Triphenylphosphoniumptoluic acid bromide Large Molecule Small Molecule Interactions

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

TPTA Binding Agent �Physical properties- 479. 35 g/mol (C 26 H 24 O 2 Br. P) �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.

Genomic (Salmon) DNA Melting TM Smart Spec Plus Spectrophotometer

Cary Spectrophotometer Native melted at same temp. ≈ 67. 5° C Treated DNA melted lower at ≈ 62. 5° C

Electrophoresis

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

Hyper. Chem TM TPTA Tube Model

Closest Distance 12 -Bp Binding the difference between the Phosphorus from the TPTA to a 12 -BP DNA in the major groove (H 5 Nitrogen base) Distance- 9. 75129 Å Energy- 5336. 171391 kcal/mol Binding the difference between the Phosphorus from the TPTA to a 12 -BP DNA in the major groove (H 5 Nitrogen base) Distance- 16. 9 Angstroms(Å) Energy- 5340. 95 kcal/mol Farthest Distance 12 -Bp

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.

Closest Distance 4 -Bp Binding the difference between the Phosphorus from the TPTA to a 4 -BP DNA in the major groove (H 5 Nitrogen base) before optimizing Distance- 8. 17853Å Energy- 1905. 35 kcal/mol Closest Distance 4 -Bp Binding the difference between the Phosphorus from the TPTA to a 4 -BP DNA in the major groove (H 5 Nitrogen group) after optimizing Distance- 7. 93616 Å Energy- -297. 980894 kcal/mol

Discussion �Spectrophotometry shows some bonding (Cary Spec) �Hyper. Chem 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 � Hyper. Chem 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 Hyper. Chem � Test the plasmid DNA melting point with the spectrophotometers