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Protein-Nucleic Acid Interactions - part 1
Blackburn & Gait, Ch. 9
Define persistence length of nucleic acid
Know four forces used in protein-nucleic acid interaction and the
details of each
Know how DNA shape affects its ability to be bound by proteins
Know other geometric constraints of dsDNA
Know geometric constraint of ss nucleic acids
Understand how proteins interact nonspecifically with DNA & RNA
HU protein
gene-5 from phage
RNase A (some slight specificity)
DNase I
polymerases (E.coli pol and HIV RT)
Protein-Nucleic Acid Interactions
Persistence length:
Length of DNA (RNA) that remains rodlike in its configuration
At 100 mM NaCl, persistence length of DNA is ~150 bp
Remember: ~1 meter of DNA in a human cell (diameter of cell ~10-5 m)
Therefore DNA is highly compacted in nucleosome (chromatin)
How does complexation with proteins cause DNA bending?
Possible forces used:
Electrostatic, Dipolar (H-bonds), Hydrophobic, Dispersion (stacking)
Protein-Nucleic Acid Interactions
Forces used:
Electrostatic, Dipolar (H-bonds), Hydrophobic, Dispersion (stacking)
Electrostatic
• salt bridges (~40 kJ/mol of stabilization per salt bridge)
• negative phosphates (DNA/RNA) with positive AA (Lys, Arg, His)
• influenced by [salt]; as [salt]  strength of salt bridge 
• pattern of salt bridges can distinguish between ss and ds DNA/RNA
and between B-DNA and Z-DNA
• overall electrostatic field of protein can orient polyanionic nucleic
acid, modeling of interactions
Protein-Nucleic Acid Interactions
Forces used:
Electrostatic, Dipolar (H-bonds), Hydrophobic, Dispersion (stacking)
Electrostatic
Protein-Nucleic Acid Interactions
Forces used:
Electrostatic, Dipolar (H-bonds), Hydrophobic, Dispersion (stacking)
Dipolar forces (H-bonds)
• between AA side chains (as well as backbone amides and carbonyls)
and Nucleic acid bases and sugar phosphate oxygens
• water mediated
X-H
- +
••• Y-R
- +
Hydrophobic (entropic forces)
• layer of water around protein or DNA
• when pro and NA interact, ordered water at interface are released
( entropy)
• hydrophobics on inside, hydrophillics on outside
Dispersion forces (base stacking)
• hydrophobic interactions and dispersion
• molecules with no net dipole can attract each other by a transient
dipole-induced dipole effect (London)
• dispersion forces important for base stacking and also for ss regions
because aromatic side chains of protein intercalate between bases in ss
nucleic acids
Protein-Nucleic Acid Interactions
Geometric Constraints
DNA shape - AT sequences/flexibility
RNA single strand - Hoogsteen pairs, triples, bulges
Protein-Nucleic Acid Interactions
Geometric Constraints
dsDNA
high (-) charge; protein domains that interact with it have a
complementary (+) surface, polar or charged side chains (used a lot by
T.F.) interact with phosphate oxygens (backbone)
Seq-specific -  repressor operator complex
Nonseq-specific - DNA polymerase I 3’5’ exonuclease
ds B-DNA
Anti-parallel -ribbon (protein) interacts with minor groove; H-bonds to
phosphates
Protein-Nucleic Acid Interactions
Geometric Constraints
ds B-DNA
-helix (protein) interacts in major groove with bases
most common because of H-bond donors and acceptors in MAJOR
groove; interaction involves at least 1 H-bond
Protein-Nucleic Acid Interactions
Geometric Constraints
ss Nucleic Acids
Hydrophobic bases exposed
SSBP will have more phobic NA binding surface
RNA - lots of regions of single-strandedness (bulges, loops,
pseudoknots)
A-form MAJOR groove deeper and bases more inaccessible
Bulges can help widen MAJOR groove
Loop structures can bind proteins
Protein-Nucleic Acid Interactions
Geometric Constraints
ss Nucleic Acids
RNA - lots of regions of single-strandedness (bulges, loops,
pseudoknots)
Loop structures can bind proteins
Protein-Nucleic Acid Interactions
Non-specific Interactions
Packaging
Euks - nucleosome
Proks - similar protein to histones that is small & basic
No nucleosome structure formed
Crystal structure of E.Coli DNA binding protein II (HU)
• Binds DNA by encircling it
• Extended -sheet arms contact DNA
• DNA binding ability increases as
#basic AAs increase
• protein wedges polymerize thus
inducing DNA to form supercoiled
structures
• HU binds ss or dsDNA so must
contact sugar-phosphate backbone
Protein-Nucleic Acid Interactions
Non-specific Interactions
ss nucleic acid binding proteins
During DNA replication in phage fd, gene-5 protein binds to ss
Lots of -strands
Lys/Arg neutralize phosphate backbone and bases stack against aromatic
amino acid side chains
Protein-Nucleic Acid Interactions
Non-specific Interactions
Exonucleases & endonucleases
RNase A
cleaves RNA but also binds ssDNA (competitive inhibitor)
Group of (+) charged residues on protein (anion binding site)
Electrostatics are main force involved so little seq-specificity
Specific for sequence with pyr 5’ to cleavage site since Thr45 H-bonds
Protein-Nucleic Acid Interactions
Non-specific Interactions
Exonucleases & endonucleases
DNase I - forces (VDW contacts, H-bonds, salt bridges)
cleaves dsDNA
Little seq-specificity
Structure of complex - exposed loop of enzyme binds in minor groove
of DNA which mimics nicked DNA
Protein-Nucleic Acid Interactions
Non-specific Interactions
Exonucleases & endonucleases
DNase I - forces (VDW contacts, H-bonds, salt bridges)
Little seq-specificity
Protein-Nucleic Acid Interactions
Non-specific Interactions
Polymerases
DNA-dependent DNA polymerase: E.Coli DNA pol I and III
Pol III
• chief replicative  subunit
Pol I
• repairs damaged DNA and converts Okazaki fragments into
complete genomic DNA
• large fragment (Klenow) - DNA pol, 3’-5’ exo
• small subunit - 5’-3’ exo
DNA pol
Catalytic AA •
(Asp705, Asp882, Glu883)
3’-5’ exo
Protein-Nucleic Acid Interactions
Non-specific Interactions
Polymerases
DNA-dependent DNA polymerase: E.Coli DNA pol I and III
Pol I - divalent cations important, may bind to catalytic AAs
Cation 1 - positions OH- to attack phosphorus and generate
pentacovalent transition state
Cation 2 - stabilizes leaving group