Download DNA Structure exercise v2.pptx

2013 Cottrell Scholars Collaborative
New Faculty Workshops in Chemistry
Exploring Watson-Crick Base Pairing and DNA Structure
Learning Goals – Content Knowledge
1)  Explore how hydrogen bond donors and acceptors of the nucleosides(tides)
influences the overall double helical structure of DNA including
isosteric nature of the W-C basepairs and groove structure.
2)  Predict the impact of a non-W-C pairing on a DNA double helix? Find evidence
to support or refute your initial prediction by using the models provided.
3)  Explore how the groove structure of a double helix might allow a protein to
“read” a DNA sequence without having to unwind the DNA duplex.
Learning Goals – Skills Development
•  Use models to visualize biomolecular structures
•  Transition between structural scales (atomic/macromolecular)
• 
Recognize links between atomic functionality and macromolecular
properties/behavior
The common nucleosides
H
H
N
HO
N
N
N
H
N
O
N
N
HO
H
N
N
N
O
O
H
OH
OH
deoxyguanosine
deoxyadenosine
H
H
O
N
H
N
N
N
HO
N
HO
O
O
O
O
OH
OH
deoxythymidine
deoxycytidine
Use the nucleotides to explore the Watson-Crick base pairing patterns. - Compare the distance between pairs
of carbon atoms (C1’-C1’ or C4’-C4’)? Are they equidistant for A•U and G•C base pairs?
0
1
2
3
4
5
6
7
8
1 Cottrell Scholars Collaborative
New Faculty Workshops in Chemistry
2013 What properties of the nucleotides give rise to the structure
of B-form DNA?
Sequence specific read out occurs in the grooves of
duplex DNA
2 2013 Cottrell Scholars Collaborative
New Faculty Workshops in Chemistry
Reading the sequence of
DNA without unfolding
the duplex
Use the models of the AT and GC base-pairs above to consider the potential
interaction surface in the major and minor grooves of the following DNA
sequences: (↑ = donor; ↓ = H-bond acceptor; ∅ - CH3 steric interaction; O - H atom)
EcoRI binding site
Major Groove
5
3
G
C
A
BamHI binding site
Minor Groove
3
5
Major Groove
3
5
G
C
T
G
A
T
A
T
T
A
C
G
G
C
T
A
A
T
T
5
3
Minor Groove
3
5
G
C
C
G
C
A
T
A
T
A
T
A
T
A
T
A
C
G
C
G
C
G
C
G
C
G
5
3
5
3
3
5
Reading the sequence of
DNA without unfolding
the duplex
Use the models of the AT and GC base-pairs above to consider the potential
interaction surface in the major and minor grooves of the following DNA
sequences: (↑ = donor; ↓ = H-bond acceptor; ∅ - CH3 steric interaction; O - H atom)
EcoRI binding site
Major Groove
5
3
G ↓ ↓! ↑ O C
BamHI binding site
Minor Groove
3
5
G ↓! ↑ ↓! C
Major Groove
3
5
G ↓ ↓! ↑ O C
Minor Groove
3
5
G ↓! ↑ ↓! C
A ↓! ↑ ↓! ∅ T
A ↓! O ↓! T
G ↓ ↓! ↑ O C
G ↓! ↑ ↓! C
A ↓! ↑ ↓! ∅ T
A ↓! O ↓! T
A ↓! ↑ ↓! ∅ T
A ↓! O ↓! T
T ∅ ↓! ↑ ↓! A
T ↓! O ↓! A
T ∅ ↓! ↑ ↓! A
T ↓! O ↓! A
T ∅ ↓! ↑ ↓! A
T ↓! O ↓! A
C O ↑ ↓! ↓! G
C ↓! ↑ ↓! G
C O ↑ ↓! ↓! G
5
3
C ↓! ↑ ↓! G
5
3
C O ↑ ↓! ↓! G
5
3
C ↓! ↑ ↓! G
3
5
3