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 nuclease- yields mononucleotides with 3’ terminal phosphates

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

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 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

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) PROKAYOTES: Escherichia coli 1 Circular 4.6 Agrobacterium tumifaciens 4 3 Circular 1 Linear 5.67 EUKARYOTES: Sacharomyces cerevisiae 16 Linear 12.1 Arabidopsis thaliana 5 125 Drosophila melanogaster 180 Homo sapiens 23 2,900

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