Showing papers on "Nucleic acid methods published in 1997"

Nucleic acid analysis techniques

Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase. In another embodiment, the end labeling can be accomplished by providing a nucleic acid, providing labeled nucleoside triphosphates, and attaching the nucleoside triphosphates to the nucleic acid using a terminal transferase.

Method of detection of methylated nucleic acid using agents which modify unmethylated cytosine and distinguishing modified methylated and non-methylated nucleic acids

Abstract: The present invention provides a method for detecting a methylated CpG-containing nucleic acid present in a specimen by contacting the specimen with an agent that modifies unmethylated cytosine and amplifying the CpG-containing nucleic acid using CpG-specific oligonucleotide primers. The present invention provides an improved method of methylation detection by facilitating the rapid identification of DNA methylation patterns in a CpG-containing nucleic acid.

High affinity nucleic acid ligands containing modified nucleotides

Abstract: Nucleic acid ligands containing modified nucleotides are described as are methods for producing such oligonucleotides. Such ligands enrich the chemical diversity of the candidate mixture for the SELEX process. Specific examples are provided of nucleic acids containing nucleotides modified at the 2'- and 5-position. Specific 2-OH and 2'-NH 2 modified RNA ligands to thrombin are described.

Invasive cleavage of nucleic acids

Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity 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.

Methods and compositions for determining the sequence of nucleic acid molecules

Abstract: Methods and compounds, including compositions therefrom, are provided for determining the sequence of nucleic acid molecules. The methods permit the determination of multiple nucleic acid sequences simultaneously. The compounds are used as tags to generate tagged nucleic acid fragments which are complementary to a selected target nucleic acid molecule. Each tag is correlative with a particular nucleotide and, in a preferred embodiment, is detectable by mass spectrometry. Following separation of the tagged fragments by sequential length, the tags are cleaved from the tagged fragments. In a preferred embodiment, the tags are detected by mass spectrometry and the sequence of the nucleic acid molecule is determined therefrom. The individual steps of the methods can be used in automated format, e.g., by the incorporation into systems.

Method for performing amplification of nucleic acid on supports

Abstract: This invention features methods, apparatus and kits for performing nucleic acid hybridization and amplification reactions on a support Such methods and apparatus are useful in diagnostic and therapeutic processes for synthesizing nucleic acid and detecting target nucleic acids in a sample

Method of Identifying a Base in a Nucleic Acid

Abstract: Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

Methods for measuring relative amounts of nucleic acids in a complex mixture and retrieval of specific sequences therefrom

Abstract: The present invention relates to a method for the comparative assessment of the level of specific nucleic acid sequences in samples derived from different sources. More specifically, the invention relates to a method using oligonucleotides covalently linked to a solid support, such as beads, to isolate specific labeled nucleic acid sequences from complex mixtures. The methods disclosed allow quantitative comparisons of the amount of nucleic acid of defined sequence in a plurality of different samples of nucleic acid, e.g., from different cells or tissues or from genetic libraries. Nucleic acids from the samples are labeled in such a fashion that the signals can be distinguished and compared following hybridization to the oligonucleotides on the beads. According to the invention, the solid supports with the hybridized nucleic acid may be retrieved, and the target nucleic acid eluted and analyzed. Furthermore, the invention provides a method for tagging individual clones from a cDNA library such that they can be identified uniquely and retrieved by hybridization to specific beads.

Methods and compositions for analyzing nucleic acid molecules utilizing sizing techniques

Abstract: Tags and linkers specifically designed for a wide variety of nucleic acid reactions are disclosed, which are suitable for a wide variety of nucleic acid reactions wherein separation of nucleic acid molecules based upon size is required.

Methods for suppressing the binding of detectable probes to non-target sequences in hybridization assays

Abstract: This invention relates to methods, kits and compositions suitable for the improved detection, analysis and quantitation of nucleic acid target sequences using probe based hybridization assays. The invention is more specifically directed to methods, kits and compositions suitable for suppressing the binding of detectable nucleic acid probes or detectable PNA probes to non-target nucleic acid sequences in an assay for a target nucleic acid sequence to thereby improve the reliability, sensitivity and specificity of the assay. The methods, kits and compositions of this invention are particularly well suited to the detection and analysis of nucleic acid point mutations.

