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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 1 1/5/2011 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 2 1/5/2011 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 3 1/5/2011 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 4