This document provides an overview of DNA microarrays (DNA chips). It discusses that DNA chips allow scientists to simultaneously measure gene expression levels or genotype multiple genomic regions. It describes the principle technologies used in DNA chips, including attaching cDNA or oligonucleotide probes to glass or silicon surfaces. The document also provides background on DNA and microarrays, their history, applications in gene expression analysis and disease research, and principle of hybridization. It discusses alternative bead-based array technologies and how microarrays enabled large-scale genomic experiments.

2. CONTENTS
 What is DNA chip?
 Principle uses of chips
 Major technologies
 Background of DNA
 DNA nomenclature
 DNA chip design
 Applying DNA principle to chips
 Why we need to know about DNA
 What you need to know about DNA
 Micro arrays
 DNA and researchers
 History
 Application
 Principle
 Micro arrays and bio-informatics
 Uses and types
 Alternative technologies

4. WHAT IS A DNA CHIP?
A DNA microarray (also commonly known as DNA chip or
biochip) is a collection of microscopic DNA spots attached to a
solid surface. Scientists use DNA microarrays to measure the
expression levels of large numbers of genes simultaneously or
to genotype multiple regions of a genome.

5. Principle uses of
chips
 Genome-scale gene expression analysis
 Differentiation
 Responses to environmental factors
 Disease processes
 Effects of drugs
 Detection of sequence variation
 Genetic typing
 Detection of somatic mutations (e.g. in oncogenes)
 Direct sequencing

6. Major technologies
 cDNA probes (> 200 nt), usually produced by PCR,
attached to either nylon or glass supports
 Oligonucleotides (25-80 nt) attached to glass
support
 Oligonucleotides (25-30 nt) synthesized in situ on
silica wafers (Affymetrix)
 Probes attached to tagged beads

7. BACKGROUND OF DNA
 Genetics started in 1866 .
 Genes were linked to DNA.
 Each DNA spot contains
picomoles (10−12 moles) of
a specific DNA sequence,
known as probes.
 These probes can be a short
section of a gene or other DNA
element.
 Probes are used to hybridize a
cDNA or cRNA sample.

8. Dna nomenclature
• Double Helix
• Four Bases

9. Dna chip design
 Probe selection
 Non-redundant set of probes
 Includes genes of interest to project
 Corresponds to physically available clones
 Chip layout
 Grouping of probes by function
 Correspondance between wells in microtitre plates and
spots on the chip

10. Applying DNA principle to chips
• Chips are designed to either “sequence” or decode genetic strands,
or to find genetic matches.
• HYBRIDIZATION
• The array provides a medium for matching known and unknown
DNA samples based on base-pairing (hybridization) rules. The
two strands basically combine automatically if correct matching
has occurred.

12. Why you need to know about
DNA Chips
•They are astonishingly powerful.
• They allow scientists to quickly and inexpensively do experiments
they could only dream about just a few years ago--like tracking
how the expression of every single gene in the human genome
changes in response to an experimental variable.
•They are cheap and fast.
•Chips make it possible to find out not just the average human
genetic sequence, but about your personal genetic sequence.
•They have consumer applications
•They are becoming big business.
• Analysts estimate that the annual sales of DNA chips will exceed
1 billion dollars within just a few years.

13. Whatyou need to know about DNA Chips
•“DNA chip” is slang for DNA microarray.
• DNA chips are a revolutionary technology. They speed up research,
helping scientists understand the primary sequence of the human
genome.
• They will also allow doctors to get important genetic information from
individual patients and thus choose the best treatments.

14. •Microarrays can have tens of thousands of
spots. This means they can look for tens of
thousands of DNA sequences all at once.
•A sequencing array is made of many
different short DNA sequences.
•Researchers use these to find the sequence
of an unknown bit of DNA.
•A researcher chops the unknown sequence
into short bits, sees where the bits bind on the
array, deduces the sequences of all the short
unknown bits, then reassembles the
overlapping sequences into one long
sequence.

