bansal jncasr 07

Molecular Biophysics Unit

DNA structure and dynamics

-as revealed by Crystallography and MD simulation

Prof Manju Bansal


• A Brief History

• DNA structure and dynamics


--Lehninger 5th Ed


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


WC base-pairing

Hoogsteen base-pairing


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


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.


B A Z

5’

5’

5’


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


NMR structure Model structure

DNA triple helix


G-quadruplex structure


G-Quadruplex

AGGGTTAGGGTTAGGGTTAGGGGGGG(Bro)UTTTGGGG


Holliday Junction

Molecular Biophysics UnitHolliday Junction


• A Brief History

• DNA structure and dynamics


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


All torsion angles vs alpha for oligomer crystallographic dataset


tRNA: schematic


tRNA


tRNA-Phe


Intra base pair parametersIntra base pair parameters


Dinucleotide parameter


Dinucleotide parameters decide the DNA structure


TATA box – TBP complex


Twist vs Roll for extended crystallographic dataset (2006):Including Oligomers and Protein bound DNA complexes


Zp


Zp vs Slide for oligomers dataset


GROOVE WIDTH:GROOVE WIDTH:

measure of minimum inter-strand P..P distance


Nucleosome Structure


Minor groove width histogram:

Oligomers crystallographic dataset


Brief Outline of MD Results


Dixit et al, Biophys J 89,2005

MD: Sugar Phase Angles for the136 unique tetranucleotides


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


Beveridge et al, Biophys J 87,2004

MD: Distribution of the values of 6 local step parameters for CG step in a GCGC tetranucleotide


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


d(CGTTTTAAAACGTTTTAAAACGTTTTAAAACG)

d(GACTAAAAATGACTAAAAAATGACTAAAAAT)

d(GCAAAATTTTGCAAAATTTTGCAAAATTTTGC)

MD : sequence dependent curvature


Biological Implications of the Sequence Dependent Variation in DNA Structure


Transcription:

Transcription

Promoter TerminatorGene

RNA polymerase

RNA


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.


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


Structure of the complex of DNA and TATA-box binding protein


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


Roll at

junction

Roll at

every step


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


• Acknowledgement:

• Arvind Marathe

• Senthil Kumar

• Prof Dhananjay Bhattacharyya (SINP, Kolkata)

• Dept of Biotech, Govt of India


G- quadruplex

bansal jncasr 07

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