligomers are labeled with a borane, or a boron-hydride moiety. The borane and boron-hydride moiety are employed to reduce a metal ion, e.g. silver, to metal or metal oxide, metal boride or other metal species, or alternatively to reduce a dye, or another organic or inorganic compound. The product of the reduction reaction can be visualized with or without signal augmentation, by one or more means, including the naked eye or a microscope, or can be detected through the use of analytical equipment that can detect conductivity, voltage, density, ultraviolet or visible light, fluorescence, luminescence, phosphorescence, paramagnetism, magnetic susceptibility, or any other detectable physical property.

Abstract: Disclosed are oligonucleoside boranophosphates, or salts thereof, comprising a chain of natural or modified ribonucleotides or deoxyribonucleotides, containing at least one boronated internucleotide phospodiester linkage of the formula: ##STR1## W is selected from the group consisting of .dbd.O, .dbd.S, --OPr, and --SPr where Pr is a base-labile protecting group. X is selected from the group consisting of --BH.sub.3, --BH.sub.2 R.sub.1, --BHR.sub.1 R.sub.2 and --BR.sub.1 R.sub.2 R.sub.3. R.sub.1 is selected from the group consisting of --R.sub.4, --COOH, --COOR.sub.4, --CONHR.sub.4, --CON(R.sub.4).sub.2, --CN.sup.+ R.sub.4 Z.sup.-, wherein Z.sup.- is an anion, --CN, carboxycholesteryl and carboxybenzyl, wherein R.sub.4 is C1 to C18 alkyl. R.sub.2 is selected from the group consisting of --R.sub.5, --COOH, --COOR.sub.5, --CONHR.sub.5, --CON(R.sub.5).sub.2, --CN.sup.+ R.sub.5 Z.sup.-, wherein Z.sup.- is an anion, --CN, carboxy- cholesteryl and carboxybenzyl, wherein R.sub.5 is C1 to C18 alkyl. R.sub.

Abstract: The phosphite-borane compounds of the present invention correspond to the formula ##STR1## where R.sub.1 is independently selected from H, C.sub.1 -C.sub.20 alkyl, alkylaryl, aryl, trialkylsilyl, with the proviso that both R.sub.1 groups cannot simultaneously be H.sub.1, andR.sub.2 is selected from H, a monovalent cation such as Li.sup.+, Na.sup.+, K.sup.+, NH.sub.4.sup.+, N(R.sub.3.sup.+).sub.4, where R.sub.3 is independently selected from H, C.sub.1 -C.sub.20 alkyl.The phosphite-borane compounds of the present invention are bioactive in character, variously exhibiting anti-tumor, anti-inflammatory, and hypolipidemic activity. Also disclosed are various synthetic methods for making such phosphite-borane compounds, and for formulating same in unit dosage forms as well as other pharmaceutically and pharmacologically acceptable formulations.

Abstract: Methods of making phosphite-borane compounds of the formula ##STR1## wherein: each R.sub.1 is independently selected from: H; C.sub.1 -C.sub.10 alkyl; alkylaryl; aralkyl; aryl; monovalent metal ions; nucleosides; and quaternary ammonium ions, (R.sub.4).sub.4 N.sup.+, in which the substituents R.sub.4 of the ammonium nitrogen atom are H or C.sub.1 -C.sub.10 alkyl;R.sub.2 is H or C.sub.1 -C.sub.10 alkyl; andR.sub.3 is CNCH.sub.2 CH.sub.3.sup.+ BF.sub.4.sup.-, COOH, carboxyl salts, COOR.sub.5, or CONHR.sub.5, wherein R.sub.5 is C.sub.1 -C.sub.10 alkyl, alkylaryl, aralkyl, or aryl;with the proviso that if at least one of the R.sub.1 substituents is H, nucleoside, monovalent metal ion, or quaternary ammonium ion, then R.sub.3 may also be CN,via synthetic routes comprising hydrolysis. The phosphorous-boron adducts of the invention are bioactive in character, variously exhibiting anti-tumor, anti-inflammatory, and hypolipidemic activity.

Abstract: A novel class of pharmaceutically active boronated compounds are provided. The boronated compounds include boronated purine and pyrimidine bases and boronated nucleosides, as well as phosphate esters and oligomers thereof. The compounds are boronated at the ring nitrogen of the purine or pyrimidine base, or at a 2', 3' or 5' amino substituent of the nucleoside sugar.

