Download - A-DNA and Z-DNA Atlases
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.
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
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
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