Biology 3594A Lecture Notes - Lecture 21: Fluorophore, Dna Supercoil, Cytogenetics

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CNV change in a segment of DNA
Can be large or small, this pic shows large structural changes, can see at cytogenetic level
Type of FISH (fluorescent in situ hybridization)
Using fluorescently labeled DNA to probe a metaphase spread of chromosomes
Green DNA control DNA, normal DNA that you have
Red DNA test DNA, often disease phenotype like tumour DNA
Colours from fluorophores
Two filters, one that’s looking for green and one that’s looking for red, take two diff pictures
Red = CNV loss or deletion in test sample
If green, CNV gain
Seeing more red = more of red DNA at that location
For your test, it means there is more red in that sample, it means that there is a gain for your test or a loss for your reference
Is there a CNV gain or loss for your test sample
Can look at many specific loci across the genome
Take the DNA, isolate it from the two samples, fragmented to 5-1500 bp samples, fluorophore
Apply to microarray they have wells that has the probes
Probes are the parts of the genome that we’re interrogating, can make them interrogate whatever you want, usually a lot of sites
Both DNAs are denatured, to make it single stranded, so it can bind to probes
Get binding at each probe
In each well there are a lot of probes so you can detect fluorescence, not just one probe
Yellow = competitive hybridization of two samples, red and green fluorescence merging to make yellow
No CNV variant here
If more red fluorescence, there is a CNV gain in our test DNA
If you see green, more of control sample binding = CNV loss in our test DNA
Test and reference DNA, both labeled with coloured fluorophores
Equal amounts of each applied to the microarray
Make huge images of fluorescence, computer analyzes the data
Does not tell you anything about the location of the CNV on the actual physical chromosome
Supercoiling large globular stuff, wont move on a gel
If you have a strand break, it starts to unwind and linearize more, supercoiling relaxes
When you have normal DNA it gets compacted and supercoiled
When supercoiling relaxes from strand breaks, it can linearize a bit only concept we need to know
Looking at single individual cells take many single cells and isolate them from a population
*the cell must have a nucleus (i.e. lymphocytes in blood)
Take control cells and more of the same cells with a DNA damaging agent added, introduces strand breaks
Take single cells and fixing them to a microscopy slide with an agarose coat, and lysing the cells
Once cells are fixed and lysed, you run them as a gel electrophoresis and stain them
GE moving molecules through a gel towards a positive and negative cathode
DNA travels to the + anode of the gel, DNA is negatively charged
Supercoil can’t travel through the gel
When you add fluorescent stain after you run on gel, dots are nuclei of the cells (top pic)
Comet tails indicative of single or double strand breaks, relaxed the supercoiling = linearization of the DNA
Tail moment length quantify the level of DNA damage
Look at diff agents and compare relative mutagenicity of those agents
Looking for 8 oxo DG
A marker in DNA for oxidative stress (ROS)
This is the primary marker, it is frequently incorporated into the DNA of almost every organism
See the adduct (don’t need to draw) - If you see extra oxygen = more reactive species
ELISA can be done in a few diff ways
Trying to detect whether there is lots of 8 oxo DG in the cell that you’re in
Tutorial 6 Mutation Detection Assays
May 13, 2018
3:04 PM
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Document Summary

Cnv change in a segment of dna. Can be large or small, this pic shows large structural changes, can see at cytogenetic level. Using fluorescently labeled dna to probe a metaphase spread of chromosomes. Green dna control dna, normal dna that you have. Red dna test dna, often disease phenotype like tumour dna. Two filters, o(cid:374)e that"s looki(cid:374)g for gree(cid:374) a(cid:374)d o(cid:374)e that"s looki(cid:374)g for red, take two diff pi(cid:272)tures. Use computers to merge the two images on the right yellow is equal hybridization of the two test and control samples, no change in cnv. Red = cnv loss or deletion in test sample. Seeing more red = more of red dna at that location. For your test, it means there is more red in that sample, it means that there is a gain for your test or a loss for your reference. Is there a cnv gain or loss for your test sample.

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