Nucleic Acids

Question 1

Base-stacking

Answer 1

Stabilises electron cloud interactions
Buries hydrophobic bases
Propeller twist of ~17o
Optimal in extended DNA configurations, and 5’-G-C-3’ sequences

Question 2

Electrostatic repulsion

Answer 2

Inter-strand: destabilises double helix, countered by Mg2+

Intra-strand, favours extended configuration, countered by Mg2+, histones

Question 3

Structural and chemical differences between RNA and DNA

Answer 3

2’-OH
Uracil - 5-methyl group
Single-stranded - more structurally versatile
Non-canonical base-pairs

Question 4

Secondary structures of RNA

Answer 4

A-form dsRNA
Stem-loop hairpins, buldge, distortions
Pseudoknots
Metal ions stabilisation
Hoogsteen

Question 5

Structure of Pro RNA Pol and how it binds to promoter

Answer 5

a2BB’w
sigma4 - -35
sigma2 - melted -10
aCTD - UP element

Question 6

Homeodomain

Answer 6

3 a-helices
Resembles HTH motif
Recognition helix inserts into major groove, forms H-bonds with base-pairs
eg. Ubx

Question 7

Zinc Fingers

Answer 7

C2H2 Zn fingers 
Coordinated by 2Cys and 2 His
BBa structure, recognition helix into major groove
Non-palindromic sites
Eg. TFIIIA

C4 Zn fingers - 4 Cys residues
Eg. Steroid hormone receptors
Dimers, non-palindromic

Question 8

Leucine Zipper

Answer 8

Two long a-helices formed by a coiled coil dimer

Dimerisation in C-terminus, DNA-binding in N-terminus
Leu every 7 residues, hydrophobic interactions mediate dimerisation
DNA-binding region has basic residues, docks on major groove on opposite sides as dimers.
Eg. AP-1, Myc

Question 9

Basic HLH

Answer 9

• Within a dimer, the DNA-binding region is formed by two long α-helices (each from a monomer), inserted into the major groove
o Long α-helix has basic amino acids that facilitates DNA-binding
• Dimerization surface is mediated by both the short and long α-helices of each monomer
o The long α-helix is involved in both DNA recognition and dimerization, while a second shorter α-helix is also involved in dimerization

Eg. MyoD, while Id has no DNA-binding domain