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Flashcards in Secondary Structure of Nucleic Acids Deck (18):
1

Structural Features of DNA

- Plectonemic
- Antiparallel
- Hydrogen Bonding
- Base Stacking

2

Plectonemic

- DNA consists of two right-handed helical chains coiled about a central axis.
- Chains can be separated only by unwinding

3

Anti-parallel

- the chains are arranged in an anti-parallel fashion with the hydrophilic phosphates on the outside and the hydrophobic bases on the inside.
- phosphates can interact directly with water
- negatively charged - hydrophilic.
- bases can interact with each other.
- bases are the main force stabilizing the double helix.

4

Hydrogen bonding

- the specificity of strand interaction and thus the basis of replication and transcription depends on AT/GC hydrogen bonds
- purines hydrogen bond to pyrimidines
- AT - 2 H bonds
- GC -3 H bonds

5

Base Stacking

- bases lie in parallel planes allowing extensive hydrophobic interactions to occur.
- These hydrophobic interactions provide the major force that stabilizes the DNA double helix.

6

biggest reason G/C more stable than A/T

- differences in hydrophobic stacking
- Driving force!

7

Relative interaction energies

- GC>AT in base pair stacking energies and bond energies
- GC 270X stronger than AT stacking
- GC hydrogen bonding 3X stronger than AT bonding
- This is sequence dependent

8

B-form DNA

- most information for protein binding found in major groove
- some proteins bind in minor groove
- not as sequence specific as major groove interactions

9

pitch of B-form DNA

- one complete turn of the helix
- takes about 10 bp
- 3.4 nm

10

diameter of B-form DNA

- 2 nm

11

A type

- bp/turn - 11
- rotation - (+)
- helical diameter - 2.3 nm

- clockwise (right handed)
- ionic conditions
- double stranded RNA
- DNA/RNA hybrid

12

B type

- bp/turn - 10.6
- rotation - (+)
- helical diameter - 2.0 nm

- clockwise (right handed)

13

Z type

- bp/turn - 12
- rotation - (-)
- helical diameter - 1.8 nm

- counterclockwise (left handed)
- left-handed so sign is (-) instead of (+)

14

A and Z form depends on

- base composition
- solvent environment
- topology

15

Ethidium bromide

- separate DNA electrophoretically on agarose gels
- interpolates between stacked base pair of DNA
- change in ionic environment greatly increases fluorescence of ethidium bromide allowing it to fluorescence orange when exposed to near UV light.
- visualize DNA bands

16

RNA secondary and tertiary structure

- t-RNA secondary structure - cloverleaf structure
- t-RNA tertiary structure - L shaped 3D structure

17

DNA secondary structure

- naked DNA
- Beta form
- in vivo only exists for short stretches. no long stretches

18

DNA tertiary structure

- 11-nm nucleosome fiber - short lived.
- 30 nm fiber
- Loop domains
- Higher order folding
- Metaphase chromosome