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Patents of Note: Dec 22, 2009

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Sequencing-Related US Patents Granted Dec. 1 — Dec. 22

US Patent 7,635,588. Apparatus and method for differentiating multiple fluorescence signals by excitation wavelength
Inventors: Howard King, Steven Boege, Eugene Young, Mark Oldham
Assignee: Applied Biosystems

Provides an apparatus and method for differentiating multiple detectable signals by excitation wavelength. The apparatus can include a light source that can emit excitation light wavelengths or wavelength ranges towards a sample, for example in a well. The sample can contain two or more detectable markers, for example, fluorescent dyes, each of which can be capable of generating increased emissions when excited in the presence of a target component. The detectable markers can have excitation wavelength ranges or emission wavelength ranges that overlap with the ranges of the other markers. A detector can be arranged for detecting an emission wavelength or wavelength range emitted from a first marker within the overlapping wavelength range of at least one of the other markers.


US Patent 7,636,159. Time-delay integration in detection of labeled beads
Inventors: Mark Oldham, Eric Nordman, Richard Reel, John Shigeura, Janice Shigeura
Assignee: Applied Biosystems

Protects an apparatus for detecting labeled beads. The apparatus can include one or more irradiation sources for irradiating one or more detection zones, at least one detector for collecting charges corresponding to light signals emitted from labeled beads in the detection zones, and a system coupled to at least one detector for effecting time delay integration of the charges by accumulating the charges before reading them at the output of the at least one detector.


US Patent 7,635,562. Methods and devices for nucleic acid sequence determination
Inventors: Timothy Harris, Philip Buzby, Mirna Jarosz, James DiMeo, Jaime Gill
Assignee: Helicos BioSciences

The invention provides surfaces for the detection of attached molecules and methods for molecular detection using these surface chemistries. Enhanced molecular signal detection is achieved on a solid support by treating the support to simultaneously reduce background and enhance signal. The invention provides surface preparation strategies, molecule attachment strategies, and washing strategies that result in improved signal detection on a surface.


US Patent 7,635,566. Methods and compositions for isolating nucleic acid sequence variants
Inventor: Sydney Brenner
Assignee: Population Genetics Technologies

Describes methods for isolating sequence variants of a genetic locus of interest using a modified iterative primer extension method. The nucleic acids analyzed are generally single stranded and have a reference sequence that is used as a basis for performing iterative single nucleotide extension reactions from a hybridized polymerization primer. The iterative polymerization reactions are configured such that polymerization of the strand will continue if the sequence of the nucleic acid being analyzed matches the reference sequence, whereas polymerization will be terminated if the nucleic acid being analyzed does not match the reference sequence. Nucleic acid strands that have mutations can be isolated using a variety of methods and sequenced to determine the precise identity of the mutation or polymorphism. By performing the method on both strands of the nucleic acid being analyzed, virtually all possible mutations can be identified, according to the patent abstract.

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US Patent 7,635,578. Massive parallel method for decoding DNA and RNA
Inventors: Jingyue Ju, Zengmin Li, John Edwards, Yasuhiro Itagaki
Assignee: The Trustees of Columbia University in the City of New York

Provides methods for attaching a nucleic acid to a solid surface and for sequencing it by detecting the identity of each nucleotide analogue after it is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues, which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the -OH group at the 3'-position of the deoxyribose.


US Patent 7,625,706. Methods and apparatus for characterizing polynucleotides
Inventors: Mark Akeson, Daniel Branton, David Deamer, Jeffrey Sampson
Assignee: Agilent Technologies, President and Fellows of Harvard College, Regents of the University of California

Provides systems and methods for analysis of polymers, for example polynucleotides. The systems are capable of analyzing a polymer at a specified rate. One such analysis system includes a structure with a nanopore aperture and a molecular motor, such as a polymerase, adjacent to it.


US Patent 7,625,701. 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 charged-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 7,626,704. Methods and systems for simultaneous real-time monitoring of optical signals from multiple sources
Inventors: Paul Lundquist, Denis Zaccarin, Yves Lacroix, Mark Maxham, Mathieu Foquet, Stephen Turner
Assignee: Pacific Biosciences of California

Describes methods and systems for real-time monitoring of optical signals from arrays of signal sources, particularly optical signal 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 7,630,073. 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, and particularly optical signal 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.

The Scan

Booster for At-Risk

The New York Times reports that the US Food and Drug Administration has authorized a third dose of the Pfizer-BioNTech SARS-CoV-2 vaccine for people 65 and older or at increased risk.

Preprints OK to Mention Again

Nature News reports the Australian Research Council has changed its new policy and now allows preprints to be cited in grant applications.

Hundreds of Millions More to Share

The US plans to purchase and donate 500 million additional SARS-CoV-2 vaccine doses, according to the Washington Post.

Nature Papers Examine Molecular Program Differences Influencing Neural Cells, Population History of Polynesia

In Nature this week: changes in molecular program during embryonic development leads to different neural cell types, and more.