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DNA Microarray: Basic Principle and It's Applications

Article · January 2017

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488 in Biosciences 10(2), Print : ISSN 0974-8431,
Trends Trends in Biosciences
488-490, 2017 10 (2), 2017

REVIEW PAPER
DNA Microarray: Basic Principle and It’s Applications
VAIBHAV CHANDRAKANT KHELURKAR1*, KRISHNANANDA PRALHAD INGLE2, DIPIKA ASHOKRAO PADOLE3
Biotechnology Centre, Dr. Panjabrao Deshmukh Krishi Vidyapeeth,
Akola, Maharashtra
*email : [email protected]

ABSTRACT only strongly paired strands will remain hybridized. So

DNA microarray is most powerful technology which can fluorescently labeled target sequences that bind to a probe
sequence generate a signal that depends on the strength
provide a high throughput and detailed view of the entire
of the hybridization determined by the number of paired
genome and transcriptome which allows scientists to
bases, the hybridization conditions (such as temperature),
understand the molecular mechanisms underlying normal
and washing after hybridization.
and dysfunctional biological processes. Microarray
technology could speed up the screening of thousands of Total strength of the signal, from a spot (feature),
DNA and protein samples simultaneously. In the present depends upon the amount of target sample binding to the
review, we discuss the basic principles behind gene probes present on that spot. Microarrays use relative
expression microarrays, it’s types and their potential quantization in which the intensity of a feature is compared
applications. to the intensity of the same feature under a different
condition, and the identity of the feature is known by its
Key words Microarray, probe, expression profiling position.
Here the unknown sample of DNA sequence is
A typical microarray experiment involves the referred as the target or sample and known sequence of
hybridization of an mRNA molecule to the DNA template DNA molecule which is referred as probe. After completion
from which it is originated. Many DNA samples are used to of hybridization the surface of chip can be analyze
construct an array. The amount of mRNA bound to each quantitatively and qualitatively by using autoradiography,
site on the array indicates the expression level of the various laser scanning, fluorescence detection device, enzyme
genes. This number may run in thousands. All the data is detection system.
collected and a profile is generated for gene expression in Types of the DNA chips
the cell. DNA microarray (also commonly known as gene
1) Oligonucleotide based chips
chip, DNA chip, or biochip) is a collection of microscopic
DNA spots attached to a solid surface. In DNA chip 2) cDNA based chips
technology, single stranded DNA molecule is immobilized Oligonucleotide based chips
on solid surface by biochemical analysis. These DNA
Large amount of oligonucleotides can synthesize on
molecules are derived from cDNA sequences of an organism
a glass support using light directed solid phase,
referred as cDNA microarray or using photolithography
combinatorial chemistry developed by Affymetrix (Santa
through synthesis of short oligonucleotide sequences.
Clara, CA USA). In this type of DNA chip the short
Scientists use DNA microarrays to measure the
oligonucleotide (10-25 mers) microarray which prepared by
expression levels of large numbers of genes simultaneously
using photolithographic technique i.e. use of light which
or to genotype multiple regions of a genome. Each DNA
synthesis the many different chemical compound on a solid
spot contains picomoles (10"12 moles) of a specific DNA
support.
sequence, known as probes (or reporters). These can be a
short section of a gene or other DNA element that are used The main feature of this technology depends upon
to hybridize a cDNA or cRNA sample (called target) under the two key technologies which is capable to synthesize of
high-stringency conditions. Probe-target hybridization is hundred and thousand of sense compound at high
usually detected and quantified by detection of flurophore- resolution in exact location on a substrate. In second
, silver-, or chemiluminescence-labeled targets to determine technique the fluorescence scanning permit the
relative abundance of nucleic acid sequences in the target. measurement of molecular interaction on array within the 1,
00,000 to 4, 00,000 oligonucleotide with an area of 1.6 CM2
Principle of DNA Microarray .
Production of cDNA from each type of mRNA is not always
The core principle behind microarrays is hybridization possible which is different and time consuming so ESTs
between two DNA strands, the property of complementary are prepared from EST library. The oligonucleotide will bind
nucleic acid sequences to specifically pair with each other with the sample DNA when target sample poured with on a
by forming hydrogen bonds between complementary oligonucleotide immobilized on a solid surface.
nucleotide base pairs.
cDNA based chips
A high number of complementary base pairs in a
cDNA based chips technique developed by Davis,
nucleotide sequence means tighter non-covalent bonding
brown and their colleagues.
between the two strands.
After washing off of non-specific bonding sequences, Hybridization and detection methods
 KHELURKAR et al., DNA Microarray: Basic Principle and It’s Applications 489

