Microarrays allow researchers to analyze gene expression and detect mutations across thousands of genes simultaneously. They consist of miniaturized spots containing DNA, proteins, or other biomolecules immobilized on a solid surface. When a fluorescently labeled sample is applied, only matching molecules will hybridize, allowing for quantification. The main types are DNA microarrays for analyzing gene expression, tissue microarrays for pathology studies, and peptide arrays for protein interactions. DNA microarrays use glass slides coated with specific DNA sequences to analyze gene expression profiles in tissues or cells.
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.
Microarray -types, DNA chip, Principle and application of microarray, Preparation of DNA Chip, Affymetrix chip, microarray in genomics and proteomics, advantages and limitations of microarray
it will help you to understand how the protein microarrays are made, what are the different types and what all purposes they are used for. its very useful ppt
A genome is an organism’s complete set of DNA or complete genetic makeup, The entire DNA complement. It describes the identity and the sequence of genes of an organism.
Genomics is the study of entire genomes(structure, function, evolution, mapping, and editing of genomes)
Executing the sequencing and analysis of entire human genome enables more rapid and effective identification of disease associated genes and provide drug companies with pre validated targets.
Proteomics is the systematic high-throughput separation and characterization of proteins within biological systems./ large scale study of protein and their functions.
Proteomics measures protein expression directly, not via gene expression, thus achieving better accuracy. Current work uses 2-dimensional polyacrylamide gel electrophoresis(2D- PAGE) and mass spectrometry.
New separation and characterization technologies, such as protein microarray and high throughput chromatography are being developed.
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.
Microarray -types, DNA chip, Principle and application of microarray, Preparation of DNA Chip, Affymetrix chip, microarray in genomics and proteomics, advantages and limitations of microarray
it will help you to understand how the protein microarrays are made, what are the different types and what all purposes they are used for. its very useful ppt
A genome is an organism’s complete set of DNA or complete genetic makeup, The entire DNA complement. It describes the identity and the sequence of genes of an organism.
Genomics is the study of entire genomes(structure, function, evolution, mapping, and editing of genomes)
Executing the sequencing and analysis of entire human genome enables more rapid and effective identification of disease associated genes and provide drug companies with pre validated targets.
Proteomics is the systematic high-throughput separation and characterization of proteins within biological systems./ large scale study of protein and their functions.
Proteomics measures protein expression directly, not via gene expression, thus achieving better accuracy. Current work uses 2-dimensional polyacrylamide gel electrophoresis(2D- PAGE) and mass spectrometry.
New separation and characterization technologies, such as protein microarray and high throughput chromatography are being developed.
A protein microarray (or protein chip) is a high-throughput method used to track the interactions and activities of proteins, and to determine their function, and determining function on a large scale. Its main advantage lies in the fact that large numbers of proteins can be tracked in parallel.
In silico drug designing is the drug design which can be carried out in silicon chip,i.e., within computers. The slides are helpful to know a brief description about in silico drug designing.
Protein microarray Preparation of protein microarray Different methods of arr...naveed ul mushtaq
Protein microarray
Preparation of protein microarray
Different methods of arraying the proteins.FUNCTIONAL PROTEIN MICROARRAYSAnalytical microarrays:-
3.REVERSE PHASE PROTEIN MICROARRAY APPLICATIONS:-
Yeast two-hybrid is based on the reconstitution of a functional transcription factor (TF) when two proteins or polypeptides of interest interact. Upon interaction between the bait and the prey, the DBD and AD are brought in close proximity and a functional TF is reconstituted upstream of the reporter gene.
A protein microarray (or protein chip) is a high-throughput method used to track the interactions and activities of proteins, and to determine their function, and determining function on a large scale. Its main advantage lies in the fact that large numbers of proteins can be tracked in parallel.
In silico drug designing is the drug design which can be carried out in silicon chip,i.e., within computers. The slides are helpful to know a brief description about in silico drug designing.
Protein microarray Preparation of protein microarray Different methods of arr...naveed ul mushtaq
Protein microarray
Preparation of protein microarray
Different methods of arraying the proteins.FUNCTIONAL PROTEIN MICROARRAYSAnalytical microarrays:-
3.REVERSE PHASE PROTEIN MICROARRAY APPLICATIONS:-
Yeast two-hybrid is based on the reconstitution of a functional transcription factor (TF) when two proteins or polypeptides of interest interact. Upon interaction between the bait and the prey, the DBD and AD are brought in close proximity and a functional TF is reconstituted upstream of the reporter gene.
Nucleic acid techniques in diagnostic microbiologymohit kumar
in this presentation, you learn about the microbiological techniques which help in the molecular diagnosis of any single pathogens. with this, you aware of some commercially available kits for polymerase chain reaction both for realtime as well as conventional PCR and genome extraction kits.
In a detail description of the two major blotting techniques. Right from its history to the result interpretation put forth in a concise way. Helps understand these protocols with ease.
B12 metabolism..................................... and role of various proteins in b12 metabolism..... necessity of supplementation..........................................
2. What is Microarray ???
Microarrays are sets of miniaturized chemical reaction areas
that may be used to test DNA fragments, antibodies,
or proteins.
Each reaction area or spot is having immobilised target which
is hybridised with complimentary probe present in the testing
sample.
3. Various types of microarrays are :
• DNA microarrays, such as cDNA microarrays, oligonucleotide
microarrays and SNP microarrays
• MMChips, for surveillance of microRNA populations
• Peptide microarrays, for detailed analyses or optimization of
protein-protein interactions
• Tissue microarrays
• Cellular microarrays (also called transfection microarrays)
• Chemical compound microarrays
• Antibody microarrays
• Carbohydrate arrays (glycoarrays)
• Phenotype microarrays
4. DNA Microarray
• commonly known as DNA chip.
