DNA Topology Flashcards
Hand rule for DNA
- point thumb and curl fingers around
- thus points in direction of axis where it is moving
clockwise
- right-handed helix
counter-clockwise
- left handed helix
Torsional stress and super coiling
- due to OVERWINDING in the primary coiling can be relieved by formation of supercoils in the OPPOSITE HANDEDNESS OF THE PRIMARY COILING.
- Conversely, torsional stress due to UNDERFUNDING in the primary coiling can be relieved by formation of supercoils of the SAME HANDEDNESS OF THE PRIMARY COILING
- Torsional stress in the primary coiling drives the supercoiling.
right handed
- twisted tight
- left-handed supercoil
- unwind - right handed supercoils.
DNA torsionally strained
- mostly DNA molecules are torsionally constrained - ends are not free to rotate - mostly covalently closed circular DNA
- linear DNA can be torsionally constrained if anchored to something - nuclear matrix.
DNA molecules of identical sequence but different LINKING NUMBERS
- degrees of coiling and supercoiling
- Topoisomers
Linking number
- invariant as long as the molecule stays uncut!
- total number of times the two DNA strands cross over each other in peace
L=W+T
T
- Twist
- property of the primary helix
- the number of times one strand crosses over the other in the primary helix.
W
- Writhe
- the twisting of the axis of the double helix about itself
- supercoiling.
Ideal linking number
- lowest energetic state
- relaxed with no withe and a twist of 10 bp/turn
if linking number lower than ideal
- molecule is under negative torsional stress
- and underwound
DNA more easily melted
- DNA under negative torsional stress
negatively supercoiled DNA
underwound
Twist right/left
RH = + LH = -
Writhe right/eft
RH = - LH = +
signs for writhe are opposite of twist
more turns/bp
- looser winding
fewer turns/bp
- tighter winding
cruciforms
- restores torsionally stressed molecules back to proper form through optimal twists.
- must contain inverted repeats
Z DNA
- must have alternating purines and pyrimidines on one strand.
4 ways of attaining optimal twist in torsionally stressed molecules
- Some bp completely unwound
- Z-DNA
- Supercoils
- Cruciforms
Gel electrophoresis
- the more highly supercoiled the faster it runs
gyrase
- Type II topoisomerase
- introduce negative coils by cutting both strands, unwinding DNA, then relegating
Type II topoisomerase
- make transient cuts in both strands of DNA and change linking numbers in increments of 2
- can introduce negative supercoils (requires energy)
- can relax positive or negative supercoils (not energy requiring)
- resolves a positive supercoils by converting it into a negative supercoil.
Type I topoisomerase
- make transient cuts in one strand of DNA and change linking numbers in increments of 1
- can relax positive or negative supercoils
Transcription and Translation
- DNA positively supercoiled in transcription and translation
- RNA polymerase melts DNA as it moves along
- overwinding DNA ahead of it and underwinding DNA behind.
Toroidal supercoil
- DNA crosses over another object and does not appear to cross over self.
- Actually does.
- left handed toroidal supercoils are actually right handed regular supercoils
