DNA Gymnastics

Question 1

bDNA twist

Answer 1

10.5 bp/turn

Question 2

what must happen when nucleosome bends dna?

Answer 2

E bend from E torsion and E stacking must be counterbalanced by E bend

Question 3

measure of flexibility of DNA

Answer 3

persistence length: length of DNA which can form a complete circle without strain @ temp T

525 bp for bdna

Question 4

E input vs. bp

Answer 4

picture

Question 5

straight dna
made of
defined as

Answer 5

poly a poly t

base pair midpoint aligns on axis

Question 6

DNA is locally flexible

Answer 6

bend over a few bp

find angle by drawing line thru midpoints.
\/ apex of theta

can still bp all

Question 7

bending and grooves

Answer 7

bending always changed groove size

good to fit things like protein pieces

Question 8

kink

Answer 8

sharp bend: bp are interrupted

Question 9

what allows protein to bind nucleics (physically)?

Answer 9

bend open DNA - can intercalate: replace base stacking with aromatic

Question 10

bendable vs bent

Answer 10

independent of each other

bendable: easily deformed, determined by stacking E
bent: lowest energy conformation isnt straight; determined by base-step roll angle

base pair (A or C, etc) determine bendability

Question 11

parameters that independently define base-step parameters

Answer 11

roll and slide!

Question 12

which base steps are the flattest? ie., have the lowest___

Answer 12

lowest roll angle

RpR and YpY

Question 13

YpR and RpY roll angle relation

Answer 13

are opposites!

Question 14

bent base steps can be straight if

Answer 14

the overall is straight even if individual base steps have nonzero roll angle

Question 15

roll of bDNA

Answer 15

slightly negtive-> slight negative writhe

Question 16

how to determine bendability

Answer 16

distribution of crystal structure has large variance

Question 17

flexibility of DNA :=

Answer 17

how easy to deform a base step away from characteristic geometry
related to stacking energy

Question 18

slide vs. roll chart tells us:

Answer 18

picture
poly A poly T straight stiff
CpA TpG TpA most flexible
stiff bents exist
CpG most bent naturally towards major (major compresse)

Question 19

circular permutation assay

finds where the bend is

Answer 19

cleave circle with 1 bend at different places-> linear with bent at different place

fastest has bend on end bc has lower radius of gyration

Question 20

bend site phasing: what happens if there is more than 1 bend?

Answer 20

phase is an angle aroud the mid axis of helix
bp are in phase if htey face same direction
ie, if angular distance =n360/10.5

if bends are in phase, the whole is more bent/less straight

Question 21

electrophoretic mobility vs. bend site phase

Answer 21

minima whenever in phase

Question 22

a-tract bending paradox A5T5

Answer 22

(cT4A4g)n straight but (cA4T4g)n highy bent
A tracts are very straight (AAAAA/TTTTT)

A tracts have very narrow minor grooves; locally bent, but a tracts bent out of phase, so overall straight

Question 23

DNA looping

Answer 23

short persistance -> bendable -> form loops easily
has less to do with sequence; more with topological constrained
topological contraight if closed or end contrained (chromosomes); linear or knicked circles has no toppo constraints-only persistence length

Question 24

supercoil density

Answer 24

Writhe/turn: 1 supercoil per 20-25 bp

can store E in supercoil like spring- release 10kcal/mol=E/ATP

Question 25

plectonemic
paranemic
toroidal

Answer 25

angle between outer strand and loop dna \0/

mmore than 90 (small loop) smaller than 90 (large loop)

Question 26

Linking number=

Answer 26

DNA twists + write (supercoil number)

Question 27

how to change twist when lk constant

Answer 27

unwinding
change from B to Z or A( z larger because left handeD)
intercalating agents
topoisomerases that ceave and religate

Question 28

2D gel to discern +- supercoiling

Answer 28

1. run gell 1 D: more supercoiled will run farther

2. add ethidium bromide(-2 T->+2w) and run 2nd D