Small Molecule Large Molecule Interactions

1. Small Molecule Large Molecule Interactions Times Squared Academy Sorys Cepeda Cheyenne Clark Instructors: Kerri Krawczyk Erick Argueta

2. Triphenyl(2-pyridylmethyl) Phosphonium Chloride • Hazard Code- Xi (Irritant) • Irritating to the skin • Irritating to the Respiratory System • Molecular weight- 423.33 AMU • Melting Point Range- 249-254°C • The chemical, physical and toxicological properties have not been thoroughly investigated.

3. Genomic Melting

4. Genomic Melting Comparison

5. Plasmid DNA Melting

6. Plasmid DNA Melting

7. Electrophoresis of Plasmid DNA • Lane 1- control uncut (1 µL uncut DNA+ 1µL buffer + 8 µL H2O) • Lane 2- uncut (1 µL uncut DNA+ 1µL TPPYD + 1µL buffer + 7 µL H2O) • Lane 3- uncut (1 µL uncut DNA+ 2µL TPPYD + 1µL buffer + 6 µL H2O) • Lane 4- Ladder • Lane 5- control cut (1 µL cut DNA+ 1µL buffer + 8 µL H2O) • Lane 6- cut (1 µL cut DNA+ 1µL TPPYD + 1µL buffer + 7 µL H2O) • Lane 7- cut (1 µL cut DNA+ 2µL TPPYD + 1µL buffer + 6 µL H2O) • Lane 8- cut (1 µL cut DNA+ 3µL TPPYD + 1µL buffer + 5 µL H2O)

9. Hyperchem Energy Data

10. Major Groove for Y Orientation After Before

11. Before After Minor Groove for Y Orientation

12. After Before Intercalating in Orientation Y

13. Energy -227.896214 Before After Intercalating TPPYD with 4 base pair of Adenine and Thymine in Orientation Z

14. Energy -329.664459 Before After Intercalating TPPYD with 4 base pair of Cytosine and Guanine in Orientation Z

15. Review • The TPPYD did not change the melting temperature of the Salmon Testes DNA • For the plasmid DNA melting, there were many inconsistencies that prevented us from determining the melting temperature. • Electrophoresis- The uncut plasmid DNA had the least movement, whether with or without the TPPYD. • In the last three lanes, most of the plasmid DNA at equal lengths, all traveling more than the DNA in the uncut lanes. • Because some plasmid DNA stayed in the wells and there were bands where the DNA did not travel as far as most of the DNA in specific lanes, we think that there may have been minor interactions between the DNA and TPPYD.

16. Discussion • The Gel Electrophoresis results for the Cut Plasmid DNA demonstrated that there could be some interaction or binding to the TPPYD. The DNA in the Hyperchem showed minor interactions with TPPYD. • The DNA denaturing experiment did not show a shift in the melting curve when the Salmon DNA was combined with TPPYD. • In the future, we would like to replicate the experiments to further validate the results. • Design similar experiments that have reduced possibilities of error. • Experiment with different chemicals on DNA to see the different interactions that can occur.