Abstract: The present invention relates to methods for identifying the location, and determining the sequence of specific genetic alterations present in a gene of interest.

Abstract: The invention provides methods and compositons for convergent synthesis of branched polymers useful as molecular probes. The invention also includes several novel branched polymeric structures particularly useful for detecting target polynucleotides. Branched polymers of the invention comprise at least two branches: at least one branch is a target binding moiety capable of specifically binding to a target molecule of interest and one or more branches are signal generation moities capable of directly or indirectly generating a detectable signal. In accordance with the method of the invention branched polymers are assembled from components having phosphorothioate groups and/or haloacyl- or haloalkylamino groups. The phosphorothioate and haloacyl- or haloalkylamino groups react rapidly and efficiently when brought into contact to form thiophosphorylacyl- or thiophosphorylalkylamino bridges which.complete the assembly of a branched polymer.

Abstract: Methods of determining whether a solid tumor has an ALL-1 gene rearrangement or an ALL-1 gene mutation are disclosed. The methods comprise the steps of obtaining a sample of a solid tumor and detecting the presence of an ALL-1 gene rearrangement or mutation in a cell in said sample. ALL-1 gene rearrangements and mutations are detected by Southern blot analysis, PCR amplification analysis, in situ hybridization analysis, Northern blot analysis or DNA sequence analysis.

Abstract: A method for amplification and detection of a low copy target nucleic acid includes coamplification of a high copy target nucleic acid. After a number of conventional amplification cycles which include a denaturation step, several cycles are carried out during which the denatured products are renatured for a brief period of time. This intermediate step in later cycles of the amplification process reduces the effective concentration of the high copy target nucleic acid available for amplification in later cycles, thereby making more DNA polymerase available for amplification of the low copy target nucleic acid.

Abstract: A reaction cassette has been designed for the highly sensitive detection of the making and breaking of chemical bonds. The system may be employed as a companion device to be used in the search for antibody and other novel catalysts. The cassette also has important clinical applications in the design of diagnostic reagents. In its fully encoded format this methodology is capable of both detecting and decoding chemical events.

Abstract: With the help of PCR it is possible to detect parasites of the genus Cryptosporidium by amplifying specific gene sequences. The disadvantage of this method is that it does not allow a statement about whether the detected gene sequences have been derived from viable and infectious parasites or from dead organisms or even from free DNA which has been released from organisms which have already disintegrated. However, by the combination of PCR with other known methods, i.e. an in vitro excystation assay and the removing or the destruction of nucleic acids which might be present in a sample material outside of Cryptosporidium oocysts before excystation this problem can be solved. Due to this combination the result of a PCR for Cryptosporidium allows a judgement on the infectivity of the examined material which would not be possible without this combination.

Abstract: A nested polymerase chain reaction (PCR) performed in a single reaction tube that remains closed after the reaction mixtures for each amplification have been introduced therein. The reaction mixture for the second PCR amplification is sequestered and preserved in an upper portion of the single, closed reaction tube during the first amplification, and subsequently introduced into the reaction space containing the end product of the first PCR amplification, without opening the reaction tube.

Abstract: Rapid and cost effective diagnosis of p53 mutations of a sample of patients is achieved by employing a selected plurality of diagnostic tools, in a hierarchy of increasing accuracy and cost per tool, in which each tool detects essentially no false positives. Diagnostic tests that may be included among the plurality of tests selected include, in order of increasing accuracy and cost:(a) immunoassays,(b) analysis of DNA from a patient sample by quantitative amplification of p53 exons using amplification primers complementary to intron regions flanking each exon and examination of the length or quantity of each amplified fragment for nucleotide insertions or deletions relative to the normal p53 gene.

Abstract: Reliable and cost effective testing for mutations in the RB1 gene can be accomplished by quantitatively amplifying exons of the sample RB1 gene using primers complementary to intron regions flanking each exon; and then determining the lengths and/or quantities of the amplification products for each exon and comparing that length or quantity to the length or quantity of amplification products obtained when a wild-type RB1 gene is amplified using the same primers. Differences in length between an amplified sample exon and the corresponding amplified wild-type exon reflect the occurrence of an insertion or deletion mutation in the sample RB1 gene. Differences in quantity reflect the complete absence of an exon, or heterozygosity for a mutant exon. Next, the nucleic acid sequence of each exon found to contain an insertion or deletion mutation is determined, or of all exons in the event no insertion or deletion mutations are identified.

Abstract: Methods for detecting, immobilizing or localizing primer extension products of a Strand Displacement Amplification reaction which are coupled to, and an indication of, amplification of the target sequence. The primer extension products are secondary, target-specific DNA products generated concurrently with SDA of the target sequence and can therefore be used to detect and/or measure target sequence amplification in real-time. In general, the secondary amplification products are not amplifiable and remain inert in the SDA reaction after they are formed without interfering with amplification of the target sequence. The secondary amplification products may be designed or modified to contain special features to facilitate their detection, immobilization or localization.

Abstract: The invention relates to the preparation, as substituents, of nucleotides possessing a fluorescent coumarin residue, the enzymic incorporation of these nucleotides into nucleic acids and the detection of nucleic acids of defined sequence by hybridization with a complementary, coumarin-labelled nucleic acid.

Abstract: A hierarchy of at least two assay techniques is utilized in testing for disease-associated mutations. The first assay in the hierarchy is selected to provide a highly specific test for the existence of the disease-associated mutation, although the accuracy of the test need not be high. The final assay in the hierarchy is selected to provide a highly accurate and highly specific test for the existence of the disease associated mutation. Intermediate tests of progressively greater accuracy may also be included in the hierarchy. Once the hierarchy has been selected for a given mutation-associated disease, a patient sample is analyzed the patient sample using the first, lowest accuracy assay in the hierarchy. If the result of the first assay is negative for the presence of a disease-associated mutation, then the next assay in the hierarchy is performed.

