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Triphenyl (2-pyridylmethyl) Phosphonium Chloride
Large Molecule – Small Molecule Interactions
Rhode Island College
July 13 – 17, 2009
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TPPYD Characteristics
Structure:
• Three benzene rings and a 2-pyridylmethyl group (functional group) attached to Phosphorous central cation with a Chloride anion
• Non-planar, aromatic rings
Cl-
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TPPYD Characteristics
CAS Number: 99662-46-1
Molecular Formula: C24H22C12NP
Molecular Weight: 426.32
Melting Point: 249-254° C
Solubility: N/A
Toxicity Levels: Properties not established
Hazards: Irritating to eyes, respiratory system & skin
Uses: Replacement for radioactive tagging
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TPPYD and DNA Predictions: Intercalating
• TPPYD will not intercalate
Evidence:
1. Best intercalators are aromatic, planar, and a multiple ringed structure.
2. Data from HyperChem
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TPPYD – 4bp dsDNA InteractionUnoptimized Optimized
Energy 2296.17 kcal/mol 76.36 kcal/mol
Gradient 278.36 0.1
Distance 4.16 Ǻ 6.66 Ǻ
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TPPYD – 12bp dsDNA InteractionUnoptimized Optimized
Energy 6612.399 kcal/mol 154.11 kcal/mol
Gradient 291.864 0.099
Distance 11.19 Ǻ 7.35 Ǻ
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Plasmid DNA Gel Electrophoresis
• Analysis of whether TPPYD interacted with plasmid DNA
• Changing migration distance or number of bands indicates interaction
• 5 Samples tested:
Well 1 ‘E’ Plasmid DNA cut with HindIII
Well 2 ‘EB’ ‘E’ with 5 µL TPPYD added
Well 3 ‘X’ Plasmid DNA, no HindIII
Well 4 ‘XB’ ‘X’ with 5 µL TPPYD added
Well 5 ‘L’ Lambda Hind III Ladder
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Electrophoresis Trial 1 Results
Conclusion• TPPYD bound, but did not alter DNA structure• Did not bind at all
Evidence
1. E and EB banding patterns identical
2. X and XB banding patterns identical
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Electrophoresis Trial 2 Results
Conclusion• TPPYD did not alter
DNA structure
Evidence
1. E and EB banding patterns identical
2. X and XB banding patterns identical
X E5
EE 10
E 15
X5
X 10
X 15
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15 20 25 30 35 40 45 50 551000
10000
100000
23130
9416
6557
4361
23222027
Lambda Hind III Band Migration
Distance (mm)
Bas
e P
airs
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100 1000 10000 1000000
100
200
300
400
500
600
477
194
135
90
4842
123
Mass (ng) of DNA lengths
Base Pairs of Hind III Ladder
Fra
gm
ent
Mas
ses
(ng
)
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Spectrophotometers
• For both:– Calibrated with water– Used two samples, a Native DNA sample
and a DNA + Compound sample. This was to see if our compound would change the melting point of DNA.
• SmartSpec:– Had too little DNA in both our Native and
DNA + Compound samples, thus results were inconclusive.
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25 35 45 55 65 75 85 95 1050.9
1
1.1
1.2
1.3
1.4
1.5
1.6
Series1
Series1
Salmon DNA Melting Curve at 260nm (Cary 100)
Native DNA
DNA -Compound
Temperature (C)
Ab
sorb
ance
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20 30 40 50 60 70 80 90 100
-0.01
0
0.01
0.02
0.03
0.04
0.05
Series1Series1
Salmon DNA Melting Point Derivative (Cary 100)
Native DNA
DNA - Com
Average Temperatute (C)
Ave
rag
e A
bso
rban
ce /
Ave
rag
e T
emp
erat
ure
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Conclusion
EWG - Savoie
Did not change melting point Did not affect distances bands travelled in
electrophoresis Did not intercalate; aromatic
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