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

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 Helix family

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

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 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 Ecoli

9 C.jejuni

10 S.cerevisiae

11 H.sapiens

12 All Organisms

13 Archaea

14 Proteobacteria

15 Tom Cavilier Smith

16 Firmicutes

17 Other Bacteria

18 Proctista

19 Protozoa

20 Leishmania major 1

21 Lmajor 1 genome

22 Lmajor 1 ADNA

23 Lmajor 1 ZDNA

24 Lmajor 4 genome

25 Lmajor 4 ADNA

26 Lmajor 4 ZDNA

27 P.falciparium 2 genome

28 P.fal 2 ADNA

29 P.fal 2 ZDNA

30 coding vs. noncoding

31 coding vs. noncoding