Antisense properties of peptide nucleic acid

Abstract: The hybridization properties of peptide nucleic acid (PNA) combined with its ease of synthesis and high chemical and biological stability rapidly made this molecule a very attractive lead compound for the development of antisense gene therapeutic drugs.

Method to detect mutations in a nucleic acid using a hybridization-ligation procedure

Abstract: The present invention provides a method for detecting a mutation in a nucleic acid molecule which comprises contacting the nucleic acid molecule with a probe. The probe comprises two covalently linked nucleic acid segments under conditions such that the unlinked end of each segment of the probe is capable of hybridizing with the nucleic acid molecule. This mixture is then contacted with a ligase under conditions such that the two hybridized probe segments will ligate and bind the nucleic acid molecule if the nucleic acid molecule contains the mutation. One would then determine the presence of bound nucleic acid molecule(s) and thereby detect the mutation in the nucleic acid molecule.

Oligonucleotide compositions and methods for the modulation of the expression of b7 protein

Abstract: Compositions and methods for the diagnosis, prevention and treatment of immune states and disorders amenable to treatment through modulation of T cell activation are provided. In accordance with preferred embodiments, oligonucleotides are provided which are specifically hybridizable with nucleic acids encoding B7 proteins.

Reagent and method for isolation and detection of selected nucleic acid sequences

Abstract: The invention relates to compositions and methods for rapidly detecting or isolating a target nucleic acid sequence in a polynucleotide-containing sample. The sample is exposed to a rapid pairing reagent, which contains a rapid capture component, effective to rapidly and non-selectively bind polynucleotides, and a target specific probe, effective to selectively bind the target nucleic acid sequence. Selectively disrupting the binding between the capture component and polynucleotides leaves only target sequence bound to the rapid pairing reagent.

Ribonuclease resistant rna preparation and utilization

Abstract: The present invention relates to nuclease resistant nucleic acids in general and ribonuclease resistant RNAs in particular. Methods of making and using such nucleic acids are disclosed.

Fen-1 endonucleases, mixtures and cleavage methods

Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to improved cleavage means for the detection and characterization of nucleic acid sequences. Structure-specific nucleases derived from a variety of thermostable organisms are provided. These structure-specific nucleases are used to cleave target-dependent cleavage structures, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Rapid detection and identification of nucleic acid variants

Abstract: The present invention relates to means for cleaving a nucleic acid cleavage structure in a site-specific manner. Enzymes, including 5' nucleases and 3' exonucleases, are used to screen for known and unknown mutations, including single base changes, in nucleic acids. Methods are provided which allow for the identification of genetic mutations and the identification bacterial and viral strains and species in a sample.

Devices and methods for detecting nucleic acid analytes in samples

Abstract: The invention provides devices and methods for use in detecting nucleic acid analytes in samples. The devices each include a solid support to which is bound a two-dimensional distribution or field of nucleic acid probes that each bind to a nucleic acid analyte, which is detected by use of amplification methods.

Method and kits for preparing multicomponent nucleic acid constructs

Abstract: The invention provides a highly efficient, rapid, and cost effective method of linking nucleic acid components in a predetermined order to produce a nucleic acid multicomponent construct The invention further provides nucleic acid components, each nucleic acid component comprising a double stranded nucleic acid molecule having at least one single stranded 5′ or 3′ terminal sequence, the terminal sequence having sufficient complementarity to either a terminal sequence in a separate nucleic acid component or to a sequence in a linking nucleic acid molecule so as to allow for specific annealing of complementary sequences and linkage of the components in a predetermined order Kits containing reagents required to practice the method of the invention are also provided

Hybridization and sequencing of nucleic acids using base pair mismatches

Abstract: Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

Methods and adaptors for generating specific nucleic acid populations

Abstract: The present invention relates to methods and kits for generating or analyzing nucleic acid populations or desired nucleic acid sequences based upon replication or amplification reactions. The invention comprises methods employing adaptors ligated to nucleic acids that preferentially permit replication or amplification of desired nucleic acid sequences or preferentially eliminate undesired nucleic acids from replication or amplification. The invention also comprises adaptors useful in the methods and in kits for replicating or amplifying nucleic acids. In one embodiment, the adaptors function to protect desired nucleic acids from cleavage by a restriction enzyme while other nucleic acids are cleaved. The protected, desired nucleic acids can then be preferentially replicated or amplified. Accordingly, the invention can be used for the amplification of desired nucleic acids and the effective removal of undesired nucleic acids from a population.

