Large Molecule ~ Small Molecule Interactions Project

Times Squared AcademySorys E. CepedaJeffrey Doddio

Instructor: Kerri Krawczyk

p-Xylylene bis (triphenyl phosphonium bromide)

• “PTPB”• C44H38Br2P2

• Structure:– Size-788.52 u – Non Planar,

Aromatic. – Hazards:

Irritant- Irritable to eyes, skin, and respiratory system.

• Physical Properties:– mp->300°C– Water SolubleUses: This compound was

created because it could be the possible solution to problems that chemists find.

Salmon DNA Meltingusing Cary Spectrophotometer

Melting Point:Native DNA- 57°CDNA + PTPB-65°C

Salmon DNA Meltingusing Cary Spectrophotometer

Melting Point:Native DNA- 57°CDNA + PTPB- 63°C

Salmon DNA Melting using Bio-Rad Smart Spec Plus

Melting Point:

Native DNA-49°CDNA + PTPB- 57°C

Salmon DNA Melting using Bio-Rad Smart Spec Plus

Melting Point:Native DNA- 51°CDNA + PTPB- 64°C

ElectrophoresisWELL #

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 DNA 1 4.0 8268 165.4

Uncut Plasmid DNA

12

4.04.7

82684125

165.482.5

Electrophoresis

Distance(cm) # of Base Pairs Mass (ng)

2.4 23130 477

3.2 9416 194

3.7 6557 135

4.3 4361 90

5.2 2322 48

5.5 2027 42

HyperChem

This is our compound, “PTPB”, via HyperChem

HyperChem PredictionsHyperChem Energy Minimizations

Test Program Algorithm Orientation Random G/C Rich A/T Rich

PTPB in Major Groove

Amber Polak-Ribiere X 5730.93 7674.50 393.64

PTPB in Major Groove

Amber Polak-Ribiere Y 309.33 5417.93 340.89

PTPB in Major Groove

Amber Polak-Ribiere Z 391.59 314.44 2211.85

PTPB in Minor Groove

Amber Polak-Ribiere X 302.46 2321. 81 322.26

PTPB in Minor Groove

Amber Polak-Ribiere Y -777.81 298.81 312.49

PTPB in Minor Groove

Amber Polak-Ribiere Z 317.07 2232.45 312.70

HyperChem Predictions

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

HyperChem Predictions

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

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.

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!!!!