1. T ETRAPHENYLPHOSPHONIUM B ROMIDE (TPP) L ARGE M OLECULE ~S MALL M OLECULE I NTERACTIONS Pilgrim High School Mr. Dubois, Mr. Lobdell C.J. Beneduce, Bryan Hallinan, Amanda Legare, Ed White

2. C HEMICAL C OMPOUND TPP: (C 6 H 5 ) 4 P(Br) Molecular Weight: 419.31 AMU 2.86E-10 mole TPP/ μl d. H20 Melting Point Range: 295 - 299°C Soluble in water Other physical properties and toxicity levels not available Hazardous Decomposition Products: Carbon monoxide, carbon dioxide, hydrogen bromide gas, thermal decomposition may produce toxic fumes of phosphorus oxides and/or phosphine.

3. G ENOMIC DNA M ELTING

5. ELECTROPHORESIS Distance (mm) 23 24 26 28 30* 34 44 51 62 Number of Bases 10,000 8,000 6,000 5,000 4,000* 3,000 2,000 1,500 1,000 According to the electrophoresis test, it appears that the cut plasmid has 4,000 bases. This supports that the plasmid had no significant effect on the DNA. Ladder *33nanoGrams (nG) (cf. Biolabs bulletin www.neb.com/nebecomm/produc ts3232.aspwww.neb.com/nebecomm/produc ts3232.asp)

6. H YPER C HEM P REDICTIONS 4 BP DNA DescriptionRandom Sequence TestProgramOrient.EnergyGradientGroove DNAAMBERXn/a DNAAMBERY14.2860.094Major DNAAMBERZ0.0290.096* Minor 12 BP DNA DescriptionRandom Sequence TestProgramOrient.EnergyGradientGroove DNAAMBERX-770.0370.376Major DNAAMBERY-779.2710.364Major DNAAMBERZ12.9370.094Major

7. H YPER C HEM P REDICTIONS 12 BP DNA DescriptionRandom Sequence TestProgramOrient.EnergyGradientGroove DNAMM+X11.7780.088Major DNAMM+Y5.6890.084Major DNAMM+Z6.4240.094Major 4 BP DNA DescriptionRandom Sequence TestProgramOrient.EnergyGradientGroove DNAMM+Xn/a DNAMM+Y18.1230.083Major DNAMM+Z20.3500.091Major For all optimization Polak Ribiere was used Both AMBER and MM+ were used

8. D ISCUSSION HyperChem analyses led to the prediction that Tetraphenylphosphonium Bromide would bond with DNA. The experimental results contrasted with this prediction. According to the results of the electrophoresis and the melting curve, TPP did not have an impact on the DNA molecule. Dr. Williams et al performed related experiments, including electrophoresis, and also found that TPP does not bond with DNA. Other compounds will be studied throughout the school year. A compound that interacts with DNA is hoped to be found using similar experiments.