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Bio-chips (Lab-on-a-chip)

System architectures

White lines correspond to metal electrodes that connect to individual nanowire devices. The position of the microfluidic channel used to deliver sample is highlighted in blue and has a total size of 6 mm × 500 μm, length × width. The image field is 4.4 × 3.5 mm.

(B) Optical image of one row of addressable device elements from the region highlighted by the red-dashed box in A. The red arrow highlights the position of a device. The image field is 500 × 400 μm.

C) Scanning electron microscopy image of one silicon nanowire device. The electrode contacts are visible at the upper right and lower left regions of the image. (Scale bar: 500 nm.)

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Bio-chips• Portable, • low cost in high volumes, • low power, • can be integrated with other components

Chii-Wann Lin et al, DEVELOPMENT OF MICROMACHINED ELECTROCHEMICAL SENSORAND PORTABLE METER SYSTEM, a Proceedings of the 20th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Vol. 20, No 4,1998

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System architectures• Chips – flat platforms, sensors below or above the chip

T. Vo-Dinh et al. , Sensors and Actuators, B 74 (2001) 2-11

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Schematic diagram of an integrated DNA biochip system

Vo-Dinh T, Alarie JP, Isola N, Landis D, Wintenberg AL, Ericson, MN (1999) Anal Chem 71 :358–363

fluorescence detection of Cy5-labeled Streptavidin using a 4X4 photodiode array IC biochip. Excitation by a 12 mW He±Ne laser (632.8 nm).

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Single detectors vs. Vectors and arrays

Single

Vector Array

DNA Arrays (Gene chips)

Example of a DNA Array(note green, yellow red colors;

also note that only part of the totalarray is depicted)

http://www.biomed.miami.edu/arrays/images/agilent_array.jpg

Example of a DNA Array(note green, yellow red colors;

also note that only part of the totalarray is depicted)

41,000+ unique human genes and transcripts represented, all with public domain annotations

an arrayed series of thousands of microscopic spots of DNA oligonucleotides, called probes, each containing picomoles of a specific DNA sequence. This can be a short section of a gene or other DNA element that are used as probes to hybridize a cDNA or cRNA sample (called target)

• Probe-target hybridization is usually detected and quantified by detection of fluorophore-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. Since an array can contain tens of thousands of probes, a microarray experiment can accomplish many genetic tests in parallel.

Colloquially known as an Affy chip when an Affymetrix chip is used. Other microarray platforms, such as Illumina, use microscopic beads, instead of the large solid support.

AffymetrixAgilent TechnologiesAppliedCombiMatrixEppendorf GE Healthcare Genetix Greiner Bio-One Illumina, Inc. Kreatech Micronit Microfluidics Nanogen, Inc. NimbleGen Ocimum Biosolutions Roche DiagnosticsSCHOTT Nexterion STMicroelectronics

• DNA microarrays can be used to measure changes in gene expression levels, to detect single nucleotide polymorphisms (SNPs) , to genotype or resequence mutant genomes.

Step 1: Create a DNA array (gene “chip”) by placing single-stranded DNA/ Oligonucleotides (probes) for each gene to be assayed into a separate “well” on the chip.

cDNAgene 1

cDNAgene 2

cDNAgene 3

cDNAgene 4

cDNAgene 5

DNA Array: Single-stranded copy DNA Oligonucleotides for each gene in a different well.

the probes are attached to a solid surface by a covalent bond to a chemical matrix (via epoxy-silane, amino-silane, lysine, polyacrylamide or others). The solid surface can be glass or a silicon chip

Step 2: Extract mRNA from biological tissues subjected to an experimental treatment and from the same tissue subjected to a control

treatment. Or from normal and from pathological tissue

• Step 3- Make single-stranded DNA from the mRNA using “color coded” nucleotides.

Extract mRNA from Control Cells

Extract mRNA from Experimental/pathological Cells

Make single-stranded cDNA using green nucleotides (e.g.

Quantum dots)

Make single-stranded cDNA using red nucleotides (e.g.

Quantum dots)

cDNA = complementary DNA (DNA synthesized from RNA)

Step 4: After making many DNA copies of the RNA, extract an equal amount of cDNA

from the controls & experimentals and place it into a container.

Control cDNA Experimental cDNA

Step 5: Extract a smallamount in a pipette.

Step 6: Insert into first well.

… insert intosecond well, etc.

Step 7: Extractmore cDNA and …

Step 8: Continue until all wells arefilled.

Step 9: Allow to hybridize, then wash away all single-stranded DNA.

Result:(1) Some wells have no color-coded cDNA (no mRNA in either type of cell)(2) Some wells have only red (i.e., expressed only in experimental cells)(3) Some wells have only green (i.e., expressed only in control cells)(4) Some wells have both red and green in various mixtures (expressed

in both experimental and control cells)

Step 10: Scan with a laser set to detect the color & process results on computer.

Results: The colors denote the degree of expression in the

experimental versus the control cells.

Gene not expressed in control or in experimental cells

Only incontrol

cells

Mostly incontrol

cells

Only inexperimental

cells

Mostly inexperimental

cells

Same inboth cells