Other

Applera Corporation

Isis Pharmaceuticals, Inc.

Pe Corporation (ny)

Qiagen Gmbh

Perseptive Biosystems Inc.

Boehringer Mannheim Gmbh

Applied Biosystems, LLC

454 Life Sciences Corporation

Pe Corporation

Michael Egholm

Peter Eigil Nielsen

Rolf Henrik Berg

Ole Buchardt

Ole Buchardt, Deceased

Caifu Chen

James M Coull

David J Ecker

John S Kiely

Kenneth J Livak

Michael W Hunkapiller

Michael C Griffith

Niels E Mollegaard

Mohamed Y Ismail

Leif Hoejslet Christensen

Richard P Hodge

By Dorte Buchardt, Representative

Christopher John Stanley

Kim L Dueholm

Pernilla Wittung

Muthiah Manoharan

John Harris Leamon

Jesper Lohse

Kelly G Sprankle

Lawrence A Haff

Roger S Lasken

Jan Berka

William E Werner

Kenton L Lohman

Benget Norden

Claudia Chiesa

Gary James Sarkis

Gyanendra Kumar

Jonathan M Rothberg

Osama A Alsmadi

Seiyu Hosono

By Dorte Buchardt, Legal Representative

Gary Schroth

Brian Christopher Godwin

Jan Fredrik Simons

Michele Wisniewski

Rene L Myers

Zhoutao Chen

Stephen Kyle Hutchison

By Dorte Buchardt, Executor

Dorte Buchardt

Carole Bornarth

Arumugham Raghunathan

Soren Holst Sonnechsen

Sharanappa B Rajur

S B Rajur

William Bloch

William Lun Lee

Jan Fredrick Simons

Brian Desany

James Drake

Mike Todd Ronan

Disclosed are compositions and a method for amplification of nucleic acid sequences of interest. The disclosed method generally involves replication of a complex nucleic acid sample such as genomic samples using one, a few, or more primers such that, during replication, the replicated strands are displaced from the nucleic acid molecules in the sample by strand displacement replication of another replicated strand. It was discovered that highly complex nucleic acid samples can be efficiently amplified using only one or a few primers having specific nucleic acid sequences. The one or few primers are complementary to nucleic acid sequences distributed throughout nucleic acid in the sample.

Nucleic acid amplification

Binary probe and clamp compositions conduct methods for target hybridization detection. Where the probe is a substrate for exonuclease cleavage, the composition provides quantitation and detection of PCR products, by real-time and end-point measurements. Where the probe is an amplification primer, the composition provides an improved method for labelling and detection of PCR products. Probes and clamps may be labelled with fluorescent dyes, quenchers, hybridization-stabilizing moieties, chemiluminescent dyes, and affinity ligands. Clamps may be nucleic acid analogs, such as 2-aminoethylglycine PNA.

Binary probe and clamp composition and methods for target hybridization detection

The present invention provides for a method of preparing a target nucleic acid fragments to produce a smaller nucleic acid which comprises the two ends of the target nucleic acid. Specifically, the invention provides cloning and DNA manipulation strategies to isolate the two ends of a large target nucleic acid into a single small DNA construct for rapid cloning, sequencing, or amplification.

Paired end sequencing

Disclosed are compositions and methods for detecting small quantities of analytes such as proteins and peptides. The method involves associating a DNA circle with the analyte and subsequent release and rolling circle replication of the circular DNA molecule. In the method, an amplification target circle is associated with analytes using a conjugate of the circle and a specific binding molecule that is specific for the analyte to be detected. Amplification target circles not associated with the proteins are removed, the amplification target circles that are associated with the proteins are decoupled from the specific binding molecule and amplified by rolling circle amplification. The amplification is isothermic and can result in the production of a large amount of nucleic acid from each primer. The amplified DNA serves as a readily detectable signal for the analytes.

Detection method using dissociated rolling circle amplification

A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker.

Peptide nucleic acids with polyamide-containing backbones

A novel class of peptide nucleic acids are described which include a conjugate attached thereto. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker.

Peptide nucleic acid conjugates

Binary probe and clamp composition

An asynchronous thermal cycling protocol for nucleic acid amplification uses two primers with thermal melting temperatures different by about 10 to 30&#xb0; C. After the higher melting primer has annealed and polymerase mediated extension, the uncopied, single-stranded target sequence may be hybridized and detected by a probe. DNA probes may be cleaved by the exonuclease activity of a polymerase. The probe may be a non-cleaving analog such as PNA. When a probe is labelled with a reporter dye and a quencher selected to undergo energy transfer, e.g. FRET, fluorescence from the reporter dye may be effectively quenched when the probe is unbound. Upon hybridization of the probe to complementary target or upon cleavage while bound to target, the reporter dye is no longer quenched, resulting in a detectable amount of fluorescence. The second, lower-melting primer may be annealed and extended to generate a double-stranded nucleic acid. Amplification may be monitored in real time, including each cycle, or at the end point. The asynchronous PCR thermal cycling protocol can generate a preponderance of the PCR amplicon in single-stranded form by repetition at the end of the protocol of annealing and extension of the higher melting primer.

Asynchronous primed PCR

The present invention provides methods and kits for isolating one strand of a double-stranded target nucleic acid. The method capitalizes on the differences in the kinetics and thermodynamic stabilities between conventional DNA/DNA, DNA/RNA and RNA/RNA duplexes and heteroduplexes in which one strand of the heteroduplexe is a nucleobase polymer having a net positively charged or net neutral backbone, such as a PNA.

Strand displacement methods employing competitor oligonucleotides for isolating one strand of a double-stranded nucleic acid

Peptide nucleic acids and analogues of peptide nucleic acids are used to form duplex, triplex, and other structures with nucleic acids and to modify nucleic acids. The peptide nucleic acids and analogues thereof also are used to modulate protein activity through, for example, transcription arrest, transcription initiation, and site specific cleavage of nucleic acids.

Higher order structure and binding of peptide nucleic acids

Synthetic procedures for peptide nucleic acids

Peptide nucleic acid synthons

A novel class of compounds known as peptide nucleic acids, bind complementary DNA and RNA strands, and generally do so more strongly than the corresponding DNA or RNA strands while exhibiting increased sequence specificity and solubility. The peptide nucleic acids comprise ligands selected from a group consisting of naturally-occurring nucleobases and non-naturally-occurring nucleobases, including 2,6-diaminopurine, attached to a polyamide backbone, and contain alkyl amine side chains.

Peptide nucleic acids having enhanced binding affinity, sequence specificity and solubility

A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and binding affinity. The peptide nucleic acids of the invention comprise ligands selected from a group consisting of naturally-occurring nucleobases and non-naturally-occurring nucleobases attached to a polyamide backbone. Some PNAs of the invention also contain C -C alkylamine side chains.

Peptide nucleic acids having 2,6-diaminopurine nucleobases

A novel class of compounds, known as peptide nucleic acids, form double-stranded structures with one another and with ssDNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker.

Modulation of cellular transcription factor activity

Growing community of inventors

Lexington, MA, United States of America

Michael Egholm