A vs B vs Z DNA, Triplexes and Quadruplexesdasher.wustl.edu/bio5357/lectures/lecture-15.pdf ·...
Transcript of A vs B vs Z DNA, Triplexes and Quadruplexesdasher.wustl.edu/bio5357/lectures/lecture-15.pdf ·...
N3
NN1
N
O N
O6N2
H
H
HN
N9
O
O
O
P
OO
O
P5'O O
O--O
H
5'
3'
H
3'
GO
OC
O
O
P
5'
P
5'
3'
3'
O
O-O
-O
5'
3'
G
5'
3'
C
O
O
O
P
N9 N3 HN2
3'
5'
OO-
O
O
N1O6
O
P
3'
5'
O O-
DIFFERENT PERSPECTIVES ON THE WATSON CRICK BASE PAIR (BP)
Looking into minor groove
minor groove side
MAJOR GROOVE SIDE
C2 pseudo axis of symmetry
TOP VIEW
SIDE VIEW
SCHEMATIC VIEW
5'-G-3'
3'-C-5'
Figure: wcbp1.cw2
5' 3'G
5'3'C
Helical parameters - [Figure 2-14]Helix axis. Line at the center of the helix parallel to thedirection of the helix.
Pitch - The distance traveled along the helix axis for a completeturn.
Helical repeat - The number of monomer units per completeturn.
Twist angle - Angle at which the pseudo dyad axis rotates ongoing from one base pair to the following base pair.
Diameter - Twice the largest radius in the helix.
Roll angle - Deviation of the angle about C6-C8 for a base pairthat is assigned zero for that in which the base pair plane isperpendicular to the helix axis.
Tilt - Deviation of the pseudodyad axis from 0 for that in whichthe base pair plane is perpendicular to the helix axis
Propellar twist - Angle between the planes of each individualbase of the base pair.
Displacement D - The distance between the helix axis and thecenter of the base pair.
Center of the base pair - The point where the C6-C8 bondcrosses the pseudodyad axis.
Helical rise per residue, h - Distance along the helix axisbetween the residues.
Dickerson Dodecamer (bdl001.pdb)
Figure BDNA1.ppt
Arnott A RNA Structure (arn0035.pdb)
Figure Adna.ppt
Comparison of groove width and depth
MAJOR
minor
MAJOR
MAJORMAJOR
minor
minor
A DNA B DNA
Figure AvsB.ppt
O
OP
O P
Base
O
OP
O P
Base
C2'-endo, 2E C3'-endo, 3E7.0 A 5.9 A
B DNA A DNA
3.4 A h = 3 A
Orientation of base pairsrelative to helix axis
h = 3.4 A3.4 A
file: c2ec3e1.cw2
Relationship between sugar pucker and helix type
C2’-endo C3’-endo
Contrasting A and B Helices A helix B helix helical repeat 11 10.5 displacement, d 4.4 -0.2 - -1.8 helical rise/residue, h 2.6-3.3 3.4 tilt 10-20 -6 twist 30-33 36-45 propellar twist sugar pucker C3’-endo, 3E C2’-endo and others, 2E intra chain P-P distance
5.9 7.0
Major groove width 2.7 11.7 depth 13.5 8.5 minor groove width 11 5.7 depth 2.8 7.5
Table: AvsB.doc
h
helic
al re
peat
minor grooveclash at 5'-Py-Pu-3'
major grooveclash at 5'-Pu-Py-3'
minimizingminor grooveclash at 5'-Py-Pu-3'
Figure calrule1.ppt
Consequences of propeller twisting on local B DNA structure and how DNA responds
Shifting BPover to minimizeclashes
Clash due to largetwist angle
Clash minimizedby decreasingtwist angle
Figure calrule2.ppt
Sequence-Dependent Variation of DNAStructure: Callidine’s rules
Local DNA structure can be viewed as aresult of two opposing effects:
1. The drive to optimize H-bonding and base stackinginteractions.
2. The drive to minimize unfavorable VDW interactionsbetween purines that result from the positive propellartwisting of the base pairs at Pu-Py (RY) and Py-Pu (YR)sequences.
