Structure of Informational
Molecules: DNA and RNA
Stryer Short course
Chapter 33
Nucleic Acid Structure
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Nucleobase
Nucleoside
Nucleotide
Nucleic acid
Chromatin
Chromosome
Polymeric Structure
• Polymer ideal for
informational
molecule
• Ribose and
deoxyribose
• Numbering
system
Directionality
• 5’  3’
directionality by
convention
• 3’  5’
phosphodiester
linkage
Base Structure
• Purines and pyrimidines
• Aromatic
• Tautomers
Nucleosides
• Ribonucleosides and deoxyribonucleoside
• Purine = osine; pyrimidine = idine (watch cytosine)
Nucleotides
• Phosphorylated
on 2’, 3’, or 5’
• 5’ unless noted
• Letter
abbreviations
• Draw these:
– dA
– ADP
– ppAp
Nucleotides
• pA is normally called _______ or ____________
Problem
• List 4 ways that ATP differs from 3’-dGMP.
Polynucleotides
• Phosphate diesters
• polyanion
• Abbreviation is
pdApdGpdTpdC
• Tetranucleotide
• Oligonucleotide
• Exonucleases and
endonucleases
Double Helix
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B-DNA
Chargoff’s Rule
Antiparallel
Right handed twist
ladder
Complementary Base Pairs
Mismatching may occur with tautomers
Double Helix Structure
• Dimensions-10 bp/turn
• Major/minor grooves
• Sugar phosphate
backbone toward
solvent
• Base pairs stacked,
perpendicular
• Edges of bases exposed
in grooves for
recognition
Weak Forces Stabilize Double Helix
• Stacking interactions
(vdW forces)
• Hydrophobic effect
• Charge-charge
• Hydrogen bonding
– Little contribution to
stability
– Large contribution to
selectivity
Denaturation
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Melting point
Melting curve
UV-absorption
cooperative
Problem
• True or False: Because a G:C base pair is
stabilized by three hydrogen bonds, whereas
an A:T base pair is stabilized by only two
hydrogen bonds, GC rich DNA is harder to
melt than AT-rich DNA.
A/T Rich and G/C Rich strands
• GC rich strands harder to denature due to
STACKING (not H-bonds)
• Cooperativity due to initial unstacking, which
exposes bases to water, which destabilizes Hbonds, which leads to further denaturation
Helical Forms
• B- form is major
• A-form is similar
to RNA/RNA and
hybrid DNA/RNA
structures
• Z-DNA not
understood, but
shows flexibility
of structure
Major/Minor Groove in B-DNA
• Many pictures
show ladder with
backbone at 180o
• Actually a
distorted ladder
with poles closer
to each other, on
one side
Semiconservative Replication
• Meselson and Stahl
• Density gradient equilibrium centrifugation
Explain the Results
Bacterial DNA
• Closed, circular
DNA
• Supercoiling
• Topology and
topoisomerases
Eukaryotic DNA
• Highly compacted (by factor of 104) into
chromatin (DNA/protein complex)
RNA Structure
RNA Structure, Stability, and Function
• Structural difference of
2’ hydroxyl
– H-bonding in RNA
structure
– Reactions of catalytic
RNA (rare)
– Hydrolysis
• Structure dictates role
difference in DNA/RNA
Why does DNA not contain U?
• DNA damage from UV
light, hydrolysis,
oxidation
• If DNA contained U, it
would be unable to
recognize a hydrolyzed
cytosine
• In RNA, damage not as
important, and T
production is costly
Recombinant DNA Techniques
Optional Lecture
DNA Sequencing
• DNA Polymerase: 5’  3’
• Sanger method
• dideoxynucleotides
Pyrosequencing
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Attach DNA to a solid surface
Run dNTPs over DNA one at a time
If reaction occurs, PPi is produced
Linked to a luciferase
Light detected
Polymerase Chain Reaction
• PCR
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Denature
Anneal primer
Polymerase
Repeat
• Taq polymerase
• Exponential production
Recombinant DNA technology
• Recombinant DNA
– Allows incorporation of gene(s) into other DNA
– Cut with exonucleases, anneal, and ligate
• Recombinant DNA serves as a cloning vector
– Incorporate into cells
– Select cells that have been transformed
Catalytic Hydrolysis: Nucleases
• Enzymes can catalyze
hydrolysis
• Very important
reactions!
• Nucleases
– RNase vs DNase
• Single/double strand
– Exonuclease vs
Endonuclease
– Orientation of
hydrolysis
Endonuclease
Restriction Enzyme
• Endonucleases recognize palindromes
• Sticky ends and blunt ends
Problem
Restriction enzymes are used to
construct restriction maps of DNA.
These are diagrams of specific DNA
molecules that show the sites
where the restriction enzymes
cleave the DNA. To construct a
restriction map, purified samples of
DNA are treated with restriction
enzymes, either alone or in
combination, and then the reaction
products are separated by agarose
gel electrophoresis. Use the results
of this gel to construct a restriction
map for this sample of DNA.
Making a Cloning Vector
Making a Cloning Vector
• ampR is gene for
ampicillin
resistance
• LacZ encodes
galactosidase
Selecting Transformed Bacteria
• Some plasmids are
recombinant, and some are
not
• Some cells accept a
plasmid, some accept
recombinant plasmid, and
some don’t accept any
• Transformed cells selected
by growing on a petri dish
with ampicilin and
galactose derivative
• Explain
Site-directed Mutagenesis
• Point mutations
• Examine
importance of a
residue
• Modify protein
function