Structure of Genome Part 2 Flashcards Preview

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Flashcards in Structure of Genome Part 2 Deck (22):
1

Rate of denaturation

- Not concentration dependent
- rapid

2

Rate of renaturation

- concentration dependent
- ssDNA molecules must find each other in solution
- more of them (more concentrated), easier to find other molecules and reanneal
- The Law of Mass Action applies.

3

Why must DNA be reduced to smaller fragments for renaturation?

If the fragments are too large, they will get tangled and won't be able to renature

4

DNA can be denatured by

- heat
- alkali
- acid

5

if one quickly removes the heat or neutralizes the DNA solution

- DNA will collapse into a compact random coil in which some bases are hydrogen bonded

6

to prevent renaturation

- boil to denature
- immerse on ice

7

if DNA slowly cooled

- the two single strands can reform a paired double helical model

8

the process requires a

- nucleation event
- slow step

9

nucleation

- regions of complementary bases on opposite strands find each other and some base pairing occurs

10

after nucleation

- rest of DNA molecule rapidly renatures if strands are complementary

11

zipping up

- when nucleation is correct
- unstable hybrids zip up to form stable hybrids

12

productive nucleation

- occurs because base pairs are complementary

13

nonproductive nucleation

- will go no further and basepairs will fall apart
- rest of DNA will not complement

14

Renaturation will never be complete

1.) Random shearing leaves some regions unpaired
2.) As renaturation progresses, the concentration of single-stranded molecules decreases and the rate of renaturation drops

15

why we use parameters for half of the molecules

- we do not use parameters for all of the molecules to renature because it will never run to completion

16

stringency

- must be correct to prevent tangles of random coils that could form in even relatively short segments of DNA

17

if stringency too low

- nonspecific hybridization can occur.

18

solution hybridization

- kinetics of hybridization are much easier to understand if all molecules are free in solution

19

blot hybridization

BUT
- blot is more convenient and makes possible some experiments that could not be done by solution hybridization

20

Nucleic acid blotting hybridization named for

- the blotted molecule
- not the probe

21

Northern blots

- RNA blots

22

Southern blots

- DNA blots