1. A-DNA and Z-DNA Atlases Dave Ussery Comparative Microbial Genomics first lecture, 18 September, 2002

2. 2 Atlases for Microbial Genomes Introduction to DNA Helix families How random is DNA? A-DNA atlases Z-DNA atlases Biological Implications – what does it MEAN? Outline

3. 3 Helix family

4. 4 A-DNA helix A-DNA A-DNA was the first DNA helix characterised by Rosalind Franklin in the early 1950’s. A-DNA helices tend to be favoured by stretches of purines (or pyrimidines) of at least 4 bp. A-DNA helices are found in RNA-DNA hybrids.

5. 5 B-DNA helix B-DNA B-DNA is the `classic´ helix described by Watson and Crick in 1953. It has, on average, about 10 bp/turn of the helix and is the AVERAGE structure for many DNA sequences.

6. 6 Z-DNA helix Z-DNA Z-DNA was the first DNA helix to be crystallised (in 1979), and came to the surprise of many biologists. It is a thin, LEFT-HANDED helix, with 12 bp/turn, and has a zig-zag backbone (hence its name). Certain alternating pyrimidine/purine sequences (e.g., CGCGCG) will form this helix.

7. 7 How Random is DNA? Consider a stretch of purines (G or A, abbreviated R) of length n: What is the probability of finding this in a random DNA sequence?

8. 8 Ecoli

9. 9 C.jejuni

10. 10 S.cerevisiae

11. 11 H.sapiens

12. 12 All Organisms

13. 13 Archaea

14. 14 Proteobacteria

15. 15 Tom Cavilier Smith

16. 16 Firmicutes

17. 17 Other Bacteria

18. 18 Proctista

19. 19 Protozoa

20. 20 Leishmania major 1

21. 21 Lmajor 1 genome

22. 22 Lmajor 1 ADNA

23. 23 Lmajor 1 ZDNA

24. 24 Lmajor 4 genome

25. 25 Lmajor 4 ADNA

26. 26 Lmajor 4 ZDNA

27. 27 P.falciparium 2 genome

28. 28 P.fal 2 ADNA

29. 29 P.fal 2 ZDNA

30. 30 coding vs. noncoding

31. 31 coding vs. noncoding