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Patents of Note: Apr 13, 2010

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Sequencing-Related US Patents Granted Jan. 27, 2010 — April 13, 2010

US Patent 7,692,783. Methods and systems for simultaneous real-time monitoring of optical signals from multiple sources
Inventors: Paul Lundquist, Denis Zaccarin, Yves Lacroix, Stephen Turner, John Dixon
Assignee: Pacific Biosciences of California

Provides methods and systems for real-time monitoring of optical signals from arrays of signal sources, particularly sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.


US Patent 7,687,236. Fluorescent nucleobase conjugates having anionic linkers
Inventors: Meng Taing, Shaheer Khan, Steven Menchen, Barnett Rosenblum
Assignee: Applied Biosystems

Describes nucleotide-dye conjugates and related compounds in which a dye is linked to a nucleobase directly or indirectly by an anionic linker. The anionic character of the linker is provided by one or more anionic moieties in the linker, such as phosphate, phosphonate, sulfonate, and carboxylate groups. When the dye is provided as a donor/acceptor dye pair, the anionic linker can be located between the donor and the acceptor, or between the nucleobase and either the donor or acceptor, or both. In one embodiment, conjugates of the invention provide enhanced electrophoretic mobility characteristics to sequencing fragments, for example for dideoxy sequencing using labeled terminators.


US Patent 7,682,809. Direct ATP release sequencing
Inventors: Jeffrey Sampson
Assignee: Agilent Technologies

Provides a method for sequencing a nucleic acid. The method includes contacting a nucleic acid template and a primer annealed to it with a reagent mix under primer extension conditions to produce an extended primer and ATP. The reagent mix may contain an adenosine-2'-deoxynucleoside tetraphosphate moiety and a polymerase. The method further includes detecting the produced ATP.


US Patent 7,682,816. Thin film coated microwell arrays and methods of using same
Inventors: Jong-Bum Kim, Steven Martin Lefkowitz, John Nobile, George Roth, Pengguang Yu
Assignee: 454 Life Sciences

The invention relates to microwell array compositions coated with one or more thin film coatings. It includes the process of fabricating and using thin film coated microwell arrays.


US Patent 7,682,791. Method of generating nested sets of double stranded DNA circles
Inventor: Stephen Macevicz
Assignee: None

Provides a method of generating nested sets of double-stranded DNA circles that may be used as size ladders in nucleic acid separations and as templates in DNA sequencing operations. It describes methods for generating nested sets of dsDNA circles in a self-sustaining enzymatic reaction, comprising the activities of at least one endonuclease, at least one single-stranded exonuclease, and at least one ligase. In another embodiment, such nested sets are generated from linear dsDNA fragments with ligatable terminators that are self-ligated to form corresponding dsDNA circles.

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US Patent 7,678,894. Nucleotide analogs
Inventor: Suhaib Siddiqi
Assignee: Helicos Biosciences

Describes nucleotide analogs and methods of their use. Analogs of the invention comprise a reporter molecule, or label, attached via the N4, N6, O4, or O6 position of the nitrogenous base portion of the analog. In a preferred embodiment, the nucleotide analogs comprise a label attached to the nitrogenous base portion of the analog via a cleavable linker at the N4, O4, N6, or O6 position.


US Patent 7,678,892. Dye-labeled ribonucleotide triphosphates
Inventors: Peter Fisher, Paolo Vatta, Shaheer Khan
Assignee: Applied Biosystems

Provides novel dye-labeled ribonucleotide analogs and methods for synthesizing them. According to the patent, the compounds of the invention are especially useful for DNA sequencing by the polymerase chain reaction.


US Patent 7,678,562. Addressable nanopores and micropores including methods for making and using same
Inventor: Xinsheng Ling
Assignee: Brown University

Features devices and systems with one or more electrically addressable solid-state nanopores for sensing and/or characterizing single macromolecules as well as sequencing DNA or RNA. The patent describes a linear or 2D electrically addressable array of nanopores, where the nanopores are located at points of intersections between V-shaped grooves formed in an upper surface of the insulating member and a V-shaped groove formed in a lower surface of the insulating member. The width and/or length of the nanopore are defined or established by sharp edges of cleaved crystals that are maintained in fixed relation during the formation of the insulating member including the nanopore.


