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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
Exercise:
List all possible dinucleotides (analysis of nearest 5’ neighbor)
Which must be present in equal frequencies if the DNA strands 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
Which must be present in equal frequencies if the DNA strands 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
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
Chromosome Sequence and Diversity
Species
# of
chromosome(s)
Form of
chromosome(s)
Genome size
(Mb)
Escherichia coli
1
Circular
4.6
Agrobacterium
tumifaciens
4
3 Circular
1 Linear
5.67
16
Linear
12.1
Arabidopsis
thaliana
5
Linear
125
Drosophila
melanogaster
4
Linear
180
Homo sapiens
23
Linear
2,900
PROKAYOTES:
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
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