Sept 20 Flashcards
What 2 factors influence the Tm of DNA?
GC has 3 H-bonds, more GC content would increase Tm because GC has lower entropy
- Ionic strength, the + ions interact with - DNA backbone and decreases the repulsion between the 2 backbones of the same helix. More salt would increase Tm
How can detect formation of ssDNA and re-annealing of DNA?
Using absorbance, DNA at 260 nm and ssDNA absorbers 40% more at 260 than DNA as the bases are more exposed.
What is DNA hybridization?
2 Similar strands denature from their other strand and come together. If a region is missing then the other strand has a bulge where it doesn’t match. on
Southern blots vs Northern blots?
Southern to detect DNA, Northern for RNA. A DNA probe is labeled and used to detect the RNA/DNA.
What is cccDNA?
It is covalently closed circular DNA for bacteria
Can straight DNA unwind more easily than bacterial DNA?
NO, proteins sit on dsDNA and so when a section of DNA unwinds, it still just creates tension as it has fixed points from bound proteins on it, generates torsional stress.
What is the linking number?
It is an interger representing the number of times DNA strand must pass through other to completely separate the strands. Has twisting and writhing
What is supercoiled DNA?
It is when DNA helix twists upon itself, determined by writhe
What are topoisomerases?
They are diff forms of DNA
What is Pos vs neg supercoiling?
Pos supercoiling is overwound. Neg is underwound. If a right handed helix (like our DNA), then twisting it more right handedly will overwind it.
Why do we have more underwound (neg supercoiled) DNA?
It is becuase neg supercoiling takes less E to unwind than pos.
Why would bacteria want to have pos supercoiling in DNA?
If in hot temp, they want to keep DNA stable and not all over the places with genes always available.
How would supercoiled DNA migrate compared to open circular and linear?
Open circular slowest, then linear, and supercoiled would be fastest.