US Patent 7,670,770. Nanochannel arrays and their preparation and use for high throughput macromolecular analysis
Inventors: Stephen Chou, Han Cao, Robert Austin, Zhaoning Yu, Jonas Tegenfeldt
Assignee: The Trustees of Princeton University

Discloses nanochannel arrays that enable high-throughput macromolecular analysis as well as methods of preparing nanochannel arrays and nanofluidic chips. The patent also describes methods of analyzing macromolecules, such as entire strands of genomic DNA, as well as systems for carrying out these methods.


US Patent 7,667,024. Oligonucleotides labeled with a plurality of fluorophores
Inventors: Fei Mao, Xing Xin
Assignee: AlleLogic Biosciences

Discloses new methods for designing labeled nucleic acid probes and primers by labeling oligonucleotides with several spectrally identical or similar dyes and optionally with one or more quencher dyes. The labeled oligonucleotides exhibit a detectable increase in signal, for example, fluorescent signal when the labeling dyes are separated from one another. Nucleic acid probes and primers of the invention have wide applications, ranging from general detection of a target nucleic acid sequence to clinical diagnostics, according to the patent.

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US Patent 7,666,593. Single molecule sequencing of captured nucleic acids
Inventor: Stanley Lapidus
Assignee: Helicos Biosciences

Provides methods and devices for detecting, enumerating, or identifying target nucleic acid molecules using immobilized capture probes and single-molecule sequencing techniques. Sequence-specific capture probes are used to isolate target nucleic acids of interest. The target population may be composed of same-sequence nucleic acids or may be a population of mixed-sequence nucleic acids.


US Patent 7,662,559. Capturing sequences adjacent to type-IIS restriction sites for genomic library mapping
Inventors: Ronald Sapolsky, Robert Lipshutz, Thomas Gingeras
Assignee: Affymetrix

Relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods described result in the "capturing" and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as markers for use in genetic mapping, screening, and manipulation.


US Patent 7,659,070. Charge switch nucleotides
Inventors: John Williams, Gregory Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi Reynolds, Pamela Sheaff
Assignee: Pacific Biosciences of California

Provides compounds, methods, and systems for sequencing nucleic acid using single-molecule detection. Using labeled nucleotides that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected, enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation without interference from unincorporated nucleotides and without illuminating the polymerase-DNA complex.


US Patent 7,658,288. Bisulfite conversion reagent
Inventors: Yafei Liu, Haley Fiske, Steven Menchen
Assignee: Applied Biosystems

Discloses a kit containing a pre-packaged bisulfite solution suitable for use in a DNA methylation analysis. The bisulfite solution comprises an aqueous deoxygenated solution of a bisulfite reagent enclosed within an oxygen-impermeable container such that the solution maintains a bisulfite concentration that is at least 90 percent of the original concentration and useable in the DNA methylation analysis reaction for a period of approximately six months after packaging.


US Patent 7,655,791. DNA amplification and sequencing using DNA molecules generated by random fragmentation
Inventors: Vladimir Makarov, Irina Sleptsova, Emmanual Kamberov, Eric Bruening
Assignee: Rubicon Genomics

Discloses methods to prepare a DNA molecule or molecules by random fragmentation. In some embodiments, this regards preparing a template for DNA sequencing by random fragmentation. The random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. A universal sequence is attached to the 3' end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase.


US Patent 7,655,443. Nucleic acid sequencing with simultaneous quantitation
Inventors: Thomas Yager, Jason August
Assignee: Siemens Healthcare Diagnostics

Describes a method for simultaneous sequencing and quantitation of a nucleic acid analyte in a sample using the same reagents for both assays. A sample containing, or suspected of containing, the nucleic acid analyte of interest is analyzed using a single set of reagents through several thermocycles to obtain a mixture of labeled polynucleotides, which are used for the determination of both sequence information about the target nucleic acid and the amount of target nucleic acid present in the sample. The fragments are separated on the basis of size, for example by electrophoresis, and the label associated with the separated fragments is detected. The positions of the separated nucleic acid fragments are evaluated to obtain information about the sequence of the target nucleic acid analyte, and the intensity of a signal derived from the label associated with one or more of the separated fragments is evaluated to determine the quantity of the target nucleic acid analyte in the sample. Only one label is needed for both sequencing and quantitation, although two or more labels may be used if bidirectional sequencing is performed.