Roche Sequencing Solutions, Inc.

Roche Nimblegen, Inc.

Thomas J Albert

Victor I Lyamichev

Jigar Patel

Frank Bergmann

Michael Schraeml

Wojtek Steffen

Roland D Green

Thomas Streidl

Matthew Rodesch

Todd Richmond

Tobias Oelschlaegel

Jason Norton

Mohamed Yosry Hassan Mohamed

Steven W Smith

Mark McCormick

Eric Sullivan

Emile Nuwaysir

Ryan Bannen

Jeffrey Jeddeloh

Jacob Kitzman

Mark D'Ascenzo

Christina Middle

Michael Molla

Steve Smith

Roland Green

In one aspect, the present disclosure provides a system and method for the identification and characterization of a transglutaminase. Further, the present disclosure provides transglutaminase enzymes for forming isopeptide bonds, methods of forming isopeptide bonds in the presence of transglutaminases, and substrate tags for use with transglutaminases. In another aspect, the present disclosure provides glutamine-containing substrates (or Q-tag substrates) that are more resistant to proteases/clipping and therefore, more stable, than other Q-tag substrates, and their uses in substrate tags for cross-linking to an amine-donor tag via an isopeptide bond mediated by a microbial transglutaminase.

System and method for identification and characterization of transglutaminase species

According to one aspect, the present disclosure provides a method of identifying a substrate of a transglutaminase using a peptide array comprising a plurality of peptides. The method includes the steps of contacting the peptides in the peptide array with the transglutaminase, allowing the transglutaminase to bind to the peptides, and identifying the substrate of the transglutaminase.

Identification of transglutaminase substrates and uses therefor

The invention comprises systems, methods and arrays for identification and optimization of novel peptide binders to protein targets. Embodiments include steps of peptide binder discovery, core peptide maturation, N-terminal and C-terminal extension and kinetics analysis of the final peptide binder.

Systematic discovery, maturation and extension of peptide binders to proteins

The present invention provides methods and systems for the capture and enrichment of target nucleic acids and analysis of the enriched target nucleic acids. In particular, the present invention provides for the enrichment of targeted sequences in a solution based format.

Methods and systems for solution based sequence enrichment

In one aspect, the present disclosure provides a system and method for the identification and characterization of a transglutaminase. Further, the present disclosure provides transglutaminase enzymes for forming isopeptide bonds, methods of forming isopeptide bonds in the presence of transglutaminases, and substrate tags for use with transglutaminases.

The invention provides novel peptide binders for streptavidin (SA), Taq polymerase and several human proteins: Prostate Specific Antigen (PSA), thrombin, Tumor Necrosis Factor Alpha (TNF&#x3b1;), and Urokinase-type Plasminogen Activator (uPA).

Specific peptide binders to proteins identified via systematic discovery, maturation and extension process

The present invention provides methods and compositions for the enrichment of target nucleic acids in a microarray system. In particular, the present invention provides methods and compositions for uniform enrichment of target nucleic acid molecules in a microarray format. The present invention also provides for intentionally non-uniform enrichment among target nucleic acid molecules.

Methods and systems for uniform enrichment of genomic regions

The present invention is a method to assist in the identification of single nucleotide polymorphisms (SNP) from microarray hybridization data. Data from hybridization protocols run on microarrays often have variations in the data resulting from variations in hybridization conditions and efficiencies and variations in optical intensities. An algorithm is described to screen the results to identify those data points most likely to be real SNPs as opposed to variations in the hybridization or sensing data.

Computer software to assist in identifying SNPS with microarrays

The present invention provides a method of amplifying target DNA by PCR or multiplex PCR on a microarray using array-immobilized DNA probes synthesized in a common area on the microarray by a maskless array synthesizer (MAS). The MAS constructed array-immobilized DNA probes include a universal primer linked to a sequence-specific probe, and optionally a calibrated probe for use in quantifying amplified target DNA.

Method of performing PCR amplification on a microarray

The present invention provides a microarray for multiple sample analysis that does not require an alignment of well walls with corresponding probe sets. Methods for building and using such a microarray are also within the scope of the present invention.

Microarrays and method for running hybridization reaction for multiple samples on a single microarray

The present invention is a method for synthesizing microarrays having different oligonucleotides present within one feature area of the array. The method utilizes the techniques common to microarray synthesis, but limits the duration in which selected feature areas on the array are initially dosed with light so as to only deprotect a calculated ratio of the compounds forming the array's binding layer. The compounds initially deprotected are capped with a non-photosensitive protecting group, such as di-methoxy-trityl, to inhibit their involvement in the synthesis of a first group of DNA strands built onto the array. Once the first group of DNA strands have been synthesized, the original deprotected group may then be further processed to build one or more groups of DNA strands in the same feature area as the first group of DNA strands. The present invention also includes microarrays manufactured using the method.

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Madison, WI, United States of America

Thomas J Albert