Nucleic Acid Structure Conformation Intro M Bansal Lehninger

Nucleic Acid Structure & Conformation - Intro M. Bansal

--Lehninger 5 th 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.

Backbone conformation a O 3’-P-O 5’-C 5’ (g-) b P-O 5’-C 4’ (t) g O 5’-C 4’-C 3’ (g+ ) d C 5’-C 4’-C 3’-O 3’ (2 E) e C 4’-C 3’-O 3’-P (t) z C 3’-O 3’-P-O 5’ (g-)

The puckering of the ribose ring is described by the phase angle P, where (ν 2+ν 4)-(ν 1+ν 3) P = arctan ----------------2ν 0[sin(π/5)+sin(2π/5)]

Torsion Angles Corresponding to A, B, Z DNA Structures Torsion angle A-DNA α -50 β B-DNA Z-DNA (dinucleotide repeat) p. G p. C -46 47 g+ -137 t 172 136 179 -140 γ 40 38 -165 56 δ 80 139 99 C 3’endo 138 C 2’ 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)