DNA compensates for the clashes by bothlocal and coupled responses:1. Local Responses
a. Decrease propellar twist to 0b. Slide base pair over (reduce d)
2. Coupled Responsesa. Reduce relative twistb. Reduce relative roll angle
Document: calladine.doc
Major Groove
Minor Groove
local responses (at a base pair)
R Y Y R
propellar twist (always decrease)
-1 -1 -2 -2
d (open purine d, decrease pyrimidine d)
+1 -1 -2 +2
coupled responses (between base pairs)
x R Y x x Y R x
twist angle (always reduce) +1-2 +1 +2 -4 +2
roll angle (+ value defined as opening in the major groove; changing the central roll angle must be equally compensated by the adjacent roll angles)
+1 -2 +1 -2 +4 -2
table calladine.ppt
Relative magnitude of responses
CD of poly (dG-dC) at pH 7 25 oCSolid line: 0.2 M NaClDotted line: after addition of more NaCl
240 260 280 300wavelength (nm)
e L-e
R
-5
+3
Fig. 4-0
Split CD curve explained by exciton chirality rule
Rich hexamer Z DNA structure (zdf002.pdb)
Figure: zdna3.ppt
CpG stepC3G4-C9G10
GpC stepG4C5-G8C9
anti
syn
Interstrandbase stacking
Intrastrandbase stacking
Figure 4-3
Structural Features of Z DNA
1. No major groove, just a surface 13.8 A wide, 2 A deep.
2. Very deep and narrow minor groove, 3.7 A wide, 8.8 Adeep.
3. 18 A wide helix (19 A for B, 23 for A)
4. Interchain phosphate-phosphate distance of 7.7 A; highcharge density.
5. 12 bp/turn, 7.4 A/dinucleotide repeat
6. Watson Crick base pairing between C and G.
7. Dinucleotide repeat with an intrastrand GC pi stack at 5’-GC-3’ steps and an interstand CC pi stack at 5’-CG-3’steps.
8. Left-handed stacking at 5’-GC-3’ site with at twist of -50o and -15o twist at 5’-CG-3’ steps.
9. Helix axis is dislocated at 5’-CG-3’ steps.
10. G is in a syn glycosyl conformation, C is in an anticonformation.
Figure: zfeature.cwg
NN
N
N
O
N
H
HH
O
O
O
N O
O
O
N
O
NHH
file: b2z1.cw2
3'-up
5'-down5'-up
3'-down
NN
N
N
O
N
H
HH
O O
O N OO
O
N
O
NH
H
3'-down5'3'-up
Base pairflips by 180o
anti anti
5'-up
OC
O
O
5'
3'
OG
O
O
OG
O
O
OC
O
O5'
3'glycosylbond rotates
wholenucleosiderotates
SIDE VIEW
TOP VIEW
Flipping of Base Pairs in B to Z transition
Figure 4-4
GC GC
GC GC
GC GC
GC GC
CG CG
CG CG
CG CG
CG CG
3' 5'
5' 3'
3'
5'
5'
3'
GC
GC
GC
GC
CG
CG
CG
CG
B DNA Z DNA
Figure: b2z1.cdr
=O
aa
a
aa
aa
aa
a
a a
a a
a a
a a
a a
a a
a a
s
s
ss
ss
ss
a= anti glycosyls = syn glycosyl
Conformational Transition BetweenB and Z DNA
Figure 4-5
A nanomechanical device based on B to Z transtion
Donor and acceptor molecules (fluorescein and Cy3) are attached to a DNA molecule containing a (GC)20section. When in B form the two dyes are close and show strong FRET, when in Z form, the DNA unwinds by about 3.5 turns, and extends about 6 A, changing the distance by 20-60 A, and greatly lowers the FRET.
