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Sequencing-Related US Patents Granted Sept. 3 – Oct. 14, 2008

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US Patent 7,435,794. Methods and compositions for selectively cleaving DNA containing duplex nucleic acids in a complex nucleic acid mixture, and nuclease compositions for use in practicing the same
Inventors: Sergey Lukyanov, Denis Rebrikov, Dmitriy Shagin 
Assignee: Evrogen JSC (Moscow)
 
Describes methods of selectively cleaving DNA containing duplex nucleic acids in a complex nucleic acid mixture, as well as nuclease containing compositions for use in these. A nuclease or composition of it is employed to provide for selective cleavage of DNA-containing duplex nucleic acids in a complex nucleic acid mixture. Also provided are novel duplex-stranded specific nucleases and nucleic acids encoding them. Kits for use in practicing the subject methods are also provided.
 

 
US Patent 7,435,572. Methods and compositions for DNA manipulation
Inventor: Jurate Bitinaite
Assignee: New England Biolabs
 
Provides methods and compositions for generating a single-stranded extension on a polynucleotide molecule, where the single-stranded extension has a desired length and sequence composition. The methods and compositions can be used to manipulate a DNA sequence, including introducing site-specific mutations into a polynucleotide molecule, and for cloning any polynucleotide molecule or set of joined polynucleotide molecules in a recipient molecule, such as a vector of choice.
 

 
US Patent 7,435,545. Method for sizing polynucleotides using electrophoresis with non-DNA size standards
Inventors: Zhaowei Liu, Thomas Kane 
Assignee: Applera
 
A sample polynucleotide is subjected to electrophoresis in the presence of a fluorescent compound with a first fluorescence spectrum. Detection of light of the first fluorescence spectrum is indicative of the presence of the sample polynucleotide. One or more size standards are also subjected to electrophoresis, optionally in the presence of the sample polynucleotide. If more than one size standard is used, the different size standards typically have different mobilities. The size standards are generally essentially or completely free of polynucleotides. Migration coordinates, e.g., migration times, of the sample polynucleotide and size standards are determined. A size of the sample polynucleotide can be determined using the migration coordinate of the sample polynucleotide and the migration coordinates of the size standards.
 

 
US Patent 7,432,058. Methods of labeling nucleic acids with energy transfer dyes
Inventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
Assignee: Applera
  
US Patent 7,423,140. Oligonucleotides and analogs labeled with energy transfer dyes
Inventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
Assignee: Applied Biosystems
 
Both patents provide novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye. These linkers facilitate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye.
 

 
US Patent 7,432,055. Dual phase multiplex polymerase chain reaction
Inventors: Alexander Pemov, Sergei Bavykin 
Assignee: University of Chicago Argonne
 
Describes highly specific and sensitive methods for multiplex amplification of nucleic acids on supports such as microarrays. Based on a specific primer design, methods include five types of amplification that proceed in a reaction chamber simultaneously. These relate to four types of multiplex amplification of a target DNA on a solid support, directed by forward and reverse complex primers immobilized to the support and a fifth type, pseudo-monoplex polymerase chain reaction of multiple targets in solution, directed by a single pair of unbound universal primers. The addition of the universal primers in the reaction mixture increases the yield over the traditional "bridge" amplification on a solid support by approximately ten times. Methods that provide multitarget amplification and detection of as little as 0.45-4.5x 10-12 g (equivalent to 100 to 1,000genomes) of a bacterial genomic DNA are disclosed.
 

 
US Patent 7,432,054. Method for separating and purifying a nucleic acid
Inventors: Toshihiro Mori, Yoshihiko Makino 
Assignee: Fujifilm
 
An object of the invention is to provide a method for separating and purifying a nucleic acid by adsorbing it in a test sample to a surface of a solid phase and desorbing it by washing and similar means. The invention provides a method for separating and purifying a nucleic acid of a predetermined length from a nucleic acid mixture, comprising a step of: adsorbing and desorbing a nucleic acid in the nucleic acid mixture containing nucleic acids with different lengths to and from a solid phase of an organic macromolecule with a hydroxyl group on the surface.
 

