# User:Mary Mendoza/Notebook/CHEM 571 Experimental Biological Chemistry I/2012/10/16

(Difference between revisions)
 Revision as of 00:54, 26 October 2012 (view source) (→PCR mutation)← Previous diff Current revision (09:00, 7 December 2012) (view source) (→Continuation of Chemiluminescence) (22 intermediate revisions not shown.) Line 12: Line 