information aspects of nucleic acids measurement technologies description of nucleic acid...
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Information Aspects of Nucleic Acids Measurement Technologies
• Description of nucleic acid measurement technologies
• Algorithmic, optimization, data analysis problems introduced by these new technologies
General Topics
• Optimization of the information measured in an assay or a set of assays.(Expression probe design)
• Optimization of information to resource ratio in molecular level assays.(Multiplexed genotyping assays)
• Biologically driven data analysis(Analysis of gene expression data)
• Algorithms for raw data interpretation(SBH, RE mapping)
Nucleic Acid Measurement Technologies (examples)
• Array based hybridization assays (DNA chips)
• MassSpectrometry based techniques
• Restriction enzyme fragmentation and length separation
• Large scale sequencing
A Few Basic Concepts of Molecular Biology
• DNA
• Proteins
• The central dogma of cellular biology
• DNA as a sequence of bases
• Watson-Crick –ery
Central Dogma
Transcription
mRNA
Cells express different subset of the genesIn different tissues and under different conditions
Gene (DNA)
Translation
Protein
DNA
• Carries the code for cellular functioning
• Variation in the code is the source for variation in properties
• Disease and disease susceptibility can be caused by changes in the DNA.
• DNA is the same for all cells of an individual.
mRNA and Proteins
• Execute the code• Relative levels are different in
different cells, depending on function and condition
• Are indicative of the state of the cell
Watson-Crick Complimentarity
A binds to TC binds to G
AATGCTTAGTCTTACGAATCAG
Perfect match
AATGCGTAGTCTTACGAATCAG
One base mismatch
FISH
• Fluorescence In-Situ Hybridiztion
• Fluorecsently labeled probes hybridize to specific chromosomal locations.
• Example application: low resolution localization of an EST.
Array Based Hybridization Assays (DNA Chips)
Unknown sequence (target)Many copies.
Array of probes
• Target hybs to WC complimentary probes only• Therefore – the fluorescence pattern is indicative of the
target sequence.
Array Based Hyb Assays
Thermal Ink Jet Arrays, by Agilent Technologies
cDNA array,Inkjet deposition
In-Situ synthesized oligonucleotide array. 25-60 mers.
Expression Profiling
• Given a set of genes of interest, measure the quantities of the corresponding mRNA, in cells in various conditions.
• Assumptions: • base sequences are known• Fluorescence levels are linear with
expression levels• Example computational problem: design
specific and sensitive probes.
Specific Probes
…
Input:Querry sequence (m:500-2000).Background message (total length of 50Mb).Probe length (20-70).
Output:For each probe candidate, its distance to the background message.
m
In future lectures and mini-projects
we will discuss/study information problems related to designing hybridization based assays and to the interpretation and data analysis of the results.
SBH