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-DNAA-DNA was the first DNA helix characterised by Rosalind Franklinin the early 1950’s. A-DNA helicestend 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-DNAB-DNA is the `classic´ helix describedby Watson and Crick in 1953. It has,on average, about 10 bp/turn of the helixand is the AVERAGE structure for many DNA sequences.

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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.

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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?

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Ecoli

9

C.jejuni

10

S.cerevisiae

11

H.sapiens

12

All Organisms

13

Archaea

14

Proteobacteria

15

Tom Cavilier Smith

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Firmicutes

17

Other Bacteria

Purine and pyr/pur tracts in "other" Bacterial Genomes

0.00

1.00

2.00

3.00

4.00

5.00

6.00

7.00

8.00

9.00

Aqui

fex a

eolic

us V

F5

pece

1

Chlam

ydia

pneu

mon

iae

AR39

Chlam

ydia

pneu

mon

iae

CWL0

29

Chlam

ydia

pneu

mon

iae

J138

Chlam

ydia

trach

omat

is D

UW_3

CX

pCHL1

Chlam

ydia

trach

omat

is M

oPn

pMoP

n

Synec

hocy

stis

PCC68

03

Chlor

obiu

m te

pidu

m T

LS

Borrelia

bur

gdor

feri

B31 M

ain+

21pl

asm

ids

Borrelia

bur

gdor

feri

B31 M

ain

Borrelia

bur

gdor

feri

B31 A

ll21p

lasm

ids

cp09

cp26

cp32

-1

cp32

-3

cp32

-4

cp32

-6

cp32

-7

cp32

-8

cp32

-9

lp05

lp17

lp21

lp25

lp28

-1

lp28

-2

lp28

-3

lp28

-4 lp

36lp

38lp

54lp

56

Trep

onem

a pa

llidum

Nich

ols

Deino

cocc

us ra

diod

uran

s R1

All

Chr. 1

Chr. 2

pCP1

pMP1

Ther

mot

oga

mar

itima

MSB8

%(R)10 %(YR)5

Spirochaetales

Chlamydiales

Expect.1.0%

18

Proctista

19

Protozoa

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Leishmania major 1

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Lmajor 1 genome

22

Lmajor 1 ADNA

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Lmajor 1 ZDNA

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Lmajor 4 genome

25

Lmajor 4 ADNA

26

Lmajor 4 ZDNA

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P.falciparium 2 genome

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P.fal 2 ADNA

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P.fal 2 ZDNA

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coding vs. noncoding

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coding vs. noncoding