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Sequencing-Related US Patents Granted April 2 – May 13, 2008

US Patent 7,371,851. Methods of cloning and producing fragment chains with readable information content
Inventor: Preben Lexow
Assignee: Complete Genomics
Provides a method for attaching a nucleic acid fragment to a second nucleic acid molecule using adapters to mediate the binding, particularly in methods of cloning and producing fragment chains with a readily readable information content.

US Patent 7,371,533. Methods for separation of polymeric compounds
Inventors: Gary Slater, Laurette McCormick, Annelise Barron, Robert Meagher
Assignee: University of Ottawa, Northwestern University
End-Labeled Free Solution Electrophoresis, or ELFSE, has proven successful for DNA sequencing. However, the importance of the ends of the polymers in determining their overall mobility was neglected in previous work. This invention determines that this "end effect" critically impacts the behavior of polymers and charged-uncharged polymer conjugates during electrophoresis. It provides for methods that exploit this "end effect" for the separation of polymeric molecules on the basis of size, including, for example DNA separation and sequencing techniques.

US Patent 7,371,532. Method and apparatus for determining base sequence of nucleic acid molecule
Inventors: Takayoshi Mamine; Atsumi Tsujimoto; Takuro Yamamoto
Assignee: Sony
Discloses a method and apparatus for determining the base sequence of a nucleic acid molecule by cleaving molecule of interest while controlling the cleavage site, measuring the change in mass which occurs after the cleavage step, and acquiring the base information of the cleaved molecule from the data about the change in mass.

US Patent 7,371,531. Use of an extraction control in a method of extracting nucleic acids
Inventors: Tobin Hellyer, Thomas Fort, Ray McMillian
Assignee: Becton Dickinson
Relates to a method for effective extraction of nucleic acid from a biological sample. The method is able to distinguish between possible defects in the extraction of nucleic acid and possible defects in a subsequent amplification step. It also relates to a packaged array for extracting nucleic acid from a biological sample.

US Patent 7,371,526. Method and materials for bisulfite conversion of cytosine to uracil
Inventors: Gerald Zon, Victoria Boyd
Assignee: Applera
Provides methods and materials for conversion of cytosine to uracil. In some embodiments, a nucleic acid, such as genomic DNA, is reacted with at least one bisulfite salt of a certain formula under conditions effective to convert at least one cytosine nucleobase to a uracil nucleobase. In another embodiments, the reacting is performed optionally in the presence of a polyamine catalyst and/or a quaternary amine catalyst. Also provided are kits that can be used to carry out these methods.

US Patent 7,368,239. Method and materials for polyamine catalyzed bisulfite conversion of cytosine to uracil
Inventors: Gerald Zon, Victoria Boyd
Assignee: Applera
Provides methods and materials for conversion of cytosine to uracil. In some embodiments, a nucleic acid, such as genomic DNA, is reacted with bisulfite and a polyamine catalyst, such as a triamine or tetra-amine. Optionally, the bisulfite comprises magnesium bisulfite. In other embodiments, a nucleic acid is reacted with magnesium bisulfite, optionally in the presence of a polyamine catalyst and/or a quaternary amine catalyst. Also provided are kits that can be used to carry out these methods.

US Patent 7,371,520. Methods and apparati using single polymer analysis
Inventors: Xiaojian Zhao, Jeffrey Randall, Bijit Kundu, Jessica Kesty, Steve Gullans, Eugene Chan, Martin Fuchs
Assignee: US Genomics
The invention relates to methods for analyzing and characterizing single polymers, such as nucleic acid molecules. In preferred embodiments, the single molecules are analyzed by single molecule detection and analysis systems. The new approach is advantageous since the amplification process is known to introduce artifacts, for example sequence errors, into the amplified product that were not present in the parent molecule.

US Patent 7,365,187. DNA amplification method and kit therefor
Inventors: Satoshi Hashiguchi, Ken Inose
Assignee: Arkray
The method comprises a PCR reaction using a sense primer and an antisense primer. The reaction is performed in the presence of an additional sense primer comprising the sense primer and an oligo with a first additional sequence and ligated to the 5' end of the sense primer, and an additional antisense primer comprising the antisense primer and an oligo  with a second additional sequence complementary to the first additional sequence and ligated to the 5' end of the antisense primer. The Tm value of the additional sequences is lower than Tm values of the sense primer and the antisense primer. The annealing temperature in the PCR is initially set to be a temperature at which the additional sequences do not anneal and changed in the course of the PCR reaction to a temperature at which the additional sequences anneal to each other.

US Patent 7,364,857. Method of purifying nucleic acid using silver nanoparticles
Inventors: Yoon-kyoung Cho, Sook-young Kim, Jin-tae Kim, Kyu-sang Lee
Assignee: Samsung Electronics
Provides a method of purifying a target substance using silver nanoparticles. The method involes mixing a sample containing molecules with a thiol group with the silver nanoparticles to obtain a complex of the molecules, and isolating and removing the complex from the mixture. By using the purification method, PCR-amplifiable DNAs can be rapidly purified, and thus, the method can be very efficiently applied to lab-on-chip procedures.

US Patent 7,364,854. Nucleotide mixture for improved nucleic acid amplification performance
Inventors: Brian Washburn, Douglas Lovern, Hwa-Tang Thomas Wang, Lawrence Burg
Assignee: BioMerieux
The invention relates to a modification of the amplification buffer used in amplification reactions. The modifications result in a significant improvement in results. In particular, the invention provides methods and buffers for performing an amplification reaction using a buffer comprising nucleotide triphosphates and treating the buffer to substitute a portion of the nucleotide triphosphates with nucleotide diphosphates.

