Why Structural Biology

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Why Structural Biology?
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Today

• Nucleic Acids History of Discovery and
  Structural Parameters

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The Key Figures

• Oswald Avery - DNA is unit of inheritance
• Erwin Chargaff - Base Pairing
• Francis Crick - DNA structure
• James Watson - DNA structure

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The Key Figures

• Rosalind Franklin -
• Fiber Diffraction Data
• Maurice Wilkins -
• Fiber Diffraction Data
• Alexander Rich -
• Crystallographic Analysis
• Jacques van Boom -
• Solid State Synthesis

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DNA as the Heritable Material
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The composition of DNA based on the findings of
Erwin Chargaff

• The base composition of DNA varies from one
  species to another.
• DNA from different tissues of the same species
  has the same base composition. This does not
  change with age or other environmental factors.
• AT CG, AGTG
• The base composition is similar from closely
  related species and very different from divergent
  species.

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Braggs law
p/2
p/2
Plane A
d
q
Plane B
Every red line is one wavelength (l) longer than
the black line Every photon that is diffracted
by angle q off a plane B that is at distance
d from plane A is in phase with every photon
diffracted by angle q off plane A if l/d
2sinq
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Fiber Diffraction
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Resulting Layer Lines
The points in 3D space where beams from a 3D
object constructively interfere.
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Diffraction from a Fiber
Continuous and discontinues helices.
reciprocal
real
The unit cell of a fiber.
The resulting diffraction pattern.
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The Real Thing!
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Watson and Cricks Model
Nature, 1953, v. 171 p.737
Note This is purely a schematic model they have
proposed. It is based on the fiber diffraction
data AND the biochemical data of Chargaff.
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The Structure of FranklinA DNA
1953
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The First Atomic Resolution Look at a Double
Helix by Alexander Rich

• 1973 crystals of GpC and ApU (RNA)
• GpC had three H-bonds between bases, not two as
  predicted by Watson and Crick.
• Also in 1973, low resolution (4 Å) structure of
  tRNA
• 1974, 3 Å structure showed some of the details.

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The First Atomic Resolution Structure of the DNA
double helix Z DNA!
Jacques van Boom chemistry Alexander Rich
Crystallography
1979
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Finally B DNA at atomic resolution!
1980, 27 years after Watson-Crick model!
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The Components of DNA
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The Sugar
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DNA Sugar Pucker
Crystal Structure of Z DNA 1DCG
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Subtle Changes Big Differences

• B-form DNA is C2 endo
• A-form DNA is C3 endo the P-P difference is
  therefore reduced to 5.5-7Å.
• RNA is generally C3 endo but can assume C2 endo
  at special points. This transition is
  energetically unfavored and therefore must be
  balanced by something else.

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Some common chemical modifications found in DNA.
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The bases are linked via a phosphodiester
bridge. Because the phosphate bridge links the 5
carbon on one side to the 3carbon on the other,
the chain has a chemical directionality.
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The shape of both base pairs is the same.
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Bond representation.
Space-filling representation.
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Dihedral angles in nucleic acids.
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The conformation of the bases in nucleic acids.
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Overview of the 3 forms of DNA.
Syn for purines
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Its possible to have greater levels of
complexity than simply duplex DNA. Here you see
Hoogsteen base pairing in triplex DNA. In DNA
where there is a higher than normal amount of
purines, triplex and even quadruplex pairing can
take place. These structures are critical for the
proper replication of chromosomal DNA and repair
of damaged DNA.
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Bond representation of triplex DNA. This view is
down the long axis. The third strand is colored.
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tRNA CPK
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tRNA bonds
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Take-Home Lessons

• Nucleic acids are built from 5 basic building
  blocks, each of which consists of a 5 carbon
  ribose sugar to which a purine or pyrimide base
  is attached to the 1 carbon and a phosphate to
  the 5 carbon.
• The sugar pucker in RNA is normally 3 endo with
  a rather large energy barrier limiting transition
  to 2 endo. In DNA the deoxyribose is generally
  2 endo with only a small energy penalty
  encountered with transition to 3 endo. The sugar
  pucker plays an important role in the
  conformation of the backbone.
• DNA is normally found in the B-form but depending
  on solution conditions and base sequence, can
  convert into the Z-form which has important
  regulatory functions within the cell. You should
  be familiar with the structural parameters of
  both types of helices.
• The Watson-Crick structure of DNA was actually a
  model based on chemical and biological data as
  well as fiber diffraction studies of DNA.
• DNA within the cell can form triplex and
  quadraplex structures. These structures have
  specific roles in recombination or in telomere
  maintenance.