DNA Topology Flashcards Preview

GN 421 > DNA Topology > Flashcards

Flashcards in DNA Topology Deck (27):
1

Hand rule for DNA

- point thumb and curl fingers around
- thus points in direction of axis where it is moving

2

clockwise

- right-handed helix

3

counter-clockwise

- left handed helix

4

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.

5

right handed

- twisted tight
- left-handed supercoil
- unwind - right handed supercoils.

6

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.

7

DNA molecules of identical sequence but different LINKING NUMBERS

- degrees of coiling and supercoiling
- Topoisomers

8

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

9

T

- Twist
- property of the primary helix
- the number of times one strand crosses over the other in the primary helix.

10

W

- Writhe
- the twisting of the axis of the double helix about itself
- supercoiling.

11

Ideal linking number

- lowest energetic state
- relaxed with no withe and a twist of 10 bp/turn

12

if linking number lower than ideal

- molecule is under negative torsional stress
- and underwound

13

DNA more easily melted

- DNA under negative torsional stress

14

negatively supercoiled DNA

underwound

15

Twist right/left

RH = +
LH = -

16

Writhe right/eft

RH = -
LH = +

signs for writhe are opposite of twist

17

more turns/bp

- looser winding

18

fewer turns/bp

- tighter winding

19

cruciforms

- restores torsionally stressed molecules back to proper form through optimal twists.
- must contain inverted repeats

20

Z DNA

- must have alternating purines and pyrimidines on one strand.

21

4 ways of attaining optimal twist in torsionally stressed molecules

- Some bp completely unwound
- Z-DNA
- Supercoils
- Cruciforms

22

Gel electrophoresis

- the more highly supercoiled the faster it runs

23

gyrase

- Type II topoisomerase
- introduce negative coils by cutting both strands, unwinding DNA, then relegating

24

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.

25

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

26

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.

27

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