MICROARRAYS/DNA CHIPS

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DNA MICROAARRAY
(DNA CHIP)

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• Introduction
• Principle
 Steps involved in DNA microarray
•Types of DNA Chips
 cDNA - based chips
 Oligonucleotide - based chips
• Applications
• Advantages and disadvantages
• Conclusion
• Reference
CONTENTS

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Introduction:
Definition: DNA microarrays are solid supports, usually of
glass or silicon, upon which DNA is attached in an organized grid
fashion. Each spot of DNA, called a probe, represents a single
gene.
There are several synonyms of DNA microarrays such as DNA
chips, gene chips, DNA arrays, gene arrays and biochips.
History: Microarray technology evolved from Southern
blotting, where fragmented DNA is attached to a substrate and
then probed with a known DNA sequence.
The use of miniaturized microarrays for gene expression profiling
was first reported in 1995, and a complete eukaryotic genome
(Saccharomyces cerevisiae) on a microarray was published in 1997.

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a) A DNA chip can be
manufactured to contain
hundreds of thousands of
synthetic single-stranded DNA
sequences.
b) Unknown DNA from a patient is
separated into single strands,
enzymatically cut and labeled with
a fluorescent dye.

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c) The unknown DNA is inserted into
the chip and allowed to hybridize
with the DNA on the chip.
d) The tagged DNA will bind only to
the complementary DNA on the chip.
The bound DNA will be detected by
its fluorescent dye and analyzed by a
computer. The red light is a gene
expressed in normal cells; green is a
mutated gene expressed in tumor
cells; and yellow, in both cells.
Fig: DNA Chip Technology

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Principle
The principle of DNA microarrays lies on the
hybridization between the nucleotide. Using this
technology the presence of one genomic or cDNA
sequence in 1,00,000 or more sequences can be
screened in a single hybridization.
The property of complementary nucleic
acid sequences is to specifically pair with each other
by forming hydrogen bonds between complementary
nucleotide base pairs.

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i. DNA Chip
ii. Target sample (Fluorescently
labelled)
ii. Enzymes
iii. Fluorescent dyes
iv. Probes
v. Scanner
Requirements:
There are certain requirements for designing a DNA
microarray system and they are:

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Design of a
DNA
Microarray
System

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1. Sample
preparation
2. Purification

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3. Reverse
Transcriptio
n
4. Labelling

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5.Hibridization
6. Scanning
7.Normalization
and analysis

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There are 2 types of DNA Chips/Microarrays:
Types of DNA chips
1. cDNA based microarray
2. Oligonucleotide based
microaaray

13. cDNA CHIPS
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This type of chips are prepared by using cDNA, it is called
cDNA chips or cDNA microarray or probe DNA. The cDNAs
are amplified by using PCR. Then these immobilized on a
solid support made up of nylon filtre of glass slide (1 x 3
inches).
The probe DNA are loaded into a spotting
spin by capillary action. Small volume of this DNA
preparation is spotted on solid surface making physical
contact between these two. DNA is delivered mechanically or
in a robotic manner.
When one DNA spotting is done, the pin is
washed and loaded with fresh DNA to Start the second cycle.
cDNA – based chips:

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Oligonucleotide-based chips
Fig: Construction of a DNA chip with attached
oligonucleotide sequences (two cycles are shown)

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The DNA chips are used in many areas as given
below:
• Gene expression profiling
• Discovery of drugs
• Diagnostics and genetic engineering
• Alternative splicing detection
• Proteomics
• Functional genomics
• DNA sequencing
• Toxicological research (Toxicogenomics)
Applications

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 Provides data for thousands of genes.
 One experiment instead of many.
 Fast and easy to obtain results.
 Huge step closer to discovering cures for diseases and cancer.
 Different parts of DNA can be used to study gene expression.
ADVANTAGES

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Disadvantages:
 The biggest disadvantage of DNA chips is that
they are expensive to create.
 The production of too many results at a time
requires long time for analysis, which is quite
complex in nature.
 The DNA chips do not have very long shelf life,
which proves to be another major disadvantage
of the technology.

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DNA Microarrays are one of the most effective
invention ever developed. A DNA Microarray is a test that allows for the
comparison of thousands of genes at once. Microarray technology uses
chips with attached DNA sequences as probes for gene expression. Any
DNA in the sample that is complementary to a probe sequence will
become bound to the chip. Microarray technology is most powerful
when it used on species with a sequenced genome. The microarray chip
can hold sequences from every gene in the entire genome and the
expression of every gene can be studied simultaneously. Gene expression
data can provide information on the function of previously
uncharacterized genes.
Conclusion

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Source:
•Lehninger, 2005, DNA Chips, Principle of Biochemistry, W.H. Freeman and Company,
Newyork, forth Edition, Pg. 326- 328.
• Presscot M. Lansing, 2002, DNA Chips, Microbiology, Athenaeum Press Ltd,
Gateshead, Tyne and Wear, Britain, Fifth Edition, 353 – 354.
• Dubey C. R, 2008, DNA Chips, A textbook for Biotechnology, S. Chand and Company
Ltd., New Delhi, 13th Edition, Pg. 194 – 197.
•Tortora J. Gerard, DNA Chips, Book for Microbiology, Pearson Education, Inc., San
Francisco, CA, tenth edition, Pg. 292 – 293.
Net Source:
• www.wikipedia.org
• www.gene-chips.com
• www.biotechnology4u.com
• www.biotechnologyforums.com
• www.ehow.com
Reference

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