US Patent 7,364,851. Nucleic acid sequencing by Raman monitoring of uptake of precursors during molecular replication
Inventors: Andrew Berlin, Steven Kirch, Gabi Neubauer, Valluri Rao, Mineo Yamakawa
Assignee: Intel
Discloses methods, compositions, and an apparatus for nucleic acid sequence determination. The methods involve isolation of one or more nucleic acid template molecules and polymerization of a nascent complementary strand of nucleic acid, using a DNA or RNA polymerase or similar synthetic reagent. As the nascent strand is extended one nucleotide at a time, the disappearance of nucleotide precursors from solution is monitored by Raman spectroscopy or FRET. The nucleic acid sequence of the nascent strand, and the complementary sequence of the template strand, may be determined by tracking the order of incorporation of nucleotide precursors during the polymerization reaction. Certain embodiments concern an apparatus comprising a reaction chamber and detection unit, of use in practicing the claimed methods. The methods, compositions, and apparatus are of use in sequencing very long nucleic acid templates in a single sequencing reaction.

US Patent 7,361,489. Nucleic acid amplification methods
Inventors: David Zhang, Wandi Zhang, Jizu Yi
Assignee: Mount Sinai School of Medicine of New York University
The invention relates to assays and kits for carrying out assays for the rapid, automated detection of infectious pathogenic agents and normal and abnormal genes. The invention further relates to methods for general amplification of genomic DNA and total mRNAs and for analyzing differential mRNA expression using the amplification methods disclosed.

US Patent 7,361,466. Nucleic acid analysis using terminal-phosphate-labeled nucleotides
Inventors: Jonas Korlach, Watt Webb, Michael Levene, Stephen Turner, Harold Craighead, Mathieu Foquet
Assignee: Cornell Research Foundation
Relates to a method of sequencing a target nucleic acid molecule with several bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. Several labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

US Patent 7,361,259. Capillary array and electrophoresis apparatus, and method
Inventors: Johan Goudberg, Syouzou Kasai
Assignee: Applera
Provides a capillary electrophoresis device, including a capillary array, and a method of manufacturing the capillary array. During the manufacture, several capillaries are arranged in a substantially parallel arrangement and are fixed with a fixing member, to form a ribbon-shaped member, on which a detection cell can be arranged. The capillary array can achieve uniform heat dissipation, thereby allowing electrophoretic velocity to be independent of the temperature characteristics of the capillaries. The capillaries are not attracted or repelled to each other by way of electrostatic effects during electrophoresis, and the productivity of the capillary array can be improved.

US Patent 7,361,465. Methods and compositions for tailing and amplifying RNA
Inventors: George Murphy, Penn Whitley 
Assignee: Applera
Provides methods and compositions that enable tagging and amplification of targeted RNA molecules. A targeted RNA molecule is any non-polyadenylated RNA molecule including, for example, miRNA, siRNA, rRNA, tRNA, synthetic RNA, or non-polyadenylated mRNA such as mRNA from bacteria. In certain aspects, the invention provides methods and compositions for the genome-wide expression analysis of bacterial genes. Significantly, the methods enable genome-wide expression analysis in circumstances where bacterial numbers were previously too low to purify adequate amounts of RNA for DNA microarray analysis or other applications. Such methods are particularly useful for the study of bacterial gene expression during host-cell infection. The invention also provides kits for tagging and amplifying targeted RNA molecules.

US Patent 7,354,742. Method for generating amplified RNA
Inventors: Fredrik Kamme, Jessica Zhu
Assignee: Ortho-McNeil Pharmaceutical
The invention provides a new method for producing amplified RNA from a selected set of cells. This method combines and utilizes known methods in a novel way to produce the gene expression profiles. The methods of the invention utilize thermostable DNA polymerases and RNase H to produce high-fidelity second strand synthesis of nucleic acids from selected cells in a highly efficient manner and in substantially reduced time.

US Patent 7,354,717. Methods and kits for amplification of RNA sequences using composite primers
Inventors: Nurith Kurn
Assignee: Nugen Technologies
Provides methods for isothermal amplification of RNA. The methods are particularly suitable for amplifying several RNA species in a sample. The methods employ a composite primer, a second primer, and strand displacement to generate multiple copies of DNA products comprising sequences complementary to an RNA sequence of interest. In another aspect, the methods employ a single primer, which is a composite primer, and strand displacement to generate multiple copies of DNA products comprising sequences complementary to an RNA sequence of interest. In some embodiments, a transcription step is included to generate multiple copies of sense RNA of an RNA sequence of interest. The methods are useful for preparation of nucleic acid libraries and substrates for analysis of gene expression of cells in biological samples. The invention also provides compositions and kits for practicing the amplification methods, as well as methods which use the amplification products.

US Patent 7,355,216. Fluidic nanotubes and devices
Inventors: Peidong Yang, Rongrui He, Joshua Goldberger, Rong Fan, Yiying Wu, Deyu Li, Arun Majumdar
Assignee: The Regents of the University of California
Describes fluidic nanotube devices in which a hydrophilic, non-carbon nanotube has its ends fluidly coupled to reservoirs. Source and drain contacts are connected to opposing ends of the nanotube, or within each reservoir near the opening of the nanotube. The passage of molecular species can be sensed by measuring current flow (source-drain, ionic, or combination). The tube interior can be functionalized by joining binding molecules so that different molecular species can be sensed by detecting current changes. The nanotube may be a semiconductor, wherein a tubular transistor is formed. A gate electrode can be attached between source and drain to control current flow and ionic flow. By way of example, an electrophoretic array embodiment is described, integrating MEMs switches. A variety of applications are described, such as nanopores, nanocapillary devices, nanoelectrophoretic, DNA sequence detectors, immunosensors, thermoelectric devices, photonic devices, nanoscale fluidic bioseparators, and imaging devices.

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.