Structure of DNA

1
Structure of DNA

• Dr. Jason Linville
• University of Alabama at Birmingham
• jglinvil_at_uab.edu

from Genetics A Molecular Approach, 3rd ed.
Brown TA.
2
Summary

• DNA is a polymeric molecule composed of
  nucleotides

• Proving the double helix

3
DNA is polymeric

• DNA is a polymer
• Monomer units are nucleotides

What is a nucleotide?
Adenine Cytosine Guanine Thymine
Phosphate Group
Base
Deoxyribose sugar
4
DNA is polymeric

• DNA deoxyribonucleic acid
• Monomer units are nucleotides

What is a nucleotide?
Adenine Cytosine Guanine Thymine
Phosphate Group
Base
Deoxyribose sugar
5
DNA is polymeric
Adenine Cytosine Guanine Thymine
Phosphate Group
Base
Deoxyribose sugar
Carbons are numbered 1 (1 prime) to 5 (5 prime)
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DNA is polymeric
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DNA is polymeric
Adenine Cytosine Guanine Thymine
Phosphate Group
Base
Deoxyribose sugar
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The 4 Nitrogenous Bases
A Adenine
C Cytosine
T Thymine
G Guanine
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The 4 Nitrogenous Bases
A
C
T
G
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The 4 Nitrogenous Bases
A and G Purines Double Rings
A Adenine
G Guanine
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The 4 Nitrogenous Bases
C and T Pyrimidines Single Rings
C Cytosine
T Thymine
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DNA is polymeric
Adenine Cytosine Guanine Thymine
Phosphate Group
Base
Deoxyribose sugar
Phosphate group is the acid of the nucleic acid
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DNA is polymeric
?
a
ß
dAMP
dATP
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DNA is polymeric

• Polynucleotides composed of nucleotides

Normally built from nucleoside triphosphate
subunits (dATP, dCTP, dGTP, dTTP)
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DNA is polymeric
Normally built from nucleoside triphosphate
subunits (dATP, dCTP, dGTP, dTTP)

• a phosphate attacks the 3 carbon of next
  nucleotide

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DNA is polymeric

• Forms phosphodiester bonds between nucleotides
• Phospho P diester 2 ester bonds
• ß ? phosphates and 3 hydroxyl are lost

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DNA is polymeric
5 end

• Polynucleotides have chemically distinct ends

3 end
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DNA is polymeric

• Polynucleotides can be any length and have any
  sequence

• Several thousand basepairs length in lab
• Millions in chromosomes

• No chemical restrictions on how they join

• 10 in length 410 1,048,576 sequences
• Variability enables genetic material to exist in
  an infinite number of forms

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DNA is polymeric

• RNA is also a polynucleotide

• Two differences

• Ribose instead of deoxyribose sugar

Deoxyribose
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DNA is polymeric

• RNA is also a polynucleotide

• Two main differences

• Ribose instead of deoxyribose sugar
• Uracil instead of Thymine

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DNA is polymeric

• RNA is also a polynucleotide

• Another important difference

• RNA occurs as single polynucleotide
• DNA occurs as two polynucleotides wrapped around
  each other in a double helix

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Summary

• DNA is a polymeric molecule composed of
  nucleotides

• Proving the double helix

23
Proving DNA is double helix

• 1950s Structure of polynucleotide known
• 3-D structure of DNA not known

• Single Polynucleotide ?
• Double Polynucleotide ?
• Triple Polynucleotide ?
• K-Fed Polynucleotide ?

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Proving DNA is double helix

• All Watson and Crick did was build a model.
• Based it on 2 key experiments

• Chargaffs base ratios
• X-ray diffraction experiments

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Chargaff

• Erwin Chargaff
• Critical of Watson and Crick and scientists in
  general.
• Nature 326199-200, 1987. Engineering a
  molecular nightmare.

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Chargaff

• Used paper chromatography to determine relative
  amounts of each base.

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Chargaff

• Procedure
• Break molecule into mononucleotide components
  using acid or alkali
• Paper chromotography with n-butanol as the
  mobile phase
• Resulting spots were cut out and dissolved in
  aqueous solution
• Concentrations were measured

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Chargaff

• Results
• Conc. A approximated Conc. T
• Conc. G approximated Conc. C
• GC content varied considerably depending on
  organism

Chargaff didnt speculate on pairing.
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Chargaff
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X-Ray Diffraction

• Rosalind Franklin and Maurice Wilkins
• Took photos of X-ray diffraction patterns of DNA
• Didnt get along

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X-Ray Diffraction
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X-Ray Diffraction

• Crystal is bombarded with x-rays
• Angles the x-rays pass through are determined by
  the structure of the molecule in the crystal.
• X-ray beam exposes film after passing through the
  crystal

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X-Ray Diffraction

• Wilkins and Franklin used x-ray diffraction
  technique on purified DNA

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X-Ray Diffraction

• Showed a helix with 2 periodicies of 3.4 angstrom
  and 34 angstroms along the axis.

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Watson and Crick
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Watson and Crick

• After earlier models proved impossible, finally
  settled on double helix.
• Based on Chargaffs ratios and X-ray diffraction

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Watson and Crick

• Features
• 2 polynucleotides
• Nitrogenous bases on the inside
• Bases interact through hydrogen bonding
• Anti-parallel double helix
• Right handed helix
• Base pairs perpendicular to the helix

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What is DNA?

• What does DNA look like?

Sugar Phosphate Backbone (Sides of Ladder)
Nitrogenous Base (Rungs of Ladder)
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The 4 Bases
The bases pair up to form the rungs of the ladder.
A pairs with T
G pairs with C
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Watson and Crick
GC
AT