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1. NUCLEIC ACID MICROARRAY
PRESENTED BY:-
MDASIF ANSARI
M.PHARMA,PHARMACOLOGY
SPER , JAMIA HAMDARD
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SEMINAR ON

2. PRESENTATION OUTLINE
 INTRODUCTION
 HISTORY
 PRINCIPLE
 TYPES OF ARRAY
 APPLICATIONS
 REFERENCES
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3. INTRODUCTION
WHAT IS MICROARRAY?
 A microarray is a laboratory tool used to detect the
expression of thousands of genes at the same time.
 Microarray helps in analyzing large amount of samples
which have either been recorded previously or new
samples.
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4.  The microarray technique is been sub-classified based on the sample to be
analyte:
oDNA microarray
oProtein microarray
oTransfection microarray
oAntibody microarray
oTissue microarray
oChemical compound microarray
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5.  A DNA microarray also commonly known as DNA chip or
biochip is a collection of microscopic DNA spots attached to
solid support surface.
 Each DNA spot contain picomoles (10-12 moles) of specific DNA
sequence known as probe or oligos.
 Each known gene or probe occupied a specific site on the chip
and varying level of fluorescent activity show varying level of
gene activity of introduced genetic material.
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6.  (1) cDNA microarrays: to enable large-scale analysis of mRNA
abundance as an indicator of gene expression.
 (2) Single nucleotide polymorphism (SNP) microarrays and
mutation arrays: to detect polymorphisms or mutations within a
population using SNP arrays or arrays designed to detect known
mutations.
 (3) Comparative genomic hybridization (CGH) microarrays to
look for genomic gains and losses, or for a change in the number
of copies of a particular gene involved in a disease.
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7. HISTORY
 Southern blotting was developed in 1975.
 The concept of DNA microarray was considered at mid 1980s.
 Quantitative monitoring of gene expression with complement
DNA microarray reported by PETRICK BROWN, MARK
SECHENA and colleagues.
 Mark Sechena was proclaimed as 'THE FATHER OF
MICROARRAYTECHNIQUE'.
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8. PRINCIPLE
 The core principle of microarray is HYBRIDIZATION.
 Samples are labelled using fluorescent dyes.
 Complementary nucleic acid get bind via hydrogen bonds.
 Washing of non specific bonding DNA.
Sample
preparation
and labelling
Hybridization Washing
Image acquisition
and data analysis
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10. SAMPLE PREPARATION AND LABELLING
 Isolate a total RNA containing mRNA that
ideally represents a quantitative copy of
genes expressed at the time of sample
collection.
 Preparation of cDNA from mRNA using a
transcriptase enzyme. reverse-transcriptase
enzyme.
 Short primer is required to initiate cDNA
synthesis.
 Each cDNA (Sample and Control) is labelled
with fluorescent cyanine dyes (i.e. Cy3 and
Cy5).
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11. ARRAY HYBRIDIZATION
 Here, the labelled cDNA
(Sample and Control) are
mixed together.
 Purification
 After purification, the mixed
labelled cDNA is competitively
hybridized against denatured
PCR product or cDNA
molecules spotted on a glass
slide.
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12. IMAGE ACQUISITION AND DATA ANALYSIS
 Slide is dried and scanned to
determine how much labelled CDNA
(probe) is bound to each target spot.
 Hybridized target produces emissions.
 Microarray software often uses green
spots on the microarray to represent
upregulated genes.
 Red to represent those genes that are
downregulated and yellow to present
in equal abundance
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13.  Fluorescently labelled target sequence that bind to the probe
sequence generate a signal.▸The signal depend on :
 1. hybridization condition (eg: temperature)
 2. washing after hybridization
 The total strength of signal depend on the amount of target
bond to probe.
