Download Brief Review of DNA Replication: Nearest Neighbor Analysis

1/5/2011
Brief Review of DNA Replication:
Nearest Neighbor Analysis (Kornberg 1956):
In vitro DNA synthesis
•Template DNA
•DNA polymerase
•dNTPs
*dATP *dCTP *dGTP
*dTTP
•Allow DNA replication to take place
•Denature DNA
•Treat with micrococcal nucleaseyields mononucleotides with 3’ terminal phosphates
ssDNA:
ssDNA treated with micrococcal nuclease:
A
A
C
C
*
G
T
T
C
*
G
T
T
C
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Exercise:
List all possible dinucleotides (analysis of nearest 5’ neighbor)
Whi h mustt be
Which
b presentt in
i equall frequencies
f
i if th
the DNA strands
t
d are:
Parallel?
Antiparallel?
Exercise:
List all possible dinucleotides (analysis of nearest 5’ neighbor)
ApA
CpA
GpA
TpA
ApC
CpC
GpC
TpC
ApG
CpG
GpG
TpG
ApT
CpT
GpT
TpT
Whi h mustt be
Which
b presentt in
i equall frequencies
f
i if th
the DNA strands
t
d are:
Parallel?
Antiparallel?
ApC = TpG
CpA = GpT
ApC = GpT
CpA = TpG
ApG = TpC
CpG = GpC
ApG = CpT
GpA = TpC
ApT = TpA
CpT = GpA
Alternative Forms of DNA
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G + C Content
DNA Melting
*Temperature at which DNA strands are ½ denatured is the
melting temperature or Tm
*GC content of DNA has a significant effect on Tm
Comparison of Typical Prokaryotic and
Eukaryotic Cells
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Chromosome Sequence and Diversity
Species
# of
chromosome(s)
Form of
chromosome(s)
Genome size
(Mb)
PROKAYOTES:
Escherichia coli
1
Circular
4.6
Agrobacterium
tumifaciens
4
3 Circular
1 Linear
5.67
16
Linear
12 1
12.1
Arabidopsis
thaliana
5
Linear
125
Drosophila
melanogaster
4
Linear
180
Homo sapiens
23
Linear
2,900
EUKARYOTES:
Sacharomyces
cerevisiae
Gene Density in Different Organisms
Species
Genome Size
Approx. # of
genes
Gene density
(genes/Mb)
Escherichia coli
4.6
4,400
950
Agrobacterium
tumifaciens
5.7
5,400
960
12
5 800
5,800
480
Arabidopsis
thaliana
125
25,500
200
Drosophila
melanogaster
180
13,700
80
Homo sapiens
2,900
27,000
9.3
PROKAYOTES:
EUKARYOTES:
Sacharomyces
cerevisiae
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