Comparison of methods for extraction of nucleic acid from hemolytic serum for PCR amplification of hepatitis B virus DNA sequences.

Abstract: The sensitivity of PCR for the amplification of target nucleic acid sequences in clinical diagnostics may often be reduced due to the presence of inhibitory factors. Hemolytic serum contains a number of PCR inhibitors, one of which is hemin. In this study we have found that conventional methods of DNA extraction were not sufficient for the removal of PCR-inhibitory compounds in hemolytic serum. We have therefore compared the efficiency of several commercial and noncommercial methods of nucleic acid purification from hemolytic serum samples prior to PCR amplification. Separation with the QIAamp HCV kit, dialysis with Millipore filters, and bovine serum albumin absorption were all found to be suitable extraction methods for eliminating inhibitors from hemolytic serum for PCR amplification. Using these methods we were able to detect very low levels of hepatitis B virus DNA in hemolytic serum.

Microfabrication technologies for integrated nucleic acid analysis

Abstract: X Chromosome Map at 75-kb STS Resolution, Revealing Extremes of Recombination and GC Content Ramaiah Nagaraja, Sandra MacMillan, Juha Kere, Carmela Jones, Stephanie Griffin, Matthew Schmatz, Jennifer Terrell, Michael Shomaker, Christopher Jermak, Christian Hott, Mochubeloa Masisi, Steven Mumm, Anand Srivastava, Giuseppe Pilia, Terence Featherstone, Richard Mazzarella, Sheila Kesterson, Brigid McCauley, Brian Railey, Frank Burough, Volker Nowotny, Michele D'Urso, David States, Bernard Brownstein, and David Schlessinger 210

High Affinity Nucleic Acid Ligands of Complement System Proteins

Abstract: Methods are described for the identification and preparation of high-affinity Nucleic Acid Ligands to Complement System Proteins. Methods are described for the identification and preparation of high affinity Nucleic Acid Ligands to Complement System Proteins C1q, C3 and C5. Included in the invention are specific RNA ligands to C1q, C3 and C5 identified by the SELEX method.

Chitosan related compositions and methods for delivery of nucleic acids and oligonucleotides into a cell

Abstract: Compositions of chitosan-based compounds and nucleic acid or oligonucleotide which are capable of delivery to a cell. Methods of preparation of the compositions. Methods of administering the compositions in vitro to cells in culture or in vivo to an organism.

Nucleic acid quantitation by co-amplification of target with multiple internal controls

Abstract: The present invention is related to an improved method for the quantification of nucleic acid, which can be performed with a minimal amount of nucleic acid amplification reactions. The method according to the invention for the quantification of analyte nucleic acid in a sample comprises the steps of: adding to the sample different respective amounts of different nucleic acid constructs, each construct being distinguishable from the analyte nucleic acid and capable of being co-amplified with the analyte nucleic acid; subjecting the sample to a nucleic acid amplification procedure, using amplification reagents capable of reacting with both the analyte nucleic acid and the nucleic acid constructs; detecting the relative amounts of amplificates derived from analyte nucleic acid and each nucleic acid construct; calculating the amount of analyte nucleic acid from said relative amounts. Each nucleic acid construct is different; the nucleic acid constructs can be distinguished from one another and from the analyte nuclic acid. The nucleic acid constructs do resemble each other, and the analyte nucleic acid, in that all are capable of reacting with the same amplification reagents.

Human Delta3 nucleic acid molecules

Abstract: The invention provides nucleic acid molecules which encode polypeptides having homology to proteins in the Delta family of proteins. The invention also provides vectors containing nucleic acid molecules of the invention and host cells containing the vectors.