The document explains DNA microarray technology for genome analysis, detailing its principles, types (cDNA and oligonucleotide microarrays), and experimental procedures. It highlights the applications of DNA chips in gene expression profiling, drug discovery, and diagnostics, while also mentioning their advantages and disadvantages, such as cost and complexity in data analysis. Overall, DNA microarrays enable the simultaneous analysis of thousands of genes, contributing to advancements in medical research.

1. NAVEED UL MUSHTAQ
Dept. : BIO-RESOURCES
UNIVERSITY OF KASHMIR

2. DEFINITION :
• DNA Microarray is a technique for genome Analysis ,
where thousands of genes are analysed at a time in a
single experiment simultaneously to determine which
genes are expressed in a particular sample
• These experiments rely on the principle of hybridisation
• Thousands of known probes are fabricated onto a smal
solid slide (Glass,Silicon ,Nylon) in a particular order
as spots and called DNA microarray or DNA chip.
• The spots can be DNA , cDNA , or oligonucleotide.

5. • The principle of DNA microarray technology is
based on the fact that complimentary sequences of
DNA can be used to hybridise , immobilised DNA
molecules.
• There are four major steps in performing a typical
microarray experiment.

7. There are major two types of Microarray :
cDNA Microarray
Oligonucleotide Microarray

8. cDNA Microarray ,first introduced by Patrick Brown ,is also
termed as spotted microarray
In this technique ,DNA fragments (genes) are amplified by
PCR and then spotted onto a glass slide in a grid like pattern.
This is a two-channeled microarray that is typically hybridised
with cDNA from two samples to be compared on the same
slide for visualisation of genes.
These samples are flourescently labelled (Cys 3-rhodamine
for red and Cys 5-fluorescin for green) for easy detection.
Data from a cDNA microarray provides information about the
relative expression of genes in two different biological
samples.

11.  In this method, a DNA microarray slide is fabricated by
synthesising 11-16 short oligonucleotides (approx.
25bp in length) at very high density for each expressed
gene on a slide.
 Here oligonucleotides are synthesised at fixed
locations by photolithographic technique and chemical
synthesis technique.
 In Affimatrix, a 25 bp long oligos are taken and a total
of 100 light masks are made for each base at each layer.
 An oligo-MA contains two sets of probes for each gene
One set for perfect match and another that contains
mismatch nucleotides.
 Here two or more samples can be compared at a time
but each sample needs different microarray slides.

12.  These arrays are used in genotyping experiments,
where sequences of alternate gene forms are
synthesised to detect polymorphisms and mutations.
 A white spot is generated for strong hybridisation and
no hybridisation produces black spots.
 In between these two colours is marginal
hybridisation.
 Oligonucleotide microarrays avoid the cross-
hybridisation that may occur with the cDNA
microarray.
 They are much expensive and also need very accurate
gene annotation to fabricate match and mismatch
probes.

15.  The DNA chips are used in many areas as given
below:
 Gene expression profiling
 Discovery of drugs
 Diagnostics and genetic engineering
 in proteomics
 Functional genomics
 DNA sequencing
 Toxicological research.

16.  Provide 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
expression.

17.  The biggest disadvantage of DNA chips is that they
are expensive to create.
 The production of too many results at a time
requires long time for analysis , which is quite
complex.
 The DNA chips do not have very long shelf life,
which proves to be another major disadvantage of
the technology.