Nature. 1999, 144-6
NN
NN
O
NHH
H
OO
OP
OO
O
O-
C
OPOO
HOMg
O
HH
H2O
OH2
OH2
H2OH
O
Figure: mg_zdna1.cw2
Ion (mM) poly d(G-C) poly d(G-m5C)
Na+ 2500 700
Mg2+ 700 0.6
Ca2+ 100 0.6
Ba2+ 40 0.6
Co(NH3)63+ 0.02 0.005
EtOH 60% v/v 20%
Mg2+ + 10% EtOH 4 mM -
Mg2+ + 20% EtOH 0.4 mM -
Minimum Salt ConcentrationRequired to Form Z DNA
Figure 4-6
NN
N
N
O
N
H
HH
H
dR
CH3
CH3
dR
H
HH
O
N
NN
m5Cm7G
Figure: zfactors.cw2
Structural factors favoring Z DNA formation
electrostatics(Z DNA has highercharge density)
hydrophobicity(methyl group occupieshydrophobic pocket)
less severe steric interactionsin the syn conformation whichis the conformation at the purinesite in Z DNA
N
NN
N
O
N
HH
HN
RO
RO O OCH3
bad steric interactionsin the anti conformation
N
NN
N
O
N
H
H
H
N
ORO
RO
CH3
O
Figure 4-7
Figure 4-8
NN
NN
N
N
O
N
H
HH
H N
O
dR
HH
H
H
dR
NN
NN
N
N
O
H
H N
O
dR
HH
H
H
dR
NN
NN
N
N
N
N
H
HH
H O
O
dR
H
H
HH
dR
inosine
2-aminopurine
Figure: 2ap_ino1.cw2
Polymer C2-NH2 group Helix
d(A)•d(T) no B
d(I)•d(C) no B
d(IIT)•d(ACC) no B
d(AG)•d(CT) yes B, A
d(AGC)•d(GCT) yes B, A
d(GC) yes B, A, Z
d(GT) yes B, A, Z
d(2AP-T) yes B, A, Z
Effect of Substituents on DNA Conformation
Figure 4-1 Figure 4-9
Figure 1 The fused hexagon motif of A-tract DNA. The four layers are coded by color with the primary layer light blue, the secondary layer magenta, the tertiary layer blue, and the quaternary layer red. The fused hexagon motif is shown in space filling representation, with van der Waal radii of oxygen atoms. (a) Stereoview into the minor groove of the DNA. The DNA is colored by CPK and shown in stick representation. (b) View across the groove, approximately down the normal of the central hexagons. Sites of potassium occupancy are indicated by plus signs. The DNA bases are shaded. Base functional groups that interact with the fused hexagon motif are indicated by circles. (c) The geometry of the sodium form fused hexagon motif. Distances are in red and angles are in white.
Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry. 1998 Dec 1;37(48):16877-87.
http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi982063o
Metal cations bind in the minor groove with water
Figure 4-9b
The role of minor groove functional groups in DNA hydration. Nucleic Acids Res. 2003 Mar 1;31(5):1536-40.
http://nar.oxfordjournals.org/cgi/content/full/31/5/1536
Loss of O2 carbonyl disrupts spine of hydration
Figure 4-9c
O
O
P
O P
Base
OH O
O
P
O P
Base
OH
C2'-endo, 2E C3'-endo, 3E
B Form of RNA A Form of RNA
Figure. zfactor2.cwg
Z DNA intrastrandphosphate hydration
Z: 6.2 A
Z: 5.6 A
P
O
OH
OH
O
O
P HOH
O
O
P
Conformational and Electrostatic Factors Favoring Various Forms of DNA or RNA
A: 5.7 A
B: 6.7 A
cannotH bond
Figure 4-10
Figure 4-11
A260
molar % dT10 molar % dT10
A260
50 50
1
0.9
0.8
0.7
0.6
File: TAT_mix1.cw2
Evidence for Triplex Helix Formation FromMixing Experiments Monitored by UV
1001000 0 66
Analysis of mixing curves of nucleic acids by UV relies on the hypochromic effect observed upon formation of stacked base apirs
d(T)10 + d(A)10 nd(T)10d(A)10
1
0.9
0.8
0.7
0.6
Figure 4-12
N
N
N
N
O
N
H
H
H
H
H
H
H
H
O
N
N
N
H
H
H
H
H
ONN
N
N
N OO
CH3
H
H
N
N
O
O
CH3
HH
H
H
H
HN
N
N
N
N
Figure: trip_bp1.cw2
Major groove
antiparallel A helix
Watson Crick base pair
parallel
helix,
Hoogsteen
base pair
protonated C required
