This document discusses bio-chips and DNA microarrays. It describes how DNA microarrays work by having thousands of probes attached to a surface to which cDNA from experimental and control samples can hybridize. The document outlines the steps of DNA microarray experiments including creating the array, extracting mRNA from samples, making cDNA, hybridizing the cDNA to the array, and scanning the array to assess gene expression differences between conditions. DNA microarrays allow analysis of expression levels of many genes in parallel.

1. 1
Bio-chips (Lab-on-a-chip)

2. System architectures

3. 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.)

4. 4
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 SENSOR
AND 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

5. System architectures
• Chips – flat platforms, sensors below or above the chip
5
T. Vo-Dinh et al. , Sensors and Actuators, B 74 (2001) 2-11

7. 7
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

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

9. 9
Single detectors vs. Vectors and arrays
Single
Vector Array

10. DNA Arrays (Gene chips)

11. Example of a DNA Array
(note green, yellow red colors;
also note that only part of the total
array is depicted)

12. Example of a DNA Array
(note green, yellow red colors;
also note that only part of the total
array is depicted)
http://www.biomed.miami.edu/arrays/images/agilent_array.jpg
41,000+ unique human genes
and transcripts represented, all
with public domain annotations

13. 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)

14. • 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.

15. 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.
Affymetrix
Agilent Technologies
Applied
CombiMatrix
Eppendorf
GE Healthcare
Genetix
Greiner Bio-One
Illumina, Inc.
Kreatech
Micronit Microfluidics
Nanogen, Inc.
NimbleGen
Ocimum Biosolutions
Roche Diagnostics
SCHOTT Nexterion
STMicroelectronics

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

17. 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.

18. DNA Array: Single-stranded copy DNA Oligonucleotides for
cDNA
gene 1
cDNA
gene 2
cDNA
gene 3
cDNA
gene 4
cDNA
gene 5
each gene in a different well.

19. 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

20. 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

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

22. 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)

23. 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.

24. Control cDNA Experimental cDNA

25. Step 5: Extract a small
amount in a pipette.

26. Step 6: Insert into first
well.

27. … insert into
second well, etc.
Step 7: Extract
more cDNA and …

28. Step 8: Continue until all wells are
filled.

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

30. 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)

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

32. 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 in
control
cells
Mostly in
control
cells
Only in
experimental
cells
Mostly in
experimental
cells
Same in
both cells