Abstract: A method of combatting, e.g., preventing as well as treating, a disease state such as cystic fibrosis, neonatal hypoxemia, pulmonary hypertension, adult respiratory distress syndrome, psoriasis, spondyloarthritis, rheumatoid arthritis, gout, inflammatory bowel disease, myocardial infarctions, and/or osteoporosis in an animal subject, by administering to the animal subject an amount of an organic boron compound which is effective thereagainst. The organic boron compounds usefully employed in the method of the invention include any suitable organic boron-containing compounds, such as Lewis base-boron adducts; a preferred class of organic boron compounds useful in such method includes boron analogs of .alpha.-amino acids, and the corresponding amides and esters of such amino acids. A method is also disclosed of inhibiting enzyme activity in in vitro or in vivo systems comprising administering to such system an enzyme-inhibiting amount of an organic boron compound.

Abstract: A gadolinium (3.sup.+) complex of polyamine polyacetate, comprising a polyamine nucleus having a pendant boron-containing substituent on one of the nitrogen or carbon atoms of the polyamine nucleus. The boron-gadolinium compound may suitably be of the formula: ##STR1## wherein: is a polyamine coordination structure capable of covalently bonding the substitutents R.sub.1, R.sub.2, R.sub.3 and R.sub.4 and of complexing with Gd;R.sub.1, R.sub.2, and R.sub.3 are independently selected from carboxyl, carboxylic salt groups, carboxylic ester groups, and carboxylate anion;R.sub.4 is a boron-containing group; andx is a number from zero to 4.

Abstract: Heterocyclic amine-borane compounds of the formula: ##STR1## wherein: A is a heterocyclic amine moiety selected from the group consisting of piperidine, substituted piperidine, piperazine, substituted piperazine, imidazole, substituted imidazole, pyrazole, substituted pyrazole, pyrazine, substituted pyrazine, pyrrole, substituted pyrrole, pyrrolidine, substituted pyrrolidine, indole, substituted indole, indoline, substituted indoline, quinoline, substituted quinoline, isoquinoline, substituted isoquinoline, thiazole, substituted thiazole, oxazole, substituted oxazole, thiazolidine, and substituted thiazolidine, wherein substitution is at any or all substituent positions, and comprises substituents selected from the group consisting of alkyl (preferably C.sub.1 -C.sub.10 linear or branched alkyl), alkylaryl, aryl, aralkyl, nitro, alkoxy, hydroxy, cyano, thiol, and halo;R.sub.1 is selected from H, alkyl (preferably C.sub.1 -C.sub.10 linear or branched alkyl), alkylaryl, aryl, and arylalkyl; andR.sub.

Abstract: A class of pharmaceutically active boronated compounds are provided. The boronated compounds include boronated phosphoramidates, and boronated nucleosides, and oligomers thereof. The compounds are boronated by an aminoalkyl substituted polyborane, carborane, metallopolyborane or metallocarborane.

Abstract: Nucleosidyl phosphite-borane compounds of the formula: ##STR1## wherein: Nucleoside is a natural or synthetic nucleoside connected to the phosphorus atom via a hydroxyl oxygen; each X is independently selected from O and BHR.sub.3 R.sub.4 ;R.sub.1 is selected from H, alkyl, aryl, alkyaryl, monovalent metal ions, and ammonium cation; R.sub.2 is selected from OR.sub.1 and N(R.sub.5).sub.2, wherein R.sub.5 is independently selected from H, C.sub.1 -C.sub.10 linear or branched alkyl or aryl; R.sub.3 is selected from H, CN, COOH, carboxyl salts, COOR.sub.6 and CONHR.sub.6, wherein R.sub.6 is selected from H, C.sub.1 -C.sub.10 alkyl, alkylaryl and aryl; R.sub.4 is selected from H and C.sub.1 -C.sub.10 alky; and n is 1 to 2.

Abstract: Phosphite-borane compounds of the formula ##STR1## wherein: each R.sub.1 is independently selected from: H; C.sub.1 -C.sub.10 alkyl; alkylaryl; aralkyl; aryl; monovalent metal ions; nucleosides; and quaternary ammonium ions, (R.sub.4).sub.4 N.sup.+, in which the substituents R.sub.4 of the ammonium nitrogen atom are H or C.sub.1 -C.sub.10 alkyl;R.sub.2 is H or C.sub.1 -C.sub.10 alkyl; andR.sub.3 is CNCH.sub.2 CH.sub.3 .sup.+ BF.sub.4.sup.-, COOH, carboxyl salts, COOR.sub.5, or CONHR.sub.5, wherein R.sub.5 is C.sub.1 -C.sub.10 alkyl, alkylaryl, aralkyl, or aryl;with the proviso that if at least one of the R.sub.1 substituents is H, nucleoside, monovalent metal ion, or quaternary ammonium ion, then R.sub.3 may also be CN.The phosphorous-boron adducts of the invention are bioactive in character, variously exhibiting anti-tumor, anti-inflammatory, and hypolipidemic activity.