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Sequencing-related US Patents, Granted February — March 2007

US Patent 7,189,503. Characterization of individual polymer molecules based on monomer-interface interactions. Inventors: Mark Akeson, Daniel Branton, George Church, David Deamer. Assignee: President and Fellows of Harvard College, Regents of the University of California.
Protects a method for detecting a double-stranded region in a nucleic acid. The method uses two separate, adjacent pools of a medium and an interface between the two pools. The interface has a channel that allows sequential monomer-by-monomer passage of a single-stranded nucleic acid, but not of a double-stranded nucleic acid, from one pool to the other pool. A nucleic acid polymer is placed in one of the two pools, and each of the nucleotide monomers of the single-stranded nucleic acid polymer passes through the channel “so as to differentiate between nucleotide monomers that are hybridized to another nucleotide monomer before entering the channel and nucleotide monomers that are not hybridized to another nucleotide monomer before entering the channel,” according to the patent abstract.

US Patent 7,188,030. Automatic threshold setting for quantitative polymerase chain reaction. Inventors: Lesley Ward, Adrian Jensen, Justin Lyon, Cameron McLeman, Bryan Tysinger. Assignee: Applera.
Covers systems and methods for identifying and quantifying the presence of one or more DNA species in a sample population through PCR amplification. The method determines a threshold fluorescence value that is used in the assessment of the PCR amplification reaction. Various embodiments of the invention incorporate an enhancement function useful in selecting appropriate threshold fluorescence values and facilitating the determination of DNA concentrations by quantitative PCR-based methodologies, according to the patent abstract.

US Patent 7,183,056. Method for performing multiplex PCR with cyclic changes of PCR parameters. Inventors: Se Ho Park, Hae Sik Yang, Dae Sik Lee, Yong Beom Shin, Kyu Won Kim, Tae Hwan Yoon, Sung Jin Kim, Yun Tae Kim. Assignee: Electronics and Telecommunications Research Institute, Korea.
Protects an improved multiplex PCR method for obtaining at least two PCR products from one PCR solution. In the method, the primer annealing temperature and the extension time are changed per cycle with constant periods. According to the patent abstract, the method eliminates “limitations in determining PCR conditions due to various sizes of PCR products or dimers” and reduces the time required for determining the PCR conditions for various samples.

US Patent 7,179,905. Nucleic acid labeling compounds. Inventors: Glenn McGall, Anthony Barone. Assignee: Affymetrix.
Protects nucleic acid labeling compounds containing heterocyclic derivatives. The compounds are synthesized by condensing a heterocyclic derivative with a cyclic group, such as a ribofuranose derivative. The labeling compounds are “suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection,” according to the patent abstract.

US Patent 7,179,602. Methods for sequencing GC-rich and CCT repeat DNA templates. Inventor: Donna Robinson. Assignee: Los Alamos National Security.
Covers a PCR-based method of cycle-sequencing DNA and other polynucleotide sequences having high CG content and regions of high GC content, including DNA strands with a high cytosine and/or guanosine content and repeated motifs such as CCT repeats.

US Patent 7,176,003. Method for determining the length of a nucleic acid molecule. Inventors: David James Squirrell, Martin Alan Lee. Assignee: The Secretary of State for Defence, UK.
Protects a method of determining the length of a particular region within a nucleic acid. The method first subjects a sample of the nucleic acid to amplification reactions, in which the time of the extension phase in each of the reactions is varied. It then monitors the progress of the amplification reactions and determines the minimum time during which the extension phase of the amplification is completed within each reaction mixture and relates that to the length of the sequence undergoing extension. The method, combined with melting point analysis, will allow the percentage GC content of a sequence to be determined, according to the patent abstract.

US Patent 7,176,002. Universal-tagged oligonucleotide primers and methods of use. Inventors: Kai Qin Lao, Caifu Chen, Ryan T. Koehler, Charles Scafe, Gary Schroth. Assignee: Applera.
Protects universal-tagged oligonucleotide primers and methods of using the primers for amplifying the genome.

US Patent 7,175,750. System and method for temperature gradient capillary electrophoresis. Inventors: Zhiyong Guo, Zhaowei Liu, Qingbo Li. Assignee: SpectruMedix.
Protects a method for determining the presence of a mutation in a sample comprising nucleotides. The sample and a reference sample that contains reference nucleotides are subjected to electrophoresis in the presence of at least one intercalating dye. During electrophoresis, the temperature of the first sample and the reference sample is changed by an amount “sufficient to change an electrophoretic mobility of at least one of the first or reference nucleotides,” according to the patent abstract. Fluorescence intensity data are then used to indicate the presence of the first and reference nucleotides. At least one of the first sample or reference samples comprises products resulting from PCR.

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