15. Researchers love DNA chips because they give a huge
amount of information, fast, at low cost.
Doctors will soon learn to love them because there are
many times when a doctor would like to know something
about a patient's genes (such as whether the patient is
likely to respond well to a certain drug). When the price
comes down enough, microarrays will likely become
routine tools in the doctor's office.
DNA AND
RESEARCHERS

16. WORKING

17. • Microarray technology evolved from
Southern blotting, where fragmented DNA is
attached to a substrate and then probed
with a known DNA sequence.
• The first reported use of this approach was
the analysis of 378 arrayed lysed bacterial
colonies each harboring a different
sequence which were assayed in multiple
replicas for expression of the genes in
multiple normal and tumor tissue.
• This was expanded to an analysis of more
than 4000 human sequences with computer
driven scanning and image processing for
quantitative analysis of the sequences in
human colonic tumors and normal tissue
and then to comparison of colonic tissues at
different genetic risk.
History
CONT…..

18.  These early gene arrays were made by spotting cDNAs onto
filter paper with a pin-spotting device. The use of miniaturized
microarrays for gene expression profiling was first reported in
1995, and a complete eukaryotic genome (Saccharomyces
cerevisiae) on a microarray was published in 1997
 The use of a collection of distinct DNAs in arrays for expression
profiling was also described in 1987, and the arrayed DNAs were
used to identify genes whose expression is modulated by
interferon.

19.  DNA microarrays have enabled biology researchers to conduct
large-scale quantitative experiments. This capacity has produced
qualitative changes in the breadth of hypotheses that can be
explored.
 It has become the dominant mode of use, changes in the
transcription rate of nearly all the genes in a genome, taking
place in a particular tissue or cell type, can be measured in
disease states, during development, and in response to
intentional experimental perturbations, such as gene disruptions
and drug treatments.
 The response patterns have helped illuminate mechanisms of
disease and identify disease subphenotypes, predict disease
progression, assign function to previously unannotated genes,
group genes into functional pathways, and predict activities of
new compounds.
.
Applications
CONT..

20.  Directed at the genome sequence itself, microarrays have been
used to identify novel genes, binding sites of transcription factors,
changes in DNA copy number, and variations from a baseline
sequence, such as in emerging strains of pathogens or complex
mutations in disease-causing human genes.
 They also serve as a general demultiplexing tool to sort spatially
the sequence-tagged products of highly parallel reactions
performed in solution

21. PRINCIPLE

22.  The core principle behind microarrays is hybridization between
two DNA strands.
 The property of complementary nucleic acid sequences to
specifically pair with each other by forming hydrogen bonds
between complementary nucleotide base pairs.
 A high number of complementary base pairs in a nucleotide
sequence means tighter non-covalent bonding between the two
strands.
 After washing off non-specific bonding sequences, only strongly
paired strands will remain hybridized.
 Fluorescently labeled target sequences that bind to a probe
sequence generate a signal that depends on the hybridization
conditions (such as temperature), and washing after
hybridization.
 Total strength of the signal, from a spot (feature), depends upon
the amount of target sample binding to the probes present on
that spot.
 Microarrays use relative quantization in which the intensity of a
feature is compared to the intensity of the same feature under a
different condition, and the identity of the feature is known by its
position
PRINCIPLE

23. Microarrays and bioinformatics
The multiple levels of replication in experimental design
(Experimental design)the number of platforms and independent
groups and data format(Standardization)the treatment of the
data (Statistical analysis)accuracy and precision (Relation
between probe and gene)the sheer volume of data and the
ability to share it (Data warehousing)
The advent of inexpensive microarray experiments created
several specific bioinformatics challenges

24. Many types of arrays exist and the broadest distinction is whether they are
spatially arranged on a surface or on coded beads:
The traditional solid-phase array is a collection of orderly microscopic
"spots", called features, each with thousands of identical and specific
probes attached to a solid surface, such as glass, plastic or silicon biochip
(commonly known as a genome chip, DNA chip or gene array). Thousands
of these features can be placed in known locations on a single DNA
microarray.
The alternative bead array is a collection of microscopic polystyrene beads,
each with a specific probe and a ratio of two or more dyes, which do not
interfere with the fluorescent dyes used on the target sequence
Uses and types

25. Alternative technologies
Advances in massively parallel sequencing has led to
the development of RNA-Seq technology, that enables
a whole transcriptome shotgun approach to
characterize and quantify gene expression. Unlike
microarrays, which need a reference genome and
transcriptome to be available before the microarray
itself can be designed, RNA-Seq can be also be used
for new model organisms whose genome has not been
sequenced yet

26. REFERENCES
 Statwww.epfl.ch/davision/…week03.ppt
 Clifton.mech.northwestern.edu
 www.seminarsonly.com
 www.Dnawikipedia.com

27. Punit Jain
punitjain5885.blogspot.com