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α -Triphenylphosphonium-p- toluic acid bromide

α -Triphenylphosphonium-p- 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 BrP) Solid Hazards XI- Irritant

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α -Triphenylphosphonium-p- toluic acid bromide

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  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 MeltingSmart Spec TM Plus Spectrophotometer

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

  5. Electrophoresis

  6. Data

  7. HyperChem TM TPTA Tube Model

  8. Farthest Distance 12-Bp Closest 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- 16.9 Angstroms(Å) • Energy- 5340.95 kcal/mol • Binding the difference between the Phosphorus from the TPTA to a 12-BP DNA in the major groove (H5 Nitrogen base) • Distance- 9.75129 Å • Energy- 5336.171391 kcal/mol

  9. 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.

  10. 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- 8.17853Å • Energy- 1905.35kcal/mol • Binding the difference between the Phosphorus from the TPTA to a 4-BP DNA in the major groove (H5 Nitrogen group) after optimizing • Distance- 7.93616 Å • Energy- -297.980894 kcal/mol

  11. 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

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