for base pairing
5 ' - TTTTTTTTTT- 3 '5 ' - AAAAAAAAAA- 3 '3 ' - TTTTTTTTTT- 5 '
HoogsteenWatson-
Crick
5 ' - CCCCCCCCCC- 3 ' ++++++++++5 ' - GGGGGGGGGG- 3 '3 ' - CCCCCCCCCC- 5 '
Hoogsteen
(+ indicates H+)
Watson-
Crick
Polypyrimidine Triplex Motif
Figure 4-13
anti parallelhelix,ReverseHoogsteenbase pair
antiparallel A helixWatson Crick base pair
Major groove
Figure: trip_bp2.cw2
N
H
NN
O
O
CH3
HH
H
H
HHN
N
N
NN
NH
N
N
N
NN
N
N
O
N
H
HH
H
H
HH
H
O
N
NN
H
HN
H
O
NN
N
N
Watson-Crick
ReverseHoogsteen
3'-GGGGGGGGGG-5'5'-GGGGGGGGGG-3'3'-CCCCCCCCCC-5'
Polypurine Triplex Motif
Watson-Crick
ReverseHoogsteen
3'-AAAAAAAAAA-5'5'-AAAAAAAAAA-3'3'-TTTTTTTTTT-5'
Figure 4-14
Figure 4-15
5'- AGGAAG GAAGGA 3'3'- TCCTTC CTTCCT 5'
5'- AGGAAG3'- TCCTTC
TCCTTC
3'5'
AGGAAG single strand
triplex
Figure: Hdna1.cw2
GAAGGA
5' 3'
CTTCCT
CTTCCT 3'GAAGGA 5'
single strand
triplex
H DNA, Hoogsteen DNA or Hinged DNAforms in reverse repeat purine DNA under high negative supercoiling
reverse repeatnot inverted repeat
The End Replication Problem
Succesive rounds of replication lead to progressive shortening of the ends of DNA
RNA RNA RNA
missingDNA
replication of this strand results in a shorter DNA
Telomerase solves the End Replication Problem, RNA templated DNA synthesis
elongationelongation
translocation
ribonucleoprotein
Annu. Rev. Pharmacol. Toxicol. 2003. 43:359–79
Figure 4-21b
Schematic structure of a telomere
single strand end protected by DNA displacement loop formation
POTprotectionof telomerebinds TTAG3
The G’s in the telomere sequence can form Quartets via HoogsteenBase Pairing,• Hoogsteen base pairing leads to circluar tetrad.• Center of quartet has large negative electrostatic
potential that can bind cations• all anti glycosyl conformation leads to parallel
stranded quadruplex
Figure 4-22
N
NN
N
O
N
H
H
H
HN
N
N N
O
NHH
H
H
N
NN
N
O
N
H
H
H
H
H
HH
HN
O
N N
NN
Figure: G_tetra1.cw2
+
Ways of forming intramolecular quadruplexformation with [GxNy]z with 3 types of loops: propeller, lateral, diagonal
Figure 4-27
3'
5'
3'
5'
5'3'
diagonal loop
lateral loop
externalloop
externalorpropellerloop
lateral loop
lateral loop
lateral loop
5'
3'
lateral loop
lateral loop
lateral loop
propeller
basketchair
hybrid
a
aa
a
aa
ss
ss
s s
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
s
s
ss
s
s
aa
a
a
aa
s
ss
s
s s
Flip centralBase quad
Glycosyl conformation depends on strand orientation. Bases in one base quad can all flip from anti to syn, and syn to anti
Figure 4-28
Front. Chem. 4:38. doi: 10.3389/fchem.2016.00038
J. Phys. Chem. B, Vol. 110, No. 32, 2006 16077
Li+ is strongly hydrated and cannot bindNa+
fits in the plane
K+ fits between the planes
Cramer and Truhlar
propellar
lateral
lateral2
3
syn
anti
A21
T20
T19
G18
G17
G16
A15T14
T13
G12
G11
G10A9
T8
T7
G6
G5
G4
A3
1
1
2
3
G11
G12
T13
T14
A15
G23
G24
T20
A21
T7
G10
A9T8
A3
G4
G5
G6
syn
anti
G22
T19
K+
T8
T7
G4
G5
G10
G11
X
T13A15
G17
G18
T19A21
G12
G16
syn
anti
T20
T14
G6
A9
Y
5'3'
diagonal
lateral lateralT8
T7G10
G11
T13
T14
A15
G17
T19
A21
G12
syn
anti
A9T18
Na+
Na+
Na+
G5
G6G18
G16 G4
laterallateral
diagonal
hybrid-1 hybrid-2
basket form 3
Characterized human telomeric DNA G-quadruplex structures in solution by NMR (See tutorial)
Folding and Unfolding Pathways for the Human Telomeric G-Quadruplex
J. Mol. Biol. (2014) 426, 1629–1650