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Molecular Biophysics Unit
DNA structure and dynamics
-as revealed by Crystallography and MD simulation
Prof Manju Bansal
Molecular Biophysics Unit
• A Brief History
• DNA structure and dynamics
Molecular Biophysics Unit
--Lehninger 5th Ed
Molecular Biophysics Unit
Molecular Biophysics Unit
Molecular Biophysics Unit
Molecular Biophysics Unit
Molecular Biophysics Unit
1. Chargaff's Rules.
Erwin Chargaff at Columbia University had, for a long time, measured the base compostion of nucleic acids. The curious feature of his data, which we now know as Chargaff's rules, was that the amount of adenine nearly always equalled the amount of thymine and the amount of cytosine nearly always equalled the amount of guanine.
The following table shows some sample data that he collected:
mol % of bases Ratios Source
A G C T A/T G/C %GC
PhiX-174 24.0 23.3 21.5 31.2 0.77
¦ 1.08 44.8
Maize 26.8 22.8 17.0 * 27.2 0.99 0.98 46.1
Octopus 33.2 17.6 17.6 31.6 1.05 1.00 35.2
Chicken 28.0 22.0 21.6 28.4 0.99 1.02 43.7
Rat 28.6 21.4 20.5 28.4 1.01 1.00 42.9
Human 29.3 20.7 20.0 30.0 0.98 1.04 40.7
Molecular Biophysics Unit
WC base-pairing
Hoogsteen base-pairing
Molecular Biophysics Unit
X-Ray fibre diffraction patters of A-DNA (left) and B-DNA (right). Images from the Maurice Wilkins 1952 Nobel Lecture at the Nobel Prize Foundation web site
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Molecular Biophysics Unit
Molecular Biophysics Unit
DNA facts:
Deoxyribose - Nucleic Acid
Base composition:
Erwin Chargaff
(A)=(T), (G)=(C)
X-ray pattern:
Rosalind Franklin
Structure:
James Watson & Francis Crick
- base pairing between
A-T and G-C
- double helical model with
10 units per turn.
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B A Z
5’
5’
5’
Molecular Biophysics Unit
Molecular Biophysics Unit
The various forms of DNA have been identified as A, B, C etc.
In fact, a detailed inspection of the literature reveals that only
the letters F, Q, U, V and Y are now available, to describe any
new DNA structure that may appear in future. It is also
apparent that it may be more relevant to talk about the A, B or
C type dinucleotide steps, since several recent structures
show mixtures of various different geometries and a careful
analysis is essential before identifying it as a ‘new structure’.
A Glossary of DNA structures from A to ZA. Ghosh & M. Bansal , Acta Cryst D, vol 59 (Apr 2003)
DNA structures from A to Z
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NMR structure Model structure
DNA triple helix
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Molecular Biophysics Unit
Molecular Biophysics Unit
G-quadruplex structure
Molecular Biophysics Unit
G-Quadruplex
AGGGTTAGGGTTAGGGTTAGGGGGGG(Bro)UTTTGGGG
Molecular Biophysics Unit
Holliday Junction
Molecular Biophysics UnitHolliday Junction
Molecular Biophysics Unit
• A Brief History
• DNA structure and dynamics
Molecular Biophysics Unit
• A Brief History
• DNA structure and dynamics
Molecular Biophysics Unit
Molecular Biophysics Unit
Molecular Biophysics Unit
Molecular Biophysics Unit
Molecular Biophysics Unit
αααα O3’-P-O5’-C5’ (g-)
ββββ P-O5’-C5’-C4’ (t)
γ γ γ γ O5’-C5’-C4’-C3’ (g+ )
δ δ δ δ C5’-C4’-C3’-O3’ (2E)
ε ε ε ε C4’-C3’-O3’-P (t)
ζ ζ ζ ζ C3’-O3’-P-O5’ (g-)
Backbone conformationBackbone conformation
Molecular Biophysics Unit
Molecular Biophysics Unit
Molecular Biophysics Unit
All torsion angles vs alpha for oligomer crystallographic dataset
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tRNA: schematic
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tRNA
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tRNA-Phe
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Intra base pair parametersIntra base pair parameters
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Dinucleotide parameter
