1. α-Triphenylphosphonium-p-toluic acid bromide
Large Molecule ~ Small Molecule Interactions Project
Juan Parra
Katherine Sochacka
Davies Career and Technical High School

2. TPTA Binding Agent Physical properties- 479.35 g/mol (C26H24O2BrP)
Solid
Hazards
XI- Irritant
May be combustible at high temperatures
Previous research- One article found on the use of binding agent. Manufactured by person using the binding agent. Not sold by chemical manufacturers.

3. Genomic (Salmon) DNA Melting Smart Spec TM Plus Spectrophotometer

6. Cary Spectrophotometer
Native melted at same temp. ≈ 67.5° C
Treated DNA melted lower at ≈ 62.5° C

7. Electrophoresis

9. Data Distance Traveled between Base pairs in mm Lane 1
Linearized Plasmid DNA
25mm
≈2,200 Bp
Lane 2
Linearized Plasmid DNA w/ TPTA
27mm
≈ ? Bp
Lane 3
Uncut Plasmid DNA
32mm
≈1,700 Bp
Lane 4
w/ TPTA
Lane 5
Lambda Hind III digest Ladder
13mm
23,130 Bp
15mm
9,416 Bp
16mm
6,557 Bp
21mm
4,361 Bp
24mm
2,332 Bp
30mm
2,027 Bp
37mm
564 Bp
39mm
125 Bp

10. HyperChem TM
TPTA Tube Model

11. Closest Distance 12-Bp Farthest Distance 12-Bp
Binding the difference between the Phosphorus from the TPTA to a 12-BP DNA in the major groove (H5 Nitrogen base)
Distance Å
Energy kcal/mol
Binding the difference between the Phosphorus from the TPTA to a 12-BP DNA in the major groove (H5 Nitrogen base)
Distance Angstroms(Å)
Energy kcal/mol
Farthest Distance 12-Bp

12. Optimization
Brings the molecule and DNA strand to its most stable energy
Molecular Mechanics- Amber 99
Geometry Optimization- Steepest descent
When the closest distance was optimized, the binding agent’s structure changed and the DNA attracted the binding agent slightly closer to it, while it lowered the energy between them.

13. Closest Distance 4-Bp Closest Distance 4-Bp
Binding the difference between the Phosphorus from the TPTA to a 4-BP DNA in the major groove (H5 Nitrogen base) before optimizing
Distance Å
Energy kcal/mol
Closest Distance 4-Bp
Binding the difference between the Phosphorus from the TPTA to a 4-BP DNA in the major groove (H5 Nitrogen group) after optimizing
Distance Å
Energy kcal/mol

14. Discussion Spectrophotometry shows some bonding (Cary Spec)
HyperChem indicates possible bonding in the major groove
Electrophoresis shows no difference with uncut plasmid
Points of Error-
Changing cuvets in the Cary Spectrophotometer changing the temp. altering results
HyperChem results depend on a lot of variables (position, angles, DNA structures)
Further investigations-
Use different plasmids with binding agent
Repeat electrophoresis using different concentrations
Investigate the minor groove with binding agent in HyperChem
Test the plasmid DNA melting point with the spectrophotometers