project 3: ru – dna binding today’s topics: 1. macromolecules 2. macromolecular interactions 3....
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Project 3:Ru – DNA Binding
Today’s topics:1. Macromolecules2. Macromolecular Interactions3. Ru-DNA Project4. Team Assignments5. Experiments
Macromolecules: DNA and Proteins
http://www.lclark.edu/~bkbaxter/200lecture/lecture_images/1_22_peptidebond.jpg
Pyrimidines : C and TPurines: A and G
www.solarnavigator.net www.wikipedia.org
Types of Interactions
• Protein - Protein– Subunits make up functional protein
• Protein – Nucleic Acid– Replication, DNA repair, Transcription,
Translation
• Protein – Small molecule– ATP-dependent enzymes
• Nucleic Acid – Small molecule– Pharmaceuticals
Protein-Protein interactions
Molecular Biology of The Cell, 4th Edition (2002)
Protein-Nucleic Acid: Replication
Molecular Biology of The Cell, 4th Edition (2002)
DNA Polymerase
Molecular Biology of The Cell, 4th Edition (2002)
Protein-Small Molecule
Molecular Biology of The Cell, 4th Edition (2002)
Hydrogen bonds and ionic interactions formed between protein and cyclic AMP
SerineArginineprotien backboneGlutamic AcidThreonineSerine
Nucleic Acid-Small Molecule: Cisplatin• Cis-platin binds
covalently to Guanine bases– Bends DNA by 35-40o
• Bent DNA mimics binding site for High Mobility Group (HMG) proteins– 100x greater affinity
• HMG proteins increase cisplatin cytotoxicity by binding onto DNA adducts and obstructing DNA repair.
+
http://pubs.acs.org/cen/coverstory/83/8325/8325cisplatin.html
Modes of Binding
• Green: surface binding
• Yellow: intercalation• Red: groove binding
• Intercalators push apart base pairs– Increase helix length
– Induce structural changes
Why is intercalation important?
Pharmaceutical applications
• Cancer chemotherapy– Daunomycin and
adriamycin
• Antibiotics
• Causes “buckle” and prevents replication by interfering with DNA-protein interaction
http://www.jonathanpmiller.com/intercalation/
Known Intercalators
Have planar aromatic cyclic structures that can “stack”
Ethidium Bromide Dipyridophenazine (dppz)
N
Ru
N
NN
N
N
N
N
N
Ru
N
NN
N
N
N
N
N
Ru
N
NN
N
N
N
NN
Ru
N
NN
N
N
N
N
N
Ru
N
NN
N
N
N
N
[Ru(bpy)2(L-pterin)]2+ [Ru(bpy)2(L-diamino)]2+
[Ru(bpy)2(L-amino)]2+
[Ru(bpy)2(L-allox)]2+ [Ru(bpy)2(L-Me2allox)]2+
NH
NH
O
O
N
N
NH2
N
NH
O
NH2
N
N
O
O
CH3
CH3
N
N
NH2
NH2
DNA-Binding Experiments: Overview
• Molecular “Light Switch”
• Viscometry: argued best method for demonstrating intercalation
• Thermal Denaturation
• Photocleavage
Do our Ru compounds intercalate DNA or bind in some other way?
Molecular Light Switch
RuDPPZ RuDPPZ+DNA RuDAP+DNA RuDAP
• Inherent fluorescence of compound quenched in aqueous buffer
• When bound to DNA, helix shields from solvent quenching
• Demonstrate by obtaining emission spectra with fluorimeter instrument
Viscometry• DNA helix can be distorted
and lengthened upon intercalation
• Lengthening increases viscosity of DNA solution, which can be monitored with a viscometer
=(t-t0)/t0 = viscosityt = flow time (seconds)t0 = flow time of buffer alone (seconds)0 = viscosity of DNA alone
Thermal Denaturation• As double stranded DNA is heated, it is
denatured to single stranded– Melting temperature defined as the inflection
point
• Intercalated molecules stabilize the helix, requiring a larger temperature to denature– RuDppz can shift melting temperature from
64.5 to 80 oC
• Measured by recording absorbance at 260 nm
Photocleavage: what is it?An intercalated Ru compound excited by UV light triggersa reaction that can cut the phosphate backbone of DNA
Monitor using Electrophoresis
Why Study DNA Cleavage?
• Activated photochemically– Rxn not initiated without irradiation
• Therapeutic agents– Activated in vivo by laser
• Selective excitation of photocleaver– Sensitive to light longer than 300nm– Nucleic acids and proteins transparent– Limited side reactions
DNA Cleavage
DNA Cleavage
FluorescenceMolecular Light SwitchFluorescenceMolecular Light Switch
ViscosityViscosity
ThermalDenaturation
ThermalDenaturation
DNA Cleavage
DNA Cleavage
FluorescenceMolecular Light SwitchFluorescenceMolecular Light Switch
ViscosityViscosity
ThermalDenaturation
ThermalDenaturation
DNABinding
Ru-DNA Project Schedule
Week 1 – April 2 Buffer, Solution PrepWeek 2 – April 9 First assigned techniqueWeek 3 – April 16 First assigned technique (repeat)Week 4 – April 23 Groups rotate: second assigned techniqueWeek 5 – April 30 Class presentation and discussion of results
DNA Cleavage
Weeks 2 & 3: Lucy & Kaylee,Yuan & Amanda
Week 4: Anna & June,Steph & Kathy,
Liz & Allison
DNA Cleavage
Weeks 2 & 3: Lucy & Kaylee,Yuan & Amanda
Week 4: Anna & June,Steph & Kathy,
Liz & Allison
FluorescenceMolecular Light SwitchWeeks 2 & 3: Liz & Allison
Week 4:TBA
FluorescenceMolecular Light SwitchWeeks 2 & 3: Liz & Allison
Week 4:TBA
ViscosityWeeks 2 & 3: Steph & Kathy
Week 4:Yuan & Amanda
ViscosityWeeks 2 & 3: Steph & Kathy
Week 4:Yuan & Amanda
ThermalDenaturationWeeks 2 & 3: Anna & June
Week 4:Lucy & Kaylee,
ThermalDenaturationWeeks 2 & 3: Anna & June
Week 4:Lucy & Kaylee,
DNA CleavageEveryone!
DNA CleavageEveryone!
FluorescenceMolecular Light Switch
Liz & Allison
FluorescenceMolecular Light Switch
Liz & Allison
ViscositySteph & Kathy
Yuan & Amanda
ViscositySteph & Kathy
Yuan & Amanda
ThermalDenaturation
Anna & June, Lucy & Kaylee
ThermalDenaturation
Anna & June, Lucy & Kaylee
ResultsOf DNABinding
Week 1 (tomorrow): Buffer, Solution Prep
Goals:
1. Make appropriate buffers for your experiment2. Make Calf Thymus DNA solution3. Make Ru solutions
Week 1 (tomorrow): sequence
1. Make appropriate buffer A or B– If needed, dilute provided buffer to assigned
concentration– Add mass of NaCl to assigned concentration
2. Make Calf Thymus DNA solution– Mass out solid DNA, add to buffer and sonicate to
dissolve (will take ~1.5-2 hours)3. Practice Pipettor Technique4. Analyze [DNA] using Abs. at 260nm and extinction
coefficient to determine DNA soln concentration5. Make Ru solutions
– Mass out solid Ru compounds and add buffer to make assigned concentration solutions
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