Nucleic Acid Structure & Conformation - Intro

M.Bansal

--Lehninger 5th Ed

WC base-pairing

Hoogsteen base-pairing

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.

O3’-P-O5’-C5’ (g-)

P-O5’-C5’-C4’ (t)

O5’-C5’-C4’-C3’ (g+ )C5’-C4’-C3’-O3’ (2E)

C4’-C3’-O3’-P (t)

C3’-O3’-P-O5’ (g-)

Backbone conformationBackbone conformation

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)]

B A Z

5’

5’

5’

Torsion angle

A-DNA B-DNA Z-DNA (dinucleotide repeat)

pG pC

α -50 -46 47g+ -137 t

β 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)

Torsion Angles Corresponding to A, B, Z DNA Structures

n 11 10 -6 h 2.56 3.3 7.2

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)

DNA structures from A to Z