Download CourseMB206_NucleicAcidStr

Nucleic Acid Structure &
Conformation - Intro
M.Bansal
--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:
Source
mol % of bases
A
G
C
Ratios
T
PhiX174
24.0 23.3 21.5 31.2
Maize
26.8 22.8
A/T G/C
%GC
0.77
1.08 44.8
¦
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
2.
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
The x-ray fibre diffraction pattern of sodium salt of
DNA-B at 90% R.H.(Rosalind Franklin 1953)
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.
Backbone conformation
a O3’-P-O5’-C5’ (g-)
b P-O5’-C5’-C4’ (t)
g O5’-C5’-C4’-C3’ (g+ )
d C5’-C4’-C3’-O3’ (2E)
e C4’-C3’-O3’-P (t)
z C3’-O3’-P-O5’ (g-)
The puckering of the ribose ring is described
by the phase angle P, where
(ν2+ν4)-(ν1+ν3)
P = arctan -------------------------------2ν0[sin(π/5)+sin(2π/5)]
5’
5’
5’
B
A
Z
Torsion Angles Corresponding to A, B, Z DNA Structures
Torsion
angle
A-DNA
α
-50
β
B-DNA
Z-DNA (dinucleotide repeat)
pG
pC
-46
47g+
-137 t
172
136
179
-140
γ
40
38
-165
56
δ
80
139
99 C3’endo
138 C2’ endo
ε
-146
-133
-104
-94
ζ
-45
-157
-69 g-
80 g+
χ
-154
-102
68 (syn)
-159 (anti)
n
h
11
2.56
10
3.3
-6
7.2
DNA structures from A to Z
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 Z
A. Ghosh & M. Bansal , Acta Cryst D, vol 59 (Apr 2003)