Applied Biosystems, LLC

The Perkin-elmer Corporation

Applera Corporation

California Institute of Technology

Other

Perkin-elmer Corporation, Applied Biosystems, Inc.

Applera Coporation

Steven Fung

Sam L Woo

Steven Menchen

Paul D Grossman

Emily S Winn-Deen

Charles R Connell

Linda G Lee

N Davis Hershey

Vergine Chakerian

Lloyd M Smith

Hongye Sun

Robert J Kaiser, Jr

Richard P Haugland

Sergei M Gryaznov

B John Bergot

Emily S Win-Deen

J Scott Eadie

A method for sequencing a nucleic acid template includes forming a nanowire assembly including a semiconductor nanowire and a probe covalently bound to the semiconductor nanowire; contacting the nanowire assembly with a template nucleic acid; contacting the nucleic acid duplexes with an extension nucleic acid, the extension nucleic acid joined to the probe; disrupting the nucleic acid duplexes; and measuring an electrical characteristic of a nanowire assembly of the set of nanowire assemblies.

Nanowire-based system for analysis of nucleic acids

System for detection and/or analysis of nucleic acids using nanowires to detect covalent modification of nucleic acids.

A system and method for analyzing nucleic acids is presented herein. The system can include a nanowire assembly including a plurality of nanowires. In some embodiments, at least two nanowires can be coupled to a different probe corresponding to a different sequence version of a polymorphism. The system can include a reagent delivery system capable of delivering a template polymorphic nucleotide, an extension nucleic acid, and an enzyme to the nanowire assembly. The system can include an electrical detector configured to measure an electrical characteristic of the nanowire assembly and/or a controller in communication with the reagent delivery system. In some embodiments, the electrical detector can be configured to collect data corresponding to changes in the electrical characteristic in response to contact with the template polymorphic nucleotide, the extension nucleic acid, and the enzyme.

Method and composition for detecting one or more selected polynucleotide regions in a target polynucleotide. In the method, a mixture of sequence-specific probes are reacted with the target polynucleotide under hybridization conditions, and the hybridized probes are treated to selectively modify those probes which are bound to the target polynucleotide in a base-specific manner. The resulting labeled probes include a polymer chain which imparts to each different-sequence probe, a distinctive ratio of charge/translational frictional drag, and a detectable label. The labeled probes are fractionated by electrophoresis in a non-sieving matrix, and the presence of one or more selected sequences in the target polynucleotide are detected according to the observed electrophoretic migration rates of the labeled probes in a non-sieving medium.

Method for distinguishing different-sequence polynucleotides

Method and composition for detecting one or more selected polynucleotide regions in a target polynucleotide. In one embodiment of the invention, a plurality of different-sequence probe pairs are added to a target polynucleotide, where each probe pair includes two polynucleotide probe elements which are complementary in sequence to adjacent portions of a selected one of the target sequences in the target polynucleotide. In each probe pair, one of the probe elements contains a non-polynucleotide polymer chain which imparts a distinctive mobility to the associated probe pair, when the elements in the pair are ligated. The other element in the pair contains a detectable reporter label. After the probe pairs have been allowed to hybridize with the target polynucleotide, the hybridized polynucleotides are treated under conditions effective to ligate the end subunits of target-bound probe elements when their end subunits are base-paired with adjacent target bases. The ligated probe pairs are then released from the target polynucleotide and separated electrophoretically in a sieving matrix, or chromatographically.

Probe composition containing a binding domain and polymer chain and methods of use

Probe composition comprising a binding polymer and polymer chain and methods of use

Long wavelength, narrow emission bandwidth fluorecein dyes are provided for detecting specially overlapping target substances. The dyes comprise 4,7-dichlorofluoresceins, and particularly 2&prime;,4&prime;,5&prime;,7&prime;-tetrachloro-4,7-dichloro-5-(and 6-) carboxyfluoresceins. Methods and kits for using the dyes in DNA analysis are provided.

4,7-dichlorofluorescein dyes as molecular probes

Long wavelength, narrow emission bandwidth fluorecein dyes are provided for detecting spacially overlapping target substances. The dyes comprise 4,7-dichlorofluoresceins, and particularly 2&prime;,4&prime;,5&prime;,7&prime;-tetrachloro-4,7-dicloro-5- (and 6-) carboxyfluoresceins. Methods and kits for using the dyes in DNA analysis are provided.

4, 7-Dichlorofluorescein dyes as molecular probes

Long wavelength, narrow emission bandwidth fluorecein dyes are provided for detecting spacially overlapping target substances. The dyes comprise 4,7-dichlorofluoresceins, and particularly 2',4',5', 7'-tetrachloro-4,7-dichloro-5- (and 6-) carboxyfluoresceins. Methods and kits for using the dyes in DNA analysis are provided.

Method and composition for detecting one or more selected polynucleotide regions in a target polynucleotide. In the method, a mixture of sequence-specific probes are reacted with the target polynucleotide under hybridization conditions, and the hybridized probes are treated to selectively modify those probes which are bound to the target polynucleotide in a base-specific manner. The resulting labeled probes include a polymer chain which imparts to each different-sequence probe, a distinctive ratio of charge/translational frictional drag, and a detectable label. The labeled probes are fractionated by electrophoresis in a non-sieving matrix, and the presence of one or more selected sequences in the target polynucleotide are detected according to the observed electrophoretic migration rates of the labeled probes in a non-sieiving medium.

Kits for DNA sequencing employing a mixed DNA-polymer chain probe

Long wavelength, narrow emission bandwidth fluorecein dyes are provided for detecting spacially overlapping target substances. The dyes comprise 4,7-dichlorofluoresceins, and particularly 2',4',5',7'-tetrachloro-4,7-dichloro-5- (and 6-) carboxyfluoresceins. Methods and kits for using the dyes in DNA analysis are provided.

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Palo Alto, CA, United States of America

Steven Fung