The above presentation consist of the definition of microarray, brief history, general principle of the same, the type of scanner that are used to read or to scan the microarray , type of DNA microarray and finally its various apliccation including the role of DNA microaarray in drug discovery.

1. NUCLEIC ACID MICROARRAY
BY: PRIYA SHUKLA

2. INDEX:
 INTRODUCTION
 HISTORY
 PRINCIPLE
 SCANNER
 Type of DNA microarray
 Application

4. 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.

5. The microarray technique is been sub-classified based
on the sample to be analyte:
 DNA microarray
 Protein microarray
 Transfection microarray
 Antibody microarray
 Tissue microarray
 Chemical compound microarray

6.  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 varing level of gene activity of introduced
genetic material.

7.  (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

8. 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 FARTHER
OF MICROARRAY TECHNIQUE’.

9. 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.

10. Sample
preparation and
labelling
HYBRIDIZATION WASHING
Image acquisition
and data analysis

12.  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.

13. SCANNING THE ARRAY:
 1. Laser Scanner:
 Excellent resolution
 Good fluorescent but may bleach the fluorochromes
 Speed: slow
 2. CCD Laser( charge coupled device)
 Less resolution
 Sensitive and easily adjustable
 Faster and cheaper as compared to laser scanner

14. TYPE OF DNA MICROARRAY:
 SPOTTED DNA ARRAYS ( cDNA):
 Develpoed by Pat Brown
 PCR product from known genes spotted on support
 Customizable
 GENE CHIPS:
 1. OLIGONUCLEOTIDE ARRAYS ( AFFYMETRIX):
 Small number of 20-25mer/ gene
 Enable by photolithography from computer industry

15.  2. INK- JET MICROARRAYS ( AGILENT);
 Large number of 25-60mer “printed” directly on glass
 Four cartridges: A,C,G and T
 Flexible, rapid, but expensive

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 utiliizers 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

18. 1. 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.

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.

21. APPLICATION
 1. gene expression analysis:
 The process of measuring gene expression via c
DNA is called expression analysis.
 Study the effect of certain treatments, diseases, and
developmental stage on gene expression.
 eg: identify genes expression changes due to
pathogens or other organisms by compairing with
uninfected cells or tissue

22. 2. Disease diagnosis:
 Earlier cancer classification on the basis of the organ
in which tumours develop.
 Earlier stage of genetic mutation in pateint.

23. 3. Drug discovery
 Applicable in pharmacogenomics
 Comparative analysis of gene
 Help the identification of specific proteins produce by
diseased cells.
 Help to produce effective drugs

24. 4.Toxicological research
 A rapid platform for the research of the impact of
toxin on the cells and their passing on to the
progeny.
 Important for toxicogenomic studies.