Bio-rad Laboratories, Inc.

Life Technologies Corporation

Applied Biosystems, LLC

Digenomix Corporation

Lei Xi

Yan Wang

Stephen P Hendricks

Peter B Vander Horn

Bin Li

Marian Peris

Dennis E Prosen

Yangzhou Wang

Swati S Ranade

Keith P Bjornson

Marc Alexander Unger

David G King

David Ruff

Zhaochun Ma

Paul M Kenney

Xiaohui Wang

Roland Nagel

This specification generally relates to non-radioactive methods of detecting nucleic acid polymerase activity and methods of detecting compounds that modulate nucleic acid polymerase activity. The activity may be measured in real-time using a real-time PCR instrument.

Polymerase assay with a FRET substrate

In some embodiments, methods for ligating nucleic acid ends comprise: conducting a nucleic acid ligation reaction in the presence of at least one agent that generates a ligatable terminal 5' phosphate group by removing an adenylate group from a terminal 5&#x2032; phosphate of a nucleic acid. In some embodiments, an aprataxin enzyme can catalyze removal of an adenylate group from a terminal 5&#x2032; phosphate of a nucleic acid. In some embodiments, methods for ligating nucleic acid ends comprise: conducting a nucleic acid ligation reaction in the presence of an aprataxin enzyme under conditions suitable for ligating nucleic acid ends.

Enhanced ligation reactions

In certain embodiments, the present invention provides a way of 'digitally' marking different the alleles of different chromosomes by using a transposase to insert differently barcoded transposons into genomic DNA before further analysis. According to this method, each allele becomes marked with a unique pattern of transposon barcodes. Because each unique pattern of transposon barcodes identifies a particular allele, the method facilitates determinations of ploidy and copy number variation, improves the ability to discriminate among homozygotes, heterozygotes, and patterns arising from sequencing errors, and allows loci separated by uninformative stretches of DNA to be identified as linked loci, thereby facilitating haplotype determinations. Also provided is a novel artificial transposon end that includes a barcode sequence in two or more positions that are not essential for transposition.

Haploidome determination by digitized transposons

The present disclosure relates to methods and compositions for making paired tags and paired tag libraries.

Method of making a paired tag library for nucleic acid sequencing

This invention provides for methods of sequencing and performing polymerase reactions using an improved generation of nucleic acid polymerases. The improvement is the fusion of a sequence-non-specific nucleic-acid-binding domain to the enzyme in a manner that enhances the processivity of the polymerase.

Methods of using improved polymerases

This disclosure relates to methods of performing activation by polyphosphorolysis (APP) reactions using at least one of the polyphosphorylating agents triphosphate, polyphosphate, imidodiphosphate, thiodiphosphate (or &#x3bc;-monothiopyrophosphate), and related compounds.

Polymerization of nucleic acids using activation by polyphosphorolysis (APP) reactions

This invention provides methods and kits for performing a quantitative amplification reaction. The method employs a polymerase enzyme and an enzyme having a 3' to 5&#x2032; exonuclease activity that cleaves the 3&#x2032; oligonucleotide of the probe.

Quantitative amplification with a labeled probe and 3' to 5&#x2032; exonuclease activity

Growing community of inventors

Foster City, CA, United States of America

Lei Xi