Steps involved in DNA microarray
• Technique used for Preparing DNA
• Types of DNA Chips
cDNA - based chips
Oligonucleotide - based chips
• Advantages and disadvantages
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.
[Ref: Presscot (Book for Microbiology), www.wikipedia.org]
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.
a) A DNA chip can be
manufactured to contain
hundreds of thousands of
synthetic single-stranded DNA
b) Unknown DNA from a patient is
separated into single strands,
enzymatically cut and labeled with
a fluorescent dye.
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
e 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.
i. DNA Chip
ii. Target sample (Fluorescently
iii. Fluorescent dyes
There are certain requirements for designing a DNA
microarray system and they are:
Design of a
Technique used for the Preparation of DNA chip
There are 2 types of DNA Chips/Microarrays:
Types of DNA chips
1. cDNA based microarray
2. Oligonucleotide based
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 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:
Fig: Construction of a DNA chip with attached
oligonucleotide sequences (two cycles are shown)
Table 1. Steps in the design and implementation of a DNA
4) Assay 5) Readout
The DNA chips are used in many areas as given
• Gene expression profiling
• Discovery of drugs
• Diagnostics and genetic engineering
• Alternative splicing detection
• Functional genomics
• DNA sequencing
• Toxicological research (Toxicogenomics)
• 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 expresion.
[Ref: www.biotechnologyforums.com, www.ehow.com]
• The biggest disadvantage of DNA chips is that they are expensive
• 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.
[Ref: www.biotechnologyforums.com, www.ehow.com]
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.
•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.