The document discusses nucleic acid microarrays, which are laboratory tools used to analyze gene expression across thousands of genes simultaneously. It covers the history, principles, types of DNA microarrays, and their applications in gene expression analysis, disease diagnosis, drug discovery, and toxicological research. The core techniques involve hybridization, fluorescence detection, and specific microarray types like cDNA and SNP microarrays.

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.