Abstract: Disclosed are stabilized ribozyme analogs having the ability to endonucleolytically cleave a sequence of 3' to 5' linked ribonucleotides. These ribozyme analogs include modifications at specific loop, catalytic core, and flanking region nucleotides which makes them more resistant to nucleases. Also disclosed are methods of preparing and utilizing the ribozyme analogs of the invention, and pharmaceutical formulations and kits containing such ribozyme analogs.

Abstract: The present invention pertains to a process which can be fully automated for accurately determining the alleles of STR genetic markers. More specifically, the present invention is related to performing PCR amplification on locations of DNA, labelling the PCR products, converting the labels into a signal, removing a reproducible PCR stutter pattern from the signal by means of a computational device, and then determining the genotype of the location of the DNA. An amplification can include multiple locations from the DNA of one or more individuals. The invention also pertains to genetics applications and systems which can effectively use this genotyping information.

Abstract: A method is provided for monitoring the progress of nucleic acid amplifications that rely on a nucleic acid polymerase having 5'.fwdarw.3' exonuclease activity. An important feature of the method is providing an oligonucleotide probe having a reporter molecule and a quencher molecule at either end such that the quencher molecule substantially quenches any fluorescence from the reporter whenever the oligonucleotide probe is in a single stranded state and such that the reporter is substantially unquenched whenever the oligonucleotide probe is in a double stranded state hybridized to a target polynucleotide.

Abstract: The invention provides a method of identification of the base in a target position in a DNA sequence wherein sample DNA is subjected to amplification; the amplified DNA is immobilised and then subjected to strand separation, the non-immobilised strand being removed and an extension primer, which hybridises to the immobilised DNA immediately adjacent to the target position, is provided; each of four aliquots of the immobilised single stranded DNA is then subjected to a polymerase reaction in the presence of a dideoxynucleotide, each aliquot using a different dideoxynucleotide whereby only the dideoxynucleotide whereby only the dideoxynucleotide complementary to the base in the target position becomes incorpored; the four aliquots are then subjected to extension in the presence of all four deoxynucleotides, whereby in each aliquot the DNA which has not reacted with the dideoxynucleotide is extended to form double stranded DNA while the dideoxy-blocked DNA remains as non-extended DNA; followed by identification

Abstract: The present invention discloses isolated nucleic acids encoding MGF and recombinant proteins encoded thereby. In addition to being useful for the production of recombinant MGF, these nucleic acids are also useful as probes. In a further aspect of the invention, transfected host cells, particularly eukaryotic cells, containing and expressing such nucleic acids are provided. Furthermore, the present invention relates to methods for using such MGF proteins to identify and characterize compounds which affect the intracellular signal transduction of a lactogenic hormone.

Abstract: A cagB gene of H. pylori is provided. This nucleic acid can be the nucleic acid consisting of nucleotides 193 through 1158 in the sequence set forth as SEQ ID NO:1, which is an example of a native coding sequence for CagB. This nucleic acid can also be in a vector suitable for expressing a polypeptide encoded by the nucleic acid. A cagC gene of H. pylori is provided. This nucleic acid can be the isolated nucleic acid consisting of nucleotides 1170 through 3830 in the sequence set forth as SEQ ID NO:3, which is an example of a native coding sequence for CagC. This nucleic acid can also be in a vector suitable for expressing a polypeptide encoded by the nucleic acid. Isolated nucleic acids that specifically hybridize with cagB and cagC are provided. CagB and CagC are associated with peptic ulceration and other clinical syndromes in humans infected with strains of H. pylori that express it.

Abstract: Oligonucleotides primers can be used to amplify and detect Hepatitis C virus nucleic acids in a process that involves reverse transcription of the viral genomic RNA to create cDNA and the subsequent amplification of the cDNA by the polymerase chain reaction. Oligonucleotide probes can be used to detect the presence of amplified DNA by hybridization. The invention provides improved methods, compositions, and kits for amplifying and detecting U.S., Japan, and HCV-C prototype nucleic acids.

Abstract: The present invention discloses a photo-induced DNA-cleaving agent composition comprises N-aryl-N-(alkyl or arylalkyl)hydroxylamine having the following formula: ##STR1## wherein R is C.sub.1 -C.sub.6 alkyl, phenyl, C.sub.1 -C.sub.6 alkoxy, phenoxy, C.sub.1 -C.sub.6 alkoxycarbonyl, halogen or halo(C.sub.1 -C.sub.6 alkyl)wherein R.sub.1 is hydrogen, C.sub.1 -C.sub.6 alkyl, phenyl, C.sub.1 -C.sub.6 alkoxy, C.sub.1 -C.sub.6 alkoxycarbonyl, halogen or halo(C.sub.1 -C.sub.6 alkyl); R.sub.2 is hydrogen; R.sub.3 is hydrogen or phenyl; R.sub.4 is hydrogen, phenyl, hydroxylphenyl, methoxyphenyl, dimethoxyphenyl, dimethylaminophenyl or naphthyl. The present N-aryl-N-(alkyl or arylalkyl)hydroxylamine is stable in dark, but it can react with O.sub.2 to form HO. radicals under irradiation of UV light for a period of 2-3 hours. The HO. radicals then react with DNA to accomplish cleavage of DNA.