 
US Patent 7,429,468. Mutant B-type DNA polymerases exhibiting improved performance in PCR
Inventors: Harald Sobek, Bruno Frey, et al.
Assignee: Roche Diagnostics
 
The invention relates to thermostable mutants of B-type DNA polymerases with a Y-GG/A amino acid motif between the N-terminal 3'-5'-exonuclease domain and the C-terminal polymerase domain whereas the tyrosine of the Y-GG/A amino acid motif is mutated and where these mutant DNA polymerases are suitable for PCR.
 

 
US Patent 7,429,453. Detection of nucleic acid sequence differences using coupled ligase detection and polymerase chain reactions
Inventors: Francis Barany, Matthew Lubin, et al.
Assignee: Cornell Research Foundation, Board of Supervisors of Louisiana State University and Agricultural and Mechanical College, Regents of the University of Minnesota
 
The invention relates to a method for identifying a target nucleotide sequence. This method involves forming a ligation product on a target nucleotide sequence in a ligase detection reaction mixture, amplifying the ligation product to form an amplified ligation product in a polymerase chain reaction mixture, detecting the amplified ligation product, and identifying the target nucleotide sequence. Such coupling of the ligase detection reaction and the polymerase chain reaction permits multiplex detection of nucleic acid sequence differences.
 

 
US Patent 7,427,673. Labelled nucleotides
Inventors: Shankar Balasubramanian, Colin Barnes, Xiaohai Liu, Harold Swerdlow
Assignee: Illumina Cambridge
 
In the invention, a nucleoside or nucleotide molecule is linked to a detectable label via a cleavable linker group attached to the base, rendering the molecule useful in techniques using labelled nucleosides or nucleotides, such as sequencing reactions, polynucleotide synthesis, nucleic acid amplification, nucleic acid hybridization assays, single nucleotide polymorphism studies, and other techniques using enzymes such as polymerases, reverse transcriptases, terminal transferases, or other DNA modifying enzymes. The invention is especially useful in techniques that use labelled dNTPs, such as nick translation, random primer labeling, end-labeling (e.g., with terminal deoxynucleotidyltransferase), reverse transcription, or nucleic acid amplification. The molecules of the present invention are in contrast to the prior art, where the label is attached to the ribose or deoxyribose sugar, or where the label is attached via a non-cleavable linker.
 

 
US Patent 7,427,479. Methods and kits for identifying target nucleotides in mixed populations
Inventors: Achim Karger, Elena Bolchakova   
Assignee: Applera
 
Discloses ligation-based methods and kits for identifying at least two target nucleotides in a mixed population sample, that is a sample that contains or potentially contains target nucleic acid sequences from more than one source. Typically, two ligation reaction compositions are formed, ligation products are generated, and the ligation products or their surrogates are analyzed to identify target nucleotides in the mixed population sample. In certain embodiments, the target nucleic acid sequences, the ligation products, or both are amplified. In certain embodiments, multiplex amplification and/or ligation reactions are performed.
 

 
US Patent 7,425,431. Polony fluorescent in situ sequencing beads
Inventors: George Church, Jay Shendure, Gregory Porreca, Jun Zhu
Assignee: President and Fellows of Harvard College
 
Provides miniaturized, high-density, bead-based arrays as well as methods of producing and using clonal beads and producing and using miniaturized, high density, bead-based arrays.
 

 
US Patent 7,424,371. Nucleic acid analysis
Inventors: Lee Kamentsky
Assignee: Helicos Biosciences

The invention relates to analyzing nucleic acid sequence data. According to one aspect of the invention, sequences obtained from a sample are collapsed into a format that is easily compared against sequence entries in a look-up table, while preserving the informational content of the sequences. In particular, this aspect of the invention comprises collapsing homopolymer regions in sample sequences such that homopolymers are represented by a single nucleotide.

 

 
US Patent 7,423,750. Configurations, systems, and methods for optical scanning with at least one first relative angular motion and at least one second angular motion or at least one linear motion
Inventors: Jon Hoshizakim, Howard Gregg King, Johannes Sluis, Steven Boege, Mark Oldham 
Assignee: Applera
 
Provides methods and optical systems for scanning of a target sample, including methods and systems using a low mass scan head and methods and systems for conducting a scanned optically transduced assay where the scanning includes at least one first relative angular motion and at least one second angular motion or at least one linear motion. The invention also relates to methods and systems for performing sample assays, and for producing and measuring optical responses and signatures.

 
The Scan

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