DNA Structure

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DNA Structure DNA Replication DNA Sequencing
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Looking down a double helix
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Major Groove
Major Groove
Minor Groove
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Normal Base Pairing
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What are hydrogen bonds? Hydrogen
Bonds Hydrogen bonds a hydrogen atom is shared
between two molecules. Partial charges
Hydrogen bonds have polarity. A
hydrogen atom covalently attached to a very
electronegative atom (N, O, or P) shares its
partial positive charge with a second
electronegative atom (N, O, or P). One example,
shown above, involves the hydrogen bonding
between water molecules.
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Alternate base possibilities
Tinoco, Jr. In Appendix 1 ofThe RNA World (R. F.
Gesteland, J. F. Atkins, Eds.), Cold Spring
Harbor Laboratory Press, 1993, pp. 603-607.
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PRYMIDINES
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PURINES
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How does DNA replication occur? Aside from the
problem of coiled coils and proteins, replication
DNA polymerases only function in a 5 to 3
direction and the DNA is anti-parallel.
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Okazaki Fragments
DNA polymerases cannot initiate DNA synthesis de
novo. They require a 3 OH group to elongate
from. RNA primers provide the 3OH that is
required by DNA polymerase.
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DNA Replication
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Okazaki Fragments
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Initiator protein binds to origin sequences and
opens the strands. Singles strand binding protein
(SSB) stabilizes open fork Helicase unwinds the
DNA, gyrase relieves the positive supercoils by
introducing negative ones.
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• Primase binds to first priming sequence on
  leading strand
• A short RNA primer is synthesized
• Replication polymerase (pol III bacteria, pol
  alpha eukaryotes) extends of the 3 OH

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• RNA primer is made for the lagging strand
• DNA polymerase extends the strand
• pol III in bacteria
• pol alpha in eukaryotes
• When a more recently synthesized Okazaki fragment
  reaches an older one, the 5 to 3exonuclease
  activity of DNA polymerase removes the RNA primer
  of the older one and it is replaced with DNA

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DNA ligase links adjacent Okazaki fragments
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Bi-Directional DNA Replication
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Rolling Circle Model
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DNA Sequencing (Dideoxy method)
Generate DNA fragments with 1 base resolution
Separate DNA fragments with 1 base
resolution Identify DNA fragments with 1 base
resolution
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DNA Sequencing (Dideoxy method)
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DNA Sequencing (Dideoxy method)