1. Large Molecule ~ Small Molecule Interactions Project Times Squared Academy Sorys E. Cepeda Jeffrey Doddio Instructor: Kerri Krawczyk

2. p-Xylylene bis (triphenyl phosphonium bromide) “PTPB” C 44 H 38 Br 2 P 2 Structure: – Size-788.52 u – Non Planar, Aromatic. – Hazards: Irritant- Irritable to eyes, skin, and respiratory system. Physical Properties: – mp->300°C – Water Soluble Uses: This compound was created because it could be the possible solution to problems that chemists find.

3. Salmon DNA Melting using Cary Spectrophotometer Melting Point: Native DNA- 57°C DNA + PTPB-65°C

4. Salmon DNA Melting using Cary Spectrophotometer Melting Point: Native DNA- 57°C DNA + PTPB- 63°C

5. Salmon DNA Melting using Bio-Rad Smart Spec Plus Melting Point: Native DNA-49°C DNA + PTPB- 57°C

6. Salmon DNA Melting using Bio-Rad Smart Spec Plus Melting Point: Native DNA- 51°C DNA + PTPB- 64°C

7. Electrophoresis WELL # 7-XB28 6-XB20 5-X 4-Ladder 3-EB28 2-EB20 1. E Band # Distance Traveled (cm) Est. Size (Base Pairs) Est. Mass (ng) Linearized DNA14.08268165.4 Uncut Plasmid DNA 1212 4.0 4.7 8268 4125 165.4 82.5

8. Electrophoresis Distance(cm)# of Base PairsMass (ng) 2.423130477 3.29416194 3.76557135 4.3436190 5.2232248 5.5202742

9. HyperChem This is our compound, “PTPB”, via HyperChem

10. HyperChem Predictions HyperChem Energy Minimizations TestProgramAlgorithmOrientationRandomG/C RichA/T Rich PTPB in Major Groove AmberPolak-RibiereX5730.937674.50393.64 PTPB in Major Groove AmberPolak-RibiereY309.335417.93340.89 PTPB in Major Groove AmberPolak-RibiereZ391.59314.442211.85 PTPB in Minor Groove AmberPolak-RibiereX302.462321. 81322.26 PTPB in Minor Groove AmberPolak-RibiereY-777.81298.81312.49 PTPB in Minor Groove AmberPolak-RibiereZ317.072232.45312.70

11. HyperChem Predictions We have discovered that our compound prefers Y-Orientation because the energy once in the DNA was the least.

12. HyperChem Predictions We have also discovered that our compound dislikes X-Orientation, because the energy once in the DNA was the greatest.

13. Discussion After having tried four different concentrations in two different Gel Electrophoresis experiments, there were no changes seen in the migration of the DNA through the gels. The DNA in the HyperChem showed possible binding with PTPB in the Y- Orientation in the minor groove with random DNA. The Cary Spectrophotometer and the Smart Spec Plus did show a shift in the melting curve when the Salmon Testes DNA was combined with PTPB. In the future, we would like to duplicate the experiments to confirm/ compare results. If the experiment was repeated with the Smart Spec Plus, a different cuvette holder should be used to eliminate the possibilities of spills and the cuvette tilting over.

14. Special Thanks.. We would just like to say thanks to Dr. Tiskus, Dr. Williams, all those who helped plan this program, and Rhode Island College for giving us this opportunity. We know we will use the skills gained here in the future, and this program has benefited us tremendously. THANK YOU!!!!