Times Squared AcademySorys Cepeda

Cheyenne ClarkInstructors:

Kerri KrawczykErick Argueta

Triphenyl(2-pyridylmethyl) Phosphonium Chloride

Hazard Code- Xi (Irritant)Irritating to the skinIrritating to the

Respiratory SystemMolecular weight- 423.33

AMUMelting Point Range- 249-

254°CThe chemical, physical

and toxicological properties have not been thoroughly investigated.

Genomic Melting

Genomic Melting Comparison

Plasmid DNA Melting

Plasmid DNA Melting

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)

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

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 -25.109259 -20.109667 2532.531982

DNA and TPPYD Amber Polak- Ribiere y -25.048698 -28.059345 -24.102997

DNA and TPPYD Amber Polak- Ribiere z -36.945206 -32.09108 4130.883301

Major Groove for Y OrientationBefore After

Minor Groove for Y Orientation

Before After

Intercalating in Orientation YBefore After

Intercalating TPPYD with 4 base pair of Adenine and Thymine in Orientation Z

Before After

Energy-

227.896214

Energy-329.664459

Intercalating TPPYD with 4 base pair of Cytosine and Guanine in Orientation Z

Before After

ReviewThe TPPYD did not change the melting temperature

of the Salmon Testes DNAFor 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.

DiscussionThe 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.