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Arrays for detecting nucleic acids

a nucleic acid and array technology, applied in the field of sequencing, fingerprinting, and polymer mapping, can solve the problems of large number of manual manipulations by practitioners, so as to reduce the number of manual manipulations, speed, accuracy, and reliability of these procedures.

Inactive Publication Date: 2005-03-10
AFFYMETRIX INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

This approach significantly enhances the speed, accuracy, and reliability of nucleotide sequencing, reduces costs, and improves reproducibility by automating the sequencing process, making it more efficient for large-scale sequencing projects like the human genome project.

Problems solved by technology

However, the need for highly rapid, accurate, and inexpensive sequencing technology is nowhere more apparent than in a demanding sequencing project such as this.
Both methods require a practitioner to perform a large number of complex manual manipulations.
These manipulations usually require isolating homogeneous DNA fragments, elaborate and tedious preparing of samples, preparing a separating gel, applying samples to the gel, electrophoresing the samples into this gel, working up the finished gel, and analyzing the results of the procedure.
Thus, a less expensive, highly reliable, and labor efficient means for sequencing biological macromolecules is needed.

Method used

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  • Arrays for detecting nucleic acids
  • Arrays for detecting nucleic acids
  • Arrays for detecting nucleic acids

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Experimental program
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Embodiment Construction

I. Overall Description A. general B. VLSIPS substrates C. binary masking D. applications E. detection methods and apparatus F. data analysis

II. Theoretical Analysis A. simple n-mer structure; theory B. complications C. non-polynucleotide embodiments

III. Polynucleotide Sequencing A. preparation of substrate matrix B. labeling target polynucleotide C. hybridization conditions D. detection; VLSIPS scanning E. analysis F. substrate reuse G. non-polynucleotide aspects

IV. Fingerprinting A. general B. preparation of substrate matrix C. labeling target nucleotides D. hybridization conditions E. detection; VLSIPS scanning F. analysis G. substrate reuse H. non-polynucleotide aspects

V. Mapping A. general B. preparation of substrate matrix C. labeling D. hybridization / specific interaction E. detection F. analysis G. substrate reuse H. non-polynucleotide aspects

VI. Additional Screening A. specific interactions B. sequence comparisons C. categorization...

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Abstract

The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.

Description

BACKGROUND OF THE INVENTION The present invention relates to the sequencing, fingerprinting, and mapping of polymers, particularly biological polymers. The inventions may be applied, for example, in the sequencing, fingerprinting, or mapping of nucleic acids, polypeptides, oligosaccharides, and synthetic polymers. The relationship between structure and function of macromolecules is of fundamental importance in the understanding of biological systems. These relationships are important to understanding, for example, the functions of enzymes, structural proteins, and signalling proteins, ways in which cells communicate with each other, as well as mechanisms of cellular control and metabolic feedback. Genetic information is critical in continuation of life processes. Life is substantially informationally based and its genetic content controls the growth and reproduction of the organism and its complements. Polypeptides, which are critical features of all living systems, are encoded b...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): B01J19/00C07B61/00C07H19/10C07H21/00C07K1/04C07K17/06C07K17/14C12Q1/68C40B40/06C40B40/10C40B60/14G01N15/14G03F7/00G03F7/26G03F7/38G11C13/02
CPCB01J19/0046B01J2219/00315B01J2219/00432B01J2219/00434B01J2219/00436B01J2219/00459B01J2219/00468B01J2219/00475B01J2219/005B01J2219/00527B01J2219/00529B01J2219/00531B01J2219/00585B01J2219/0059B01J2219/00596B01J2219/00605B01J2219/00608B01J2219/0061B01J2219/00612B01J2219/00617B01J2219/00626B01J2219/0063B01J2219/00637B01J2219/00641B01J2219/00648B01J2219/00659B01J2219/00689B01J2219/00695B01J2219/00711B01J2219/00722B01J2219/00725B82Y10/00B82Y30/00C07B2200/11C07H19/10C07H21/00C07K1/042C07K1/045C07K17/06C07K17/14C12Q1/6804C12Q1/6809C12Q1/6816C12Q1/6827C12Q1/6834C12Q1/6837C12Q1/6874C40B40/06C40B40/10C40B60/14G01N15/1475G03F7/00G03F7/265G03F7/38G11C13/0014G11C13/0019C12Q2565/513C12Q2565/507C12Q2545/101C12Q2525/185C12Q2565/514C12Q2563/173C12Q2563/119C12Q2563/149C12Q2525/151C12Q2525/179C12Q2525/204G01N15/1433
Inventor FODOR, STEPHEN P.A.SOLAS, DENNIS W.DOWER, WILLIAM J.
Owner AFFYMETRIX INC