Nanogen, Inc.

The Scripps Research Institute

Nanogen/becton Dickinson Partnership

Gamida for Life B.v.

Michael I Nerenberg

Carl Frederick Edman

Ronald George Sosnowski

Isao Kitajima

Eugene Tu

Michael James Heller

William Frank Butler

Lorelei P Westin

Ray R Radtkey

John J Carrino

James P O'Connell

David Canter

Ling Wang

Geoffrey C Landis

Prashant P Mehta

Dana Vollmer

Lana L Feng

A method for electronically stabilizing hybridization of nucleic acids bound at a test site of a microelectronic device is described. First and second negatively charged nucleic acids are provided, the second nucleic acid being bound to the test site. A zwitterionic buffer having a conductance of less than 100 mS/cm is applied to the microelectronic device. A current is applied to the test site to positively bias the test site, such that the first negatively charged nucleic acid is transported to the positively biased test site having the bound the second negatively charged nucleic acid. At the test site, the first and second negatively charged nucleic acids hybridize. The zwitterionic buffer acquires a net positive charge under influence of the current, such that the positively charged zwitterionic buffer stabilizes the hybridization by reducing the repulsion between the first and second negatively charged nucleic acids.

Self-addressable self-assembling microelectronic integrated systems, component devices, mechanisms, methods, and procedures for molecular biological analysis and diagnostics

Antisense oligonucleotides which hybridize with nuclear factor-&#x3ba;B (NF-&#x3ba;B) mRNA and methods of using these oligonucleotides.

Suppression of nuclear factor-&#x3ba;B dependent processes using oligonucleotides

This application includes methods for detecting single nucleotide polymorphisms (SNPs) in a sample using an electronically addressable microchip having a plurality of test sites. A sample nucleic acid is electronically biased, concentrated at, and immobilized to a test site on the microchip. A mixture comprising a first labeled probe and a second labeled probe is electronically hybridized to the sample nucleic acid to form first or second hybridized complexes. The first labeled probe is perfectly complementary to the first sample nucleic acid and the second labeled probe is complementary to the sample nucleic acid and contains a nucleotide that forms a mismatch with the nucleotide at the site of the polymorphism. The first or second hybridized complexes are detected by determining a signal intensity of the label of the first or second probe.

Methods for determination of single nucleic acid polymorphisms using a bioelectronic microchip

Antisense oligonucleotides which hybridize with nuclear factor-&#x3ba;B(NF-&#x3ba;B) mRNA and methods of using these oligonucleotides.

Novel polymorphisms of prokaryotic topoisomerase type II Gyr A, Gyr B and parC gene loci are provided. These polymorphisms differentiate very closely related organisms and provide a means to identify pathogenicity and drug resistance. For example, drug resistance such as resistance to methicillin, a drug which is not metabolically tied to topoisomerase function, may be determined by polymorphisms in the Gyrase A locus. Identification of such drug resistance by such unrelated loci is indicative of heretofore unrecognized [sub]species of

Topoisomerase type II gene polymorphisms and their use in identifying drug resistance and pathogenic strains of microorganisms

A method of improving amplification of nucleic acids using a nucleic acid sequence-based amplification ('NASBA') method is provided wherein target nucleic acids and NASBA primers are electronically addressed to electronically addressable capture sites of a microchip. This improvement uses electronically induced hybridization of the target nucleic acids to the primers. The primers may be solution-based or immobilized on the capture sites of the microchip.

Electronically mediated nucleic acid amplification in NASBA

A method for amplifying nucleic acids is provided wherein detection of amplified species is enhanced by the use of asymmetric amplification. Such amplification is made asymmetric by using divergent ratios of amplification primers or by using non-extending and/or non-cleavable amplification primers. Detection of the amplicons is improved because maintenance of single stranded species of amplicons during amplification facilitates their direct capture by immobilized probes without having to include denaturing steps.

Multiplex amplification and separation of nucleic acid sequences on a bioelectronic microchip using asymmetric structures

Methods and compositions of matter are provided for the strand displacement amplification of target nucleic acids of interest using primer pair sets that are anchored to electronically addressable capture sites on a microarray. The primer pair sets may be individually bound to the capture sites or may comprise a unique branched primer pair moiety. The anchored primers allow for the simultaneous multiplex capture, amplification and detection of a target nucleic acid derived from any sample source.

Anchored strand displacement amplification on an electronically addressable microchip

A self-addressable, self-assembling microelectronic device is designed and fabricated to actively carry out and control multi-step and multiplex molecular biological reactions in microscopic formats. These reactions include nucleic acid hybridizations, antibody/antigen reactions, diagnostics, and biopolymer synthesis. The device can be fabricated using both microlithographic and micro-machining techniques. The device can electronically control the transport and attachment of specific binding entities to specific microlocations. The specific binding entities include molecular biological molecules such as nucleic acids and polypeptides. The device can subsequently control the transport and reaction of analytes or reactants at the addressed specific microlocations. The device is able to concentrate analytes and reactants, remove non-specifically bound molecules, provide stringency control for DNA hybridization reactions, and improve the detection of analytes. The device can be electronically replicated.

Method for enhancing the hybridization efficiency of target nucleic acids using a self-addressable, self-assembling microelectronic device

Antisense oligonucleotides which hybridize with nuclear factor- B(NF- B) mRNA and methods of using these oligonucleotides.

Suppression of nuclear factor-&kgr;b dependent processes using oligonucleotides

Methods are provided for the analysis and determination of the nature of single nucleic acid polymorphisms (SNPs) in a genetic target. In one method of this invention, the nature of the SNPs in the genetic target is determined by the steps of providing a plurality of hybridization complexes arrayed on a plurality of test sites on an electronically bioactive microchip, where the hybridization complex includes at least a nucleic acid target containing a SNP, a stabilizer probe having a sequence complementary to the target sequence and/or reporter probe, and a reporter probe having a selected sequence complementary to either the stabilizer or the same target sequence strand wherein a selected sequence of the reporter includes either a wild type nucleotide or a nucleotide corresponding to the SNP of the target. In accordance with the invention, the stabilizer, reporter and target amplicons are hybridized using electronic assistance of the microchip system such that base-stacking energies are utilized in discerning among other identifying indicators, the presence of wild type or polymorphism sequence. Applications include disease diagnostics, such as for the identification of polymorphisms in structural genes, regulatory regions, antibiotic or chemotherapeutic resistance conferring regions, or for SNPs associated with speciation or used for determination of genetic linkage.

Methods for determination of single nucleic acid polymorphisms using bioelectronic microchip

A method of improving amplification of nucleic acids using a nucleic acid sequence-based amplification (&ldquo;NASBA&rdquo;) method is provided wherein target nucleic acids and NASBA primers are electronically addressed to electronically addressable capture sites of a microchip. This improvement uses electronically induced hybridization of the target nucleic acids to the primers. The primers may be solution-based or immobilized on the capture sites of the microchip.

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San Diego, CA, United States of America

Michael I Nerenberg