Secondary Structure of Nucleic Acids Flashcards
1
Q
Structural Features of DNA
A
- Plectonemic
- Antiparallel
- Hydrogen Bonding
- Base Stacking
2
Q
Plectonemic
A
- DNA consists of two right-handed helical chains coiled about a central axis.
- Chains can be separated only by unwinding
3
Q
Anti-parallel
A
- 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
Q
Hydrogen bonding
A
- 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
Q
Base Stacking
A
- 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
Q
biggest reason G/C more stable than A/T
A
- differences in hydrophobic stacking
- Driving force!
7
Q
Relative interaction energies
A
- 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
Q
B-form DNA
A
- most information for protein binding found in major groove
- some proteins bind in minor groove
- not as sequence specific as major groove interactions
9
Q
pitch of B-form DNA
A
- one complete turn of the helix
- takes about 10 bp
- 3.4 nm
10
Q
diameter of B-form DNA
A
- 2 nm
11
Q
A type
A
- bp/turn - 11
- rotation - (+)
- helical diameter - 2.3 nm
- clockwise (right handed)
- ionic conditions
- double stranded RNA
- DNA/RNA hybrid
12
Q
B type
A
- bp/turn - 10.6
- rotation - (+)
- helical diameter - 2.0 nm
- clockwise (right handed)
13
Q
Z type
A
- bp/turn - 12
- rotation - (-)
- helical diameter - 1.8 nm
- counterclockwise (left handed)
- left-handed so sign is (-) instead of (+)
14
Q
A and Z form depends on
A
- base composition
- solvent environment
- topology
15
Q
Ethidium bromide
A
- 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
