Structure of Genome Part 2

Question 1

Rate of denaturation

Answer 1

• Not concentration dependent

- rapid

Question 2

Rate of renaturation

Answer 2

• 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.

Question 3

Why must DNA be reduced to smaller fragments for renaturation?

Answer 3

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

Question 4

DNA can be denatured by

Answer 4

• heat
• alkali
• acid

Question 5

if one quickly removes the heat or neutralizes the DNA solution

Answer 5

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

Question 6

to prevent renaturation

Answer 6

• boil to denature

- immerse on ice

Question 7

if DNA slowly cooled

Answer 7

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

Question 8

the process requires a

Answer 8

• nucleation event

- slow step

Question 9

nucleation

Answer 9

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

Question 10

after nucleation

Answer 10

• rest of DNA molecule rapidly renatures if strands are complementary

Question 11

zipping up

Answer 11

• when nucleation is correct

- unstable hybrids zip up to form stable hybrids

Question 12

productive nucleation

Answer 12

• occurs because base pairs are complementary

Question 13

nonproductive nucleation

Answer 13

• will go no further and basepairs will fall apart

- rest of DNA will not complement

Question 14

Renaturation will never be complete

Answer 14

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

Question 15

why we use parameters for half of the molecules

Answer 15

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

Question 16

stringency

Answer 16

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

Question 17

if stringency too low

Answer 17

• nonspecific hybridization can occur.

Question 18

solution hybridization

Answer 18

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

Question 19

blot hybridization

Answer 19

BUT

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

Question 20

Nucleic acid blotting hybridization named for

Answer 20

• the blotted molecule

- not the probe

Question 21

Northern blots

Answer 21

• RNA blots

Question 22

Southern blots

Answer 22

• DNA blots