Individually addressable micro-electromagnetic unit array chips

Details Individually addressable micro-electromagnetic unit array chips Individually addressable micro-electromagnetic unit array chips

2001-09-18

2004-10-19

Chin, Christopher L. (Department: 1641)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C435S004000, C435S007100, C435S287100, C435S287200, C422S082010, C436S149000, C436S150000, C436S151000, C436S518000, C436S526000, C436S806000

Reexamination Certificate

active

06806050

ABSTRACT:

FIELD OF THE INVENTION
The present application concerns micromachined or microfabricated devices known as “biochips” and more particularly biochips employing magnetic forces and methods of utilizing such biochips for performing chemical, biological and biochemical reactions and assays.
DESCRIPTION OF RELATED ART
As a novel and emerging technology in life science and biomedical research during last several years, biochip technology can be applied to many areas of biology, biotechnology and biomedicine including point-mutation detection, DNA sequencing, gene expression, drug screening and clinical diagnosis. Biochips refer to miniaturized devices having characteristic dimensions in the micrometer to millimeter range that can be used for performing chemical and biochemical reactions. Biochips are produced using microelectronic and microfabrication techniques as used in semiconductor industry or other similar techniques, and can be used to integrate and shrink the currently discrete chemical or biochemical analytical processes and devices into microchip-based apparatus. Recent scientific literature shows a plethora of uses for these devices.
The reader's attention is drawn to the following articles for an appreciation of the breadth of biochip uses. “Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control” by Sosnowski, R. G. et al. (Proc. Natl. Acad. Sci., USA, 94:1119-1123 (1997)) and “Large-scale identification, mapping and genotyping of single-nucleotide polymorphisms in the human genome” by Wang, D. G. et al. (Science, 280: 1077-1082 (1998)) show current biochip use in detection of point mutations. “Accurate sequencing by hybridization for DNA diagnostics and individual genomics.” by Drmanac, S. et al. (Nature Biotechnol. 16: 54-58 (1998)), “Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy” by Shoemaker, D. D. et al. (Nature Genet., 14:450-456 (1996)), and “Accessing genetic information with high density DNA arrays.” by Chee, M et al., (Science, 274:610-614 (1996)) show biochip technology used for DNA sequencing. The use of biochip technology to monitor gene expression is shown in “Genome-wide expression monitoring in
Saccharomyces cerevisiae
” by Wodicka, L. et al. (Nature Biotechnol. 15:1359-1367 (1997)), “Genomics and human disease—variations on variation,” by Brown, P. O. and Hartwell, L. and “Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays.” by Ruan, Y. et al. (The Plant Journal 15:821-833 (1998)). The use of biochips in drug screening is illustrated in “Selecting effective antisense reagents on combinatorial oligonucleotide arrays.” by Milner, N. et al. (Nature Biotechnol., 15:537-541 (1997)), and “Drug target validation and identification of secondary drug target effects using DNA microarray.” by Marton, M. J. et al. (Nature Medicine, 4:1293-1301 (1998)). Examples of clinical diagnostic use of biochips are illustrated in “Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays.” by Cronin, M. T. et al. (Human Mutation, 7:244-255 (1996)), and “Polypyrrole DNA chip on a silicon device: Example of hepatitis C virus genotyping.” by Livache, T. et al. (Anal. Biochem. 255:188-194 (1998)). These references are intended to give a notion of the wide range of biochip uses.
A variety of biochips have biomolecules (e.g., oligonucleotides, cDNA and antibodies) immobilized on their surfaces. There are a number of different approaches to make such chips. For example, the light-directed chemical synthesis process developed by Affymetrix (see, U.S. Pat. Nos. 5,445,934 and 5,856,174) is a method of synthesizing biomolecules on chip surfaces by combining solid-phase photochemical synthesis with photolithographic fabrication techniques. The chemical deposition approach developed by Incyte Pharmaceutical uses pre-synthesized cDNA probes for directed deposition onto chip surfaces (see, e.g., U.S. Pat. No. 5,874,554). The contact-print method developed by Stanford University uses high-speed, high-precision robot-arms to move and control a liquid-dispensing head for directed cDNA deposition and printing onto chip surfaces (see, Schena, M. et al. Science 270:467-70 (1995)). The University of Washington at Seattle has developed a single-nucleotide probe synthesis method using four piezoelectric deposition heads, which are loaded separately with four types of nucleotide molecules to achieve required deposition of nucleotides and simultaneous synthesis on chip surfaces (see, Blanchard, A. P. et al. Biosensors & Bioelectronics 11:687-90 (1996)). Hyseq, Inc. has developed passive membrane devices for sequencing genomes (see, U.S. Pat. No. 5,202,231).
There are two basic types of biochips, i.e., passive and active. Passive biochips refer to those on which chemical or biochemical reactions are dependent on passive diffusion of sample molecules. In active biochips reactants are actively moved or concentrated by externally applied forces so that reactions are dependant not only on simple diffusion but also on the applied forces. The majority of the available biochips, e.g., oligonucleotide-based DNA chips from Affymetrix and cDNA-based biochips from Incyte Pharmaceuticals, belongs to the passive type. There are structural similarities between active and passive biochips. Both types of biochips employ of arrays of different immobilized ligands or ligand molecules. Herein, “ligands or ligand molecules” refers to bio/chemical molecules with which other molecules can react. For instance, a ligand may be a single strand of DNA to which a complementary nucleic acid strand can hybridize. A ligand may be an antibody molecule to which the corresponding antigen (epitope) can bind. A ligand may also include a particle on whose surface are a plurality of molecules to which other molecules may react. By using various markers and indicator molecules (e.g.: fluorescent dye molecules), the reaction between ligands and other molecules can be monitored and quantified. Thus, an array of different ligands immobilized on a biochip enables the-reaction and monitoring of multiple analyte molecules.
Many current passive biochip designs do not take full advantage of microfabrication and microelectronic technologies. Passive biochips cannot be readily used to achieve fully integration and miniaturization of the entire bioanalytical system from the front-end sample preparation to final molecular quantification/detection. In addition, passive biochips have other disadvantages including low analytical sensitivity, a long reaction time, and difficulties associated with control of temperature, pressure, and electrical fields at individual sites (called units) on the chip surfaces as well as difficulties in controlling the local concentrations of molecules.
On the other hand, active biochips allow versatile functions of molecular manipulation, interaction, hybridization reaction and separation (such as PCR and capillary electrophoresis) by external forces through means such as microfluidic manipulation and electrical manipulation of molecules. However, many such biochips cannot be readily used in high throughput applications. The electronic biochips developed by Nanogen can manipulate and control sample biomolecules with electrical field generated by microelectrodes, leading to significant improvement in reaction speed and detection sensitivity over passive biochips (see, U.S. Pat. Nos. 5,605,662, 5,632,957, and 5,849,486). However, to effectively move biomolecules in their suspension/solutions with electrical fields, the electrical conductivity of solutions has to be very low. This significantly limits the choice of buffer solutions used for biochemical assays because enzymes and other biomolecules are denatured under conditions of low ionic strength and/or serious non-specific binding occurs to chip surfaces.
The present invention provides a new type of active biochips in which magnetic forces are generated by individually addres

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