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14. SCANNINGTHE ARRAY
 1. Laser Scanner:
Excellent resolution
Good fluorescent but may bleach the fluorochromes
Speed: slow
 2. CCD( charge coupled device) Laser
Less resolution
Sensitive and easily adjustable
Faster and cheaper as compared to laser scanner
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15. TYPE OF DNA MICROARRAY
SPOTTED DNA ARRAYS (cDNA):
 Developed by Patrick Brown
 PCR product from known genes spotted on support
 Customizable
OLIGONUCLEOTIDE ARRAYS
• Small number of 20-25 mer/ gene
 Enable by photolithography from computer industry
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16. SPOTTED DNA ARRAYS
 The probes are oligonucleotides, cDNA, or small
fragments of PCR products that correspond to
mRNAs, there probes are synthesized prior to
deposition or the array surface and are then
spotted' onto glass.
 A common approach utilizes an array of fine pins or
needles controlled by a robotic arm that is dipped
into wells containing DNA probes and then
depositing each probe at designated locations on
the array surface.
 The resulting 'grid' of probe represents the nucleic
acid profiles of the prepared probes and is ready to
receive c DNA derived from experimental or clinical
samples.
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18. OLIGONUCLEOTIDE ARRAYS
 Here, probes are short sequences
designed to match parts of the sequence
of known or predicted open reading
frames.
 Oligonucleotide array are produced by
printing short oligonucleotide sequences
designed to represent a single gene by
synthesizing this sequence directly onto
the array surface instead of depositing
intact sequences.
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19.  Sequences may be longer or shorter depending on desired
purpose; longer probes are more specific to individual target
genes, shorter probes may be spotted in higher density across
the array and are cheaper to manufacture.
 One technique used to produce oligonucleotide arrays include
photolithographic synthesis (Agilent and Affymetrix) on a silica
substrate where light and light-sensitive masking agents are
used to build' a sequence one nucleotide at a time across the
entire array.
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20. APPLICATION OF MICROARRAY
TECHNOLOGY
As gene
expression
profiling tool
As comparative
genomics tool
Drug discovery
Disease
diagnosis
Toxicological
research
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21. MICROARRAY AS A GENE EXPRESSION
PROFILINGTOOL
 The principle aim of using microarray technology as a gene
expression profiling tool is to answer some of the fundamental
questions in biology such as "when, where, and to what
magnitude genes of interest are expressed.
 Microarray analysis measure changes in the multigene patterns
of expression to better understand about regulatory
mechanisms and broader bioactivity functions of genes.
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22. MICROARRAY AS A COMPARATIVE
GENOMICSTOOL
 Microarray technology have widespread use in comparative
gene mutation analysis to analyze genomic alterations such as
sequence and single nucleotide polymorphisms.
 In microbiology microarray gene mutation analysis is directed to
characterization of genetic differences among microbial
isolates, particularly closely related species.
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23. DISEASE DIAGNOSIS
 Different types of cancer have been classified on the basis of the
organs in which the tumors develop.
 Now, with the evolution of microarray technology, it will be
possible for the researchers to further classify the types of
cancer on the basis of the patterns of gene activity in the tumor
cells.
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24. DRUG DISCOVERY
 Microarray technology has extensive application in
Pharmacogenomics.
 Comparative analysis of the genes from a diseased and a normal
cell will help the identification of the biochemical constitution of
the proteins synthesized by the diseased genes.
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25. TOXICOLOGICAL RESEARCH
 Microarray technology provides a robust platform for the
research of the impact of toxins on the cells and their passing on
to the progeny.
 Toxicogenomic establishes correlation between responses to
toxicants and the changes in the genetic profiles of the cells
exposed to such toxicants.
 The microarray permits researchers to examine thousands of
different genes in the same experiment and thus to obtain a
good understanding of the relative levels of expression between
different genes in an organism.
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26. REFERENCES
• DNA Microarrays and Related GenomicsTechniques: Design,
Analysis, and Interpretation of Experiment by David B.
Allison & Grier P. Page &T. Mark Beasley & JodeW. Edwards.
• Microarray for the neuroscience : An essential guide (Cellular
and molecular Neuroscience) edited by Daniel H. Geschwind and
Jeffrey P. Gregg
 Stoughton, RB. Applications of DNA microarrays in biology.
Annual Review of Biochemistry. 2005;74: 53-82
 M. Schena, Microarray Analysis, JohnWiley & Sons, Hobokon,
New Jersey, 2003
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