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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)