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US Patent 7,513,984. Capillary array electrophoresis apparatus
Inventors: Ryoji Inaba, Satoshi Takahashi, Miho Ozawa, Yoshitaka Kodama
Assignee: Hitachi

Describes an apparatus where an irradiating laser beam is positioned on the side face of an capillary array, and the optical axis of the laser beam is inclined in vertical direction with respect to a plane face formed by the capillary array. Reflection light by the capillary array and returning light is thus prevented from entering into a laser beam source, so instability of laser oscillation is eliminated.


US Patent 7,511,811. Pulsed-multiline excitation for color-blind fluorescence detection
Inventors: Graham Scott, Carter Kittrell, Robert Curl, Michael Metzker
Assignee: Baylor College of Medicine and Rice University

Describes a technology called pulsed-multiline excitation, or PME, that provides a novel approach to fluorescence detection, with application for high-throughput identification of informative SNPs. The PME technology has two main advantages that significantly increase fluorescence sensitivity, according to the patent abstract: optimal excitation of all fluorophores in the genomic assay; and "color-blind" detection, which collects more light than standard wavelength resolved detection. This technology differs significantly from current state-of-the-art DNA sequencing instrumentation, which features single source excitation and color dispersion for DNA sequence identification, the abstract states.


US Patent 7,511,285. Methods and apparatus for biomolecule identification
Inventor: Jonathan Bernstein
Assignee: The Charles Stark Draper Laboratory

Describes an apparatus and methods that provide improved-resolution, high-throughput biomolecule identification by exciting sub-wavelength regions of biomolecules drawn through a microfluidic channel.


US Patent 7,504,505. Synthetic nanopores for DNA sequencing
Inventors: Devanand Shenoy, Enrico Dalcanale, Sander Willems, Marco Busi
Assignee: The US of America as represented by the Secretary of the Navy, Washington, DC

Discloses a compound of a certain composition and methods for making it. The invention is related to cyclic oligomeric compounds. The approach disclosed can utilize robust, synthetic organic nanopores to replace proteinaceous ion pores currently used for studying DNA translocation. The interaction forces between the translocating molecule and the organic nanopore may be tuned by engineering the pore to achieve single-base-pair resolution.


US Patent 7,504,496. Water-soluble rhodamine dye conjugates
Inventors: Linda Lee, Ronald Graham, William Werner, Elana Swartzman, Lily Lu
Assignee: None

Provides novel, water-soluble, red-emitting fluorescent rhodamine dyes and red-emitting fluorescent energy-transfer dye pairs, as well as labeled conjugates comprising the same and methods for their use. The dyes, energy-transfer dye pairs, and labeled conjugates are useful in a variety of aqueous-based applications, particularly in assays involving staining of cells, protein binding, and/or analysis of nucleic acids, such as hybridization assays and nucleic acid sequencing.


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US Patent 7,504,261. Method for highly sensitive nucleic acid detection using nanopore and non-specific nucleic acid-binding agent
Inventors: Kui-hyun Kim, Jun-hong Min, In-ho Lee, Ah-gi Kim
Assignee: Samsung Electronics

Provides a method for the sensitive detection of nucleic acids in a nucleic acid sample. The nucleic acid sample is contacted with a non-specific nucleic acid binding agent in an electrically conductive fluid medium, the sample is contacted with a nanopore, a voltage is applied to the nanopore, and current change through the nanopore is monitored. The nucleic acid can be detected with high sensitivity because a change in current amplitude through the nanopore is greater than when nucleic acid detection is performed without using an intercalator.


US Patent 7,501,254. Methods and compositions for amplification and capture of nucleic acid sequences
Inventor: Daniel Shoemaker
Assignee: GHC Technologies

Provides methods for the amplification and capture of nucleic acid sequences. A forward primer is annealed to a DNA or RNA template in a first reaction vessel including fewer than four different dNTPs; an extended primer is formed that terminates when an omitted dNTP is required for further extension; the extended primer is released and exponentially amplified in a second reaction vessel that includes a reverse primer, four different dNTPs, and a capture probe that includes n oligonucleotides with fewer than n locking nucleic acids; and one of the extended primers is captured concurrently with a capture probe while the extended primer is amplified. The steps of annealing, extending, and releasing can occur at a first reaction temperature that is substantially isothermal and in the absence of a helicase. The steps of exponentially amplifying and capturing can occur at a second reaction temperature that is substantially isothermal.


US Patent 7,501,245. Methods and apparatuses for analyzing polynucleotide sequences
Inventors: Stephen Quake, Emil Kartalov
Assignee: Helicos BioSciences

The patent claims a surface for nucleic acid sequencing, comprising several chemical layers. A polyethylene glycol layer is positioned between a polydimethylsiloxane layer and a polyelectrolyte multilayer, and a nucleic acid linkage layer attaches a nucleic acid layer to a polyelectrolyte multilayer.


US Patent 7,501,240. Method for bisulfite treatment
Inventors: Christian Birkner, Christine Markert-Hahn, Herbert von der Eltz
Assignee: Roche Molecular Systems

The invention is related to the detection of a methylated cytosine in a nucleic acid, where guanidinium hydrogen sulfite is used for the preparation of a solution containing guanidinium ions and sulfite ions and subsequent modification of the nucleic acid. In the process, a non-methylated cytosine is converted to uracil. The invention also discloses kits for performing the methods.


US Patent 7,501,252. Use of predetermined nucleotides having altered base pairing characteristics in the amplification of nucleic acid molecules
Inventors: David Schuster, Ayoub Rashtchian
Assignee: Life Technologies

Provides improved methods for amplifying a nucleic acid molecule, using primers with equivalent priming efficiency.

The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.