Triphenyl (2-pyridylmethyl) Phosphonium Chloride

Large Molecule – Small Molecule Interactions

Rhode Island College

July 13 – 17, 2009

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-

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

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

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

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

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

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

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

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

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

)

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.

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

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

Conclusion

EWG - Savoie

Did not change melting point Did not affect distances bands travelled in

electrophoresis Did not intercalate; aromatic

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