Fig. 1. Steps involved in microarray

Hybridization of the target DNA to microarray yields monitored to study the effects of certain treatments,
sequence information. Target DNA of unknown sequence diseases, and developmental stages on gene expression.
is hybridizing with probe if the target DNA has For example, microarray-based gene expression profiling
complementary region. After hybridization , the hybridized can be used to identify genes whose expression is changed
target sequence can be detected by various methods. The in response to pathogens or other organisms by comparing
hybridized sample can be detected by various techniques gene expression in infected to that in uninfected cells or
like radioactive and non-radioactive detection system. The tissues. In toxicological research, microarray technology
hybridization pattern can be analyzed by using automatic provides a robust platform for the research of the impact of
scanning system by using scanner like Scan Array 3000. toxins on the cells and their passing on to the progeny.
This detection system is based on charged coupled device Toxicogenomics establishes correlation between responses
system and lens based system, lens based system is not to toxicants and the changes in the genetic profiles of the
appropriate analysis to the small quantities of array bound cells exposed to such toxicants.
molecules.
Comparative genomic hybridization
Double Stranded DNA chips Assessing genome content in different cells or closely
Presently, DNA chip technology has been extended related organisms.
to fabrication of double stranded DNA chips on a solid GeneID
surface. In one of the approaches single stranded
oligonucleotide are immobilized on to a surface via 3’ end. Small microarrays to check IDs of organisms in food
To these 16 mer primer is hybridized which can be extended and feed (like GMO),mycoplasms in cell culture,
with klenow fragment, thereby converting the immobilized or pathogens for disease detection, mostly combining
DNA into double stranded form. Incorporation of the PCR and microarray technology.
fluorescent label into DNA as a marker, it was shown that Chromatin immunoprecipitation on Chip
double stranded DNA is accessible to protein. An
DNA sequences bound to a particular protein can be
alternative approach is to couple 12-mer oligonucleotide to
isolated by immunoprecipitating that protein (ChIP), these
gold support and then these oligos are hybridized to double
fragments can be then hybridized to a microarray (such as
stranded DNA with complementary single stranded end,
a tiling array) allowing the determination of protein binding
followed by treatment with DNA ligase which results in
site occupancy throughout the genome. Example protein
surface coupled double stranded DNA.
to immunoprecipitate are histone modifications (H3K27me3,
Application of DNA chips H3K4me2, H3K9me3, etc.), Polycomb-group protein
Gene expression profiling (PRC2:Suz12, PRC1:YY1) and trithorax-group protein (Ash1)
to study the epigenetic landscape or RNA Polymerase II to
In an mRNA or gene expression profiling the study the transcription landscape.
expression levels of thousands of genes are simultaneously
490 Trends in Biosciences 10 (2), 2017

DamID microarrays. The oligo design strategy enables combined

Analogously to ChIP, genomic regions bound by a measurements of chimeric transcript junctions with exon-
wise measurements of individual fusion partners.
protein of interest can be isolated and used to probe a
microarray to determine binding site occupancy. Unlike Tiling array
ChIP, DamID does not require antibodies but makes use of Characterization of the selected mutant population
adenine methylation near the protein’s binding sites to can be analyzed with using this microarray technique this
selectively amplify those regions, introduced by expressing method of mutants analysis is depend upon the fitness
minute amounts of protein of interest fused to bacterial DNA value of the variety of alleles for each of the large number
adenine methyltransferase. of genes in a species. This technique is useful where the
SNP detection complete genome sequence is known by this method the
deletion, insertions or substitution can be analyzed this
Identifying single nucleotide polymorphism
method also called the reverse genetics.
among alleles within or between populations. Several
applications of microarrays make use of SNP detection, The gene expression in a plant genome have different
including genotyping, forensic analysis, measuring expression pattern with respective the different
predisposition to disease, identifying drug-candidates, environmental condition. It can be analysis with the help of
evaluating germline mutations in individuals or somatic this microarray technique.
mutations in cancers, assessing loss of heterozygosity, CONCLUSION
or genetic linkage analysis.
Microarray technology has been extensively used
Alternative splicing detection by the scientific community for the novel applications. The
An exon junction array design uses probes specific main advantage of this method is the genomic wide
to the expected or potential splice sites of information provided at reasonable costs.
predicted exons for a gene. It is of intermediate density, or LITERATURE CITED
coverage, to a typical gene expression array (with 1-3 probes
Drmanac, S., Kita, D., Labat, I., Hauser, B., Schmidt, C., Burczak,
per gene) and a genomic tiling array (with hundreds or
J.D., and Drmanac, R. 1998. Accurate sequencing by hybridization
thousands of probes per gene). It is used to assay the for DNA diagnostics and individual genomics. Nat. Biotechnol.
expression of alternative splice forms of a gene. Exon 16:54–58.
arrays have a different design, employing probes designed Gupta, P. K. , Roy, J. K. and M. Prasad. 1999. DNA chips, microarray
to detect each individual exon for known or predicted genes, and genomics. Curr. Sci. 77:875-884
and can be used for detecting different splicing isoforms. Pollack JR; Perou CM; Alizadeh AA; Eisen MB; Pergamenschikov
Fusion genes microarray A; Williams CF; Jeffrey SS; Botstein D; Brown PO. 1999.
“Genome-wide analysis of DNA copy-number changes using
A Fusion gene microarray can detect fusion cDNA microarrays”. Nat Genet. 23 (1): 41–46.
transcripts, e.g. from cancer specimens. The principle Syvanen AC. 2005. Toward genome-wide SNP genotyping. Nat. Genet.
behind this is building on the alternative splicing 37:S5–10.

Received on 07-01-2017 Accepted on 12-01-2017

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