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Dinucleotide parameters decide the DNA structure
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Molecular Biophysics Unit
TATA box – TBP complex
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Molecular Biophysics Unit
Twist vs Roll for extended crystallographic dataset (2006):Including Oligomers and Protein bound DNA complexes
Molecular Biophysics Unit
Zp
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Zp vs Slide for oligomers dataset
Molecular Biophysics Unit
GROOVE WIDTH:GROOVE WIDTH:
measure of minimum inter-strand P..P distance
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Nucleosome Structure
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Minor groove width histogram:
Oligomers crystallographic dataset
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Brief Outline of MD Results
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Dixit et al, Biophys J 89,2005
MD: Sugar Phase Angles for the136 unique tetranucleotides
Molecular Biophysics Unit
Dixit et al, Biophys J 89,2005
State 1
State 2
State 3
State 4
State 5
State 6
State 7
MD: α/γ/ε-ζ/ distribution for the136 unique tetranucleotides
Molecular Biophysics Unit
Beveridge et al, Biophys J 87,2004
MD: Distribution of the values of 6 local step parameters for CG step in a GCGC tetranucleotide
Molecular Biophysics Unit
12.2(1.0)
11.7(1.6)
12.7(1.4)
G:C
13.6(1.0)
12.5(1.8)
12.8(1.5)
T:A
11.4(1.3)
11.4(1.1)
11.0(1.1)
T:A
10.4(1.0)
10.4(0.7)
10.1(0.7)
T:A
10.2(0.9)
10.4(0.8)
10.1(0.7)
A:T
10.7(0.9)
11.3(1.1)
10.7(0.9)
A:T
11.9(1.1)
12.6(1.2)
12.3(1.0)
A:T
12.7(1.0)
12.0(1.5)
13.3(1.2)
C:G
A3T3 (Ber,
rand)
Å
A3dU3 (Ber)
ÅA3T3 (Ber)
Å
MD results: 6-7ns mean minor groove width
Molecular Biophysics Unit
d(CGTTTTAAAACGTTTTAAAACGTTTTAAAACG)
d(GACTAAAAATGACTAAAAAATGACTAAAAAT)
d(GCAAAATTTTGCAAAATTTTGCAAAATTTTGC)
MD : sequence dependent curvature
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Biological Implications of the Sequence Dependent Variation in DNA Structure
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Transcription:
Transcription
Promoter TerminatorGene
RNA polymerase
RNA
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How does RNA polymerase know
where to start transcription?
It is through sequence motifs which match the consensus sequences in -10 and -35 regions,
but large variability seen. Also similar sequences seen in non-promoter regions.
Molecular Biophysics Unit
Some typical sequence motifs
• There are few sequence motifs which exactly match the consensus sequence, large variability seen.
• Similar sequences seen in non-promoter regions.
-35 -10
TATAATTACTGTGACACTTATGGT
TSS
17 bp
SPACER1
TTGACACTGACGTGGACTGTCACA
ConsensusaraBADaraCgalP1
Molecular Biophysics Unit
Structure of the complex of DNA and TATA-box binding protein
Molecular Biophysics Unit
Dinucleotide Rollo
Tilto
Twisto
CA/TG(BI)* 5.10 -0.31 31.03
GG/CC 5.02 -1.83 32.4
AG/CT 4.30 2.68 29.46
CG/CG 3.50 0.15 34.1
TA/TA 2.94 0.04 39.94
AA/TT 2.60 -1.66 35.58
AC/GT -0.70 -0.15 33.29
AT/AT -1.79 0.21 32.49
GA/TC -2.31 -0.88 38.55
GC/GC -6.49 -0.18 38.61
CA/TG(BII)* -7.50 0.68 47.62
Dinucleotide parameters in Free Oligomers
Bansal M (1996) Biological Structure and Dynamics, Proceedings of the Ninth Conversation (Vol. I) pp 121-134
Molecular Biophysics Unit
Roll at
junction
Roll at
every step
Molecular Biophysics Unit
Radiu
sdl
max
A B
D
Imax
Imin
C
Successiv
e bending
angle , (i
=1)
Cumulative bending angle = Σ(i
=1 to n)
4. Bending Angle
1. Least square circle fit 2. d/lmax
3. Imax/Imin
Measures
of DNA curvature
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Molecular Biophysics Unit
• Acknowledgement:
• Arvind Marathe
• Senthil Kumar
• Prof Dhananjay Bhattacharyya (SINP, Kolkata)
• Dept of Biotech, Govt of India
Molecular Biophysics Unit
G- quadruplex