Active Motif, Inc.

Life Technologies Corporation

Invitrogen Corporation

Sloan-Kettering Institute for Cancer Research

Centre National De La Recherche Scientifique

Molecular Biology Resources, Inc.

Chimer

Joseph M Fernandez

James P Hoeffler

Marc Nasoff

John Archdeacon

Mary Anne Jelinek

Brian Stanley Egan

Lloyd M Smith

Stewart Shuman

Corinna Herrnstadt

David A Mead

JoAnn Sekiguchi

John Comiskey

Robert Marcil

Vladimir Efimov

Dorothy Archdeacon

Oksana Chakhmakhcheva

Alla Buryakova

Mikhail Choob

Kyle Hondorp

Gilles Divita

May Catherine Morris

Jean Mery

Kyle Horndorp

Disclosed herein are compositions, methods and kits useful for epigenetic analysis based on the use of transposons that are targeted to specific regions of chromatin based on DNA-DNA interactions, protein-protein interactions, RNA-RNA interactions, and nucleic acid-protein interactions.

Targeted transposition for use in epigenetic studies

The invention provides novel methods and materials for genetic and genomic analysis using single or multiplex isolation of protein-associated nucleic acids, including transposase-assisted chromatin immunoprecipitation (TAM-ChIP) and antibody-oligonucleotide proximity ligation. These methods comprise tagging and isolating chromatin or other protein-associated nucleic acids and using antibody-oligonucleotide complexes that recognize the proteins associated with such nucleic acids.

Multiplex isolation of protein-associated nucleic acids

Methods of using microarrays to simplify analysis and characterization of genes and their function are provided. Such methods can be used to identify and characterize antibodies having binding affinity for a specific target antigen. A method of determining gene expression at the protein level by contacting an array of characterized or uncharacterized antibodies on a solid surface with one or more proteins and identifying the antibodies to which said protein(s) binds also is provided. This method can be used to compare the protein expression in two different populations of cells, such as normal cells and cancer cells or resting cells and stimulated cells. In addition, a method of determining gene expression at the protein level by contacting a microarray of nucleic acid samples derived from a variety of different sources with one or more nucleic acid probes then identifying the sample or samples to which the probe binds is provided.

Microarrays and uses therefor

The present invention provides a method of covalently joining a DNA strand to an RNA strand, a method of tagging a 5' end of an RNA molecule, a DNA-RNA molecule which has been joined in vitro by the use of a topoisomerase, a method of tagging a 5&#x2032; end of an mRNA, and a method of isolating and cloning full-length gene sequences using capped mRNA after subtraction of non-capped RNA.

Covalent joining of DNA strands to RNA strands catalyzed by vaccinia topoisomerase

The invention disclosed herein comprises methods of using microarrays to simplify analysis and characterization of genes and their function. In one aspect of the invention the methods are used to identify and characterize antibodies having binding affinity for a specific target antigen. The invention further comprises a method of determining gene expression at the protein level comprising contacting an array of characterized or uncharacterized antibodies on a solid surface with one or more proteins and identifying the antibodies to which said protein(s) binds. This method can be additionally used to compare the protein expression in two different populations of cells, such as normal cells and cancer cells or resting cells and stimulated cells. A further aspect of the invention comprises a method of determining gene expression at the protein level comprising contacting a microarray of nucleic acid samples derived from a variety of different sources with one or more nucleic acid probes then identifying the sample or samples to which the probe binds.

Microarray and uses therefor

The present invention provides a method of covalently joining a DNA strand to an RNA strand comprising (a) forming a topoisomerase-DNA intermediate by incubating a DNA cleavage substrate comprising a topoisomerase cleavage site with a topoisomerase specific for that site, wherein the topoisomerase-DNA intermediate has one or more 5' single-strand tails; and (b) adding to the topoisomerase-DNA intermediate an acceptor RNA strand complementary to the 5&#x2032; single-strand tail under conditions permitting a ligation of the covalently bound DNA strand of the topoisomerase-DNA intermediate to the RNA acceptor strand and dissociation of the topoisomerase, thereby covalently joining the DNA strand to the RNA strand. The present invention also provides a method of tagging a 5&#x2032; end of an RNA molecule. The present invention further provides a DNA-RNA molecule which has been joined in vitro by the use of a topoisomerase. The present invention also provides a method of tagging a 5&#x2032; end of an mRNA. The present invention provides a method of isolating and cloning full-length gene sequences using capped mRNA after subtraction of non-capped RNA.

Covalent joining of DNA to RNA by vaccinia topoisomerase and uses thereof

Compounds are described and claimed comprising general formula: The compounds have substituents as described herein and are useful, e.g., for their ability to bind nucleic acids and thereby effect purifications, probing techniques and gene inhibition.

Hydroxyproline/phosphono oligonucleotide analogues, methods of synthesis and methods of use

The present invention relates generally to oligonucleotide analogues that include novel protein nucleic acid molecules (PNAs), particularly monomers, dimers, oligomers thereof and methods of making and using these oligonucleotide analogues. The PNAs of the present invention are characterized as including a variety of classes of molecules, such as, for example, hydroxyproline peptide nucleic acids (HypNA), and serine peptide nucleic acids (SerNA). The invention includes monomers, homodimers, heterodimers, homopolymers and heteropolymers of these and other oligonucleotide analogues. The present invention includes methods of using these oligonucleotide analogues in the detection and separating of nucleic acid molecules, including uses that include the utilization of oligonucleotide analogues on a solid support. The present invention also includes methods for purifying or separating nucleic acids, such as mRNA molecules, by hybridization with the oligonucleotides of the present invention. The present invention also includes the use of oligonucleotides of the present invention in antisense and homologous recombination constructs and methods.

Oligonucleotide analogues, methods of synthesis and methods of use

Peptides that are useful as transfection agents are described. The peptides can facilitate the efficient cellular internalization of a broad range and size of compounds that when non-covalently complexed therewith are efficiently internalized into a cell. Advantages include but are not limited to excellent transfection efficiency, relatively low toxicity, internalization by a broad host cell spectrum, and the simplicity and cost-effectiveness that arise from not having to covalently complex the peptide with a specific molecule to be delivered. Applications include but are not limited to the delivery of diagnostics and therapeutics, as well as drug discovery, gene discovery, and the analysis and/or manipulation of other cellular and molecular biological functions. Claims are made for transfection agents, compositions of matter, including pharmaceutical compositions, reagent kits, methods of delivery, and methods of identification of additional peptides for performing and/or including in the same.

Peptide-mediated transfection agents and methods of use

Methods are described for producing recombinant DNA molecules from suitable host vectors and nucleic acids subjected to 3'-terminal transferase activity. In one embodiment, the method takes advantage of the single 3'-deoxy-adenosine monophosphate (dAMP) residues attached to the 3' termini of PCR generated nucleic acids. Vectors are prepared with recognition sequences that afford single 3'-terminal deoxy-thymidine monophosphate (dTMP) residues upon reaction with a suitable restriction enzyme. Thus, PCR generated copies of genes can be directly cloned into the vectors without need for preparing primers having suitable restriction sites therein. The invention also contemplates associated plasmid vectors and kits for implementing the methods.

Direct cloning of PCR amplified nucleic acids

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Carlsbad, CA, United States of America

Joseph M Fernandez