-Bio chip is a small rectangular solid surface that is made of glass or
silicone.
-short DNA or RNA targets are anchored to its surface. (no. may vary
from 10-20 to hundreds of thousands)
- Each known gene occupies a particular “spot” on the chip.
-the DNA sample which is to be analysed is amplified by PCR.
-now sample DNA is labelled with fluorescent tag
-this fluorescent DNA sample is loaded on chip
-Hybridization occurs between sample DNA and target, allowing
thousands of hybridization reactions to occur at the same time.
-complete sequence matching result in bright
fluorescence and even a single base mismatching
result in a dimmer fluorescence signal.
5.
6. The solid surface of Biochip
• Substrates for arrays are usually silicon chips or glass
microscope slides.
• Glass is a readily available and inexpensive support medium
that has a relatively homogeneous chemical surface whose
properties have been well studied and is amenable to
chemical modification using very versatile and well developed
silanization chemistry.
• The two-dimensional surface is typically prepared by treating
the glass or silicon surface with an amino silane which results
in a uniform layer of primary amines or epoxides.
7. • These modifications results in several advantages:
1. the linkages are chemically stable,
2. sufficiently long to eliminate undesired steric interference
from the support, and
3. hydrophilic enough to be freely soluble in aqueous solution
and not produce non-specific binding to the support.
• Once these modifications have activated the surface, the
efficiency of attaching the oligonucleotides depends largely on
the chemistry used and how the oligonucleotide targets are
modified.
8. Fabrication of the surface with oligonucleotide
• Fabrication is done by two methods:
1. Spotted microarray
2. In situ synthesised array / oligonucleotide microarrays
9. • Spotted microarray:
In spotted microarrays, the probes can be
i. oligonucleotides,
ii. cDNA or
iii. small fragments of PCR products that correspond to
mRNAs.
The probes are synthesized prior to deposition on the array
surface and are then "spotted" onto glass.
Spotting is done by a technique
which utilises atomic force
microscopy;
known as Dip Pen Nanolithography
10. • This technique is used by research scientists around the world
to produce "in-house" printed microarrays from their own
labs.
• These arrays may be easily customized for each experiment,
because researchers can choose the probes and printing
locations on the arrays, synthesize the probes in their own lab
(or collaborating facility), and spot the arrays.
• This provides a relatively low-cost microarray that may be
customized for each study, and avoids the costs of purchasing
often more expensive commercial arrays that may represent
vast numbers of genes that are not of interest to the
investigator.
• In-house spotted microarrays may not provide the same level
of sensitivity compared to commercial oligonucleotide
arrays, possibly owing to the small batch sizes and reduced
printing efficiencies when compared to industrial
manufactures of oligo arrays.
11. • Oligonucleotide array:
• Oligonucleotide arrays are produced by printing short
oligonucleotide sequences designed to represent a single
gene or family of gene splice-variants.
• Printing is done by synthesizing this sequence directly onto
the array surface instead of depositing intact sequences as
done in spotted microarray.
• technique used to produce oligonucleotide arrays
include photolithographic synthesis (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.
14. Fluoroscence tagging of DNA sample
• Fluorescent dyes commonly used for cDNA labeling
include Cy3, which has a fluorescence emission wavelength of
570 nm (corresponding to the green part of the light
spectrum), and Cy5 with a fluorescence emission wavelength
of 670 nm (corresponding to the red part of the light
spectrum).
18. Two channel microarray
Relative intensities of each fluorophore may then be used in ratio-based
analysis to identify up-regulated and down-regulated genes.
19. Single channel microarray
• In single-channel microarrays or one-color microarrays, the
arrays provide intensity data for each probe or probe set
indicating a relative level of hybridization with the labelled
target.
• One strength of the single-dye system lies in the fact that an
aberrant sample cannot affect the raw data derived from other
samples, because each array chip is exposed to only one sample
(as opposed to a two-colour system in which a single low-quality
sample may drastically impinge on overall data precision even if
the other sample was of high quality).
• Another benefit is that data are more easily compared to arrays
from different.
• A drawback to the one-color system is that, when compared to
the two-colour system, twice as many microarrays are needed to
compare samples within an experiment.
21. Analysis of Gene Expression
• Examining expression during development
or in different tissues
• Comparing genes expressed in normal vs.
diseased states
• Analyzing response of cells exposed to
drugs or different physiological conditions
22. Monitoring Changes in Genomic DNA
• Identify mutations
• Examining genomic instability such as in certain
cancers and tumors (gene amplifications,
translocations, deletions)
• Identifying polymorphisms (SNPs)
• Diagnosis: chips have been designed to detect
mutations in p53, HIV, and the breast cancer
gene BRCA-1
23. Applications in Medicine
• Inferring regulatory networks
• Pathogen analysis (rapid genotyping)
• Staging of leukemias
24. Applications in Drug Discovery
Drug Discovery
• Identify appropriate molecular targets for
therapeutic intervention (small molecule / proteins)
• Monitor changes in gene expression in response
to drug treatments (up / down regulation)
• Analyze patient populations (SNPs) and response
Targeted Drug Treatment
• Pharmacogenomics: individualized treatments
• Choosing drugs with the least probable side
effects
25.
26.
27. Nucleic acid
techniques
Detection Discrimination
techniques techniques
UV absorbance electrophoresis
Fluoroscence HPLC & mass
staining spectrophotom
etry
Hybridization
assay
Solid phase Solution phase
hybridization hybridization
Dot-blot and line RT-PCR
probe assay
Arrays (micro and PCR melting assay
medium density)
In situ hybridization others
Southern and
northern blotting