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Sequencing-Related US Patents, Granted April – May 2007

US Patent 7,223,568. Methods for determining nucleotide sequences of single nucleic acid molecules. Inventors: Tamotsu Kondow, Fumitaka Mafune, Yoshihiro Takeda. Assignee: Toyota Jidosha, Genesis Research Institute.
Protects a method for determining a nucleotide sequence of a nucleic acid by detecting a single dye molecule. According to the patent claims, users first immobilize a nucleic acid molecule onto the surface of a solid and then anneal a primer to the nucleic acid molecule. The primer has a sequence complementary to a part of a sequence of the nucleic acid molecule. A solution containing a DNA polymerase and only one type of dye-labeled dNTP, where N is A, T or U, G or C, or an RNA polymerase and only one type of dye-labeled NTP, where N is A, U, G or C, is provided, and the dye-labeled dNTP or NTP reacts with the 3' end of the primer so that the dye-labeled dNTP or NTP forms a base pair with a base in the nucleic acid molecule. The sequence of the nucleic acid molecule is determined based on the types of the sequentially bound dNTPs or NTPs.

US Patent 7,223,326. Capillary electrophoresis system. Inventors: Takashi Anazawa, Takashi Irie, Masao Kamahori. Assignee: Hitachi.
Protects a capillary electrophoresis system that includes capillaries arranged in parallel on a vertical plane at an identical distance from each other, each of which has a sample injection end immersed in a cathode buffer and pointed downward vertically to facilitate connection between the cathode buffer and a sample solution.

US Patent 7,222,059. Electrophoretic trace simulator. Inventors: Alexandre Izmailov, Thomas Yager. Assignee: Siemens Medical Solutions Diagnostics.
The patent describes a method for creating a simulated electrophoretic trace for use in sequencing a sample polynucleotide sequence. Users first obtain an input file with a base sequence comprising a string of letters (A, C, G and/or T) in an order corresponding to the input base sequence, and then modify the input file using one or more functions to take into account perturbations associated with changes in peak intensity as a function of base number; peak shape as a function of base number; peak skew; spacing between peaks; background; noise; spectral cross-talk; instrumental effects and/or gel electrophoresis effects to produce a modified file representing a simulated electrophoretic trace.

US Patent RE39,663. Electron-deficient nitrogen heterocycle-substituted fluorescein dyes. Inventors: Krishna Upadhva, Steven Menchen, Weiguo Zhen. Assignee: Applera.
Protects electron-deficient nitrogen heterocycle-substituted fluorescein dyes and methods in which the dyes are conjugated to substrates and used as detection labels in molecular biology experiments. The electron-deficient nitrogen heterocycles include pyridine, quinoline, pyrazine, and the like. Substrates include polynucleotides, nucleosides, nucleotides, peptides, proteins, carbohydrates, and ligands. According to the inventors, the fluorescent detection methods described in the patent are useful for automated DNA sequencing, oligonucleotide probe methods, detection of polymerase-chain-reaction products, immunoassays, and other applications.

US Patent 7,220,549. Stabilizing a nucleic acid for nucleic acid sequencing. Inventors: Philip Richard Buzby. Assignee: Helicos BioSciences.
Protects methods for sequencing a nucleic acid that include stabilizing a primer/target nucleic acid duplex on a substrate. Methods of the invention “generally contemplate the use of a dual-anchored primer/target nucleic acid duplex, or a stabilizing molecule in a single molecule sequencing reaction,” according to the patent abstract.

US Patent 7,220,543. Method and support for biological analysis using oligonucleotides comprising a marker capable of enzymatic activation. Inventors: Jean-Luc Decout, Marc Fontecave, Ce Dueymes. Assignee: Commissariat a l'Energie Atomique.
Covers a method for analyzing biological targets of DNA or RNA in which the difference between two signals indicates the presence of complementary targets of oligonucleotide probes. “This support and method find applications in numerous areas, in particular in biology for sequencing genomes, the search for mutations, the development of new medicinal products, etc,” according to the patent claims.

US Patent 7,214,783. Universal bases for nucleic acid analyses, methods for using universal bases, and kits comprising universal bases. Inventors: Geunsook Jeon, Shaheer Khan. Assignee: Applera.
Covers compounds, methods, and kits for making and analyzing primer extension products that incorporate one or more universal bases, including methods and kits for nucleic acid sequencing and microsatellite analysis.

US Patent 7,211,390. Method of sequencing a nucleic acid. Inventors: Jonathan Rothberg, Joel Bader, Scott Dewell, Keith McDade, John Simpson, Jan Berka, Christopher Colangelo. Assignee: 454 Life Sciences.
Protects methods and apparatuses for sequencing a nucleic acid. In one aspect, the method includes “annealing a population of circular nucleic acid molecules to a plurality of anchor primers linked to a solid support, and amplifying those members of the population of circular nucleic acid molecules which anneal to the target nucleic acid, and then sequencing the amplified molecules by detecting the presence of a sequence byproduct such as pyrophosphate,” according to the patent abstract.

US Patent 7,211,382. Primer extension using modified nucleotides. Inventors: Xiaodong Zhao, Craig Gelfand, Rolf Swenson.
Protects methods and compositions that reduce target-independent primer extension or enhance template-dependent primer extension. The methods are useful in PCR, nucleic acid sequencing, genotyping, and other applications that employ primer extension, according to the patent abstract.

US Patent 7,211,184. Capillary electrophoresis devices. Inventors: James Russell Webster, Yuan-Fong Kuo, Shao-Tsu Wang, Chun-Hsien Lee. Assignee: AST Management.
The patent describes a capillary electrophoresis and a process for fabrication of the device. The device includes a series of reservoirs for loading a sample, and rows of grooves transversely defined to be connected with the reservoirs for receiving a capillary electrophoresis chip. The chip comprises a straight main separation channel, an injection channel, and sample transport channels “in liquid communication with the reservoirs,” according to the patent abstract.

The Scan

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.