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 AMU
Melting Point Range °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)

8. Distance (mm)
Number of Bases
33.5
10000 34
8000 36
6000 38
5000
40.5
4000
46.5
3000 58
2000 79
1500 89
1000

9. Molecular Mechanic Method Geometry Optimization Algorithm
Hyperchem Energy Data
Test
Molecular Mechanic Method
Geometry Optimization Algorithm
Orientation
Major Groove Energy
Minor Groove Energy
Intercalating Energy
DNA and TPPYD
Amber
Polak- Ribiere x y z

10. Major Groove for Y Orientation
After
Before

11. Minor Groove for Y Orientation
Before
Minor Groove for Y Orientation
After

12. After
Before
Intercalating in Orientation Y

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

14. Energy
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.