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Nucleotide Structure: Pentose sugar. Nucleotide Structure: Nitrogenous Bases. DNA Linkage. Phosphate group/phosphodiester bond Nucleotides contain one, two, or three phosphate groups. *nucleoside *nucleotide. Nucleic Acid Polarity. *Top of molecule has free 5’-phosphate group
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DNA Linkage • Phosphate group/phosphodiester bond • Nucleotides contain one, two, or three phosphate groups *nucleoside *nucleotide
Nucleic Acid Polarity *Top of molecule has free 5’-phosphate group This is the 5’ end *Bottom has a free 3’ hydroxyl group This is the 3’ end
Structural analysis of DNA *Early 1950’s Rosalind Franklin *1953 Watson and Crick
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 treated with micrococcal nuclease: A A C C C * G G T T T T C ssDNA: *
Exercise: List all possible dinucleotides (analysis of nearest 5’ neighbor) Which must be present in equal frequencies if the DNA strands are: Parallel ?Antiparallel?