1. Brief Review of DNA Replication:

2. 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 nuclease-
yields mononucleotides with 3’ terminal phosphates

3. ssDNA:
ssDNA treated with micrococcal nuclease: A C G T * A C G T *

4. Exercise:
List all possible dinucleotides (analysis of nearest 5’ neighbor)
Which must be present in equal frequencies if the DNA strands are:
Parallel ? Antiparallel?

5. Exercise:
List all possible dinucleotides (analysis of nearest 5’ neighbor)
ApA
ApC
ApG
ApT
GpA
GpC
GpG
GpT
CpA
CpC
CpG
CpT
TpA
TpC
TpG
TpT
Which must be present in equal frequencies if the DNA strands are:
Parallel ? Antiparallel?
ApC = TpG CpA = GpT
ApG = TpC CpG = GpC
ApT = TpA CpT = GpA
ApC = GpT CpA = TpG
ApG = CpT GpA = TpC

6. Alternative Forms of DNA

7. G + C Content

8. 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

9. Comparison of Typical Prokaryotic and Eukaryotic Cells

10. 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 Linear
5.67
EUKARYOTES:
Sacharomyces cerevisiae 16
Linear
12.1
Arabidopsis thaliana 5
125
Drosophila melanogaster
180
Homo sapiens 23
2,900

11. Gene density (genes/Mb)
Gene Density in Different Organisms
Species
Genome Size
Approx. # of genes
Gene density (genes/Mb)
PROKAYOTES:
Escherichia coli
4.6
4,400
950
Agrobacterium tumifaciens
5.7
5,400
960
EUKARYOTES:
Sacharomyces cerevisiae 12
5,800
480
Arabidopsis thaliana
125
25,500
200
Drosophila melanogaster
180
13,700 80
Homo sapiens
2,900
27,000
9.3