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Sequencing-Related US Patents Granted July 16 – Aug. 5, 2008

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US Patent 7,408,051. Modified oligonucleotides and applications thereof
Inventors: Zhaochun Ma, Khairuzzaman Bashar Mullah
Assignee: Applera
 
Discloses primers containing modified nucleobases in their 3' terminal region that help reduce the formation of primer-dimers during amplification reactions. The patent also describes various methods for their use.
 

 
US Patent 7,407,757. Genetic analysis by sequence-specific sorting
Inventor: Sydney Brenner 
Assignee: Population Genetics Technologies
 
Provides methods for sorting polynucleotides from a population, based on predetermined sequence characteristics. The method can be carried out by extending a primer annealed to polynucleotides with predetermined sequence characteristics to incorporate a terminator with a capture moiety, capturing polynucleotides with extended primers by a capture agent that specifically binds to the capture moiety, and melting the captured polynucleotides from the extended primers to form a subpopulation of polynucleotides with the predetermined sequence characteristics. The method can also be carried out on a population of tagged polynucleotides, so that after a subpopulation is selected, the members of the subpopulation may be simultaneously analyzed using the unique tags on the polynucleotides to convey analytical information to a hybridization array for a readout.
 

 
US Patent 7,407,747. Method for drying dye-terminator sequencing reagents
Inventors: Kathleen Perry, Robert Ruhfel, Sandra Spurgeon, Peter Ma 
Assignee: Applera
 
Provides a dry composition, comprising a nucleotide linked to a fluorescent dye. The patent also describes a method for making a dry composition, comprising drying a solution with a nucleotide linked to a fluorescent dye. Another method is provided for performing a reaction on a nucleic acid substrate, involving a vessel containing a dried composition with a nucleotide linked to a fluorescent dye, and adding an aqueous solution and the nucleic acid substrate. A kit is provided for determining the sequence of a nucleic acid, consisting of a dry composition of a nucleotide linked to a fluorescent dye.
 

 
US Patent 7,406,385. System and method for consensus-calling with per-base quality values for sample assemblies
Inventor: Jon Sorenson 
Assignee: Applera
 
Discloses a method for evaluating a polynucleotide sequence using a consensus-based analysis approach. The sequence analysis method uses quality values for several aligned sequence fragments to identify consensus base calls and calculate associated consensus quality values. The method is applicable to resolution of single nucleotide polymorphisms, mixed-based sequences, heterozygous allelic variants, and heterogeneous polynucleotide samples.
 

 
US Patent 7,405,281. Fluorescent nucleotide analogs and uses therefor
Inventors: Yue Xu, Jeffrey Wegener, Arek Bibillo 
Assignee: Pacific Biosciences of California
 
Discloses labeled nucleotide analogs used in place of naturally occurring nucleoside triphosphates or other analogs in template-directed nucleic acid synthesis reactions and other nucleic acid reactions, and various analyses based on these, including DNA sequencing, single base identification, hybridization assays, and others.
 

 
US Patent 7,405,042. Method of extracting nucleic acid or protein using dendrimers and dendrimer-compositional substances
Inventors: Tadashi Matsunaga, Haruko Takeyama, Brandon Yoza, Kazuhisa Fukushima, Saya Satou 
Assignee: Yokogawa Electric
 
The invention relates to a method for extracting nucleic acids or proteins, in which multi-layer dendrimers are formed on the surface of fine particles, amino radicals for capturing nucleic acids or proteins are formed on the surface of these dendrimers, and nucleic acids or proteins are extracted using these amino radicals.
 

 
US Patent 7,402,671. UV excitable fluorescent energy transfer dyes
Inventor: Linda Lee 
Assignee: Applera
 
Discloses novel energy transfer dyes which can be used with shorter wavelength light sources. These dyes include a donor dye with an absorption maximum at a wavelength between about 250 to 450 nm and an acceptor dye which is capable of absorbing energy emitted from the donor dye. One of the energy transfer dyes has a donor dye which is a member of a class of dyes with a coumarin or pyrene ring structure and an acceptor dye which is capable of absorbing energy emitted from the donor dye, where the donor dye has an absorption maximum between about 250 and 450 nm and the acceptor dye has an emission maximum at a wavelength greater than about 500 nm.
 

 
US Patent 7,402,422. Systems and methods for detecting and analyzing polymers
Inventors: Martin Fuchs, John Harris, Ray Meyer 
Assignee: US Genomics
 
Describes a detection system and methods for improving its ability to recognize labels that are disposed on a polymer. Embodiments of the invention include schemes for selecting emitters and labels used within the system in a manner that allows an increase in the number of distinct labels that can be used together in a system. In other embodiments, the detection system and methods are directed to identifying portions of a detection signal that may be associated with extra labels residing within a detection zone. In other embodiments, the detection system and methods relate to using wide field imaging detectors while reducing out-of-focus noise contributions to detection signals of the system. Still other embodiments relate to the use of linear array detectors to detect labels.
 

 
US Patent 7,402,654. PHI 15 DNA polymerase
Inventors: Carl Fuller, Cuong Lam 
Assignee: GE Healthcare Bio-Sciences
 
Describes a purified recombinant DNA polymerase with high processivity and strand-displacement activity, an isolated nucleic acid that encodes the bacteriophage DNA polymerase, and a kit and method for amplifying DNA.
 

 
US Patent 7,402,390. Method of isolating nucleic acid using material positively charged at first pH and containing amino group and carboxyl group
Inventors: Kyu-youn Hwang, Joon-ho Kim, Chang-eun Yoo, Hun-joo Lee, Hee-kyun Lim; Sung-young Jeong, Jeo-young Shim
Assignee: Samsung Electronics
 
Provides a method of isolating nucleic acids from a sample. The method includes contacting the sample with a bifunctional material that contains an amino group and a carboxyl group and is positively charged at a first pH to allow binding of the nucleic acid to the bifunctional material; and extracting the nucleic acid at a second pH higher than the first pH from the complex.
 

 
US Patent 7,402,386. Global amplification using random priming by a composite primer
Inventors: Nurith Kurn, Shenglong Wang
Assignee: NuGen Technologies
 
The invention relates to the field of polynucleotide amplification. More particularly, it provides methods, compositions, and kits for the amplification of many different polynucleotide template sequences using a randomly primed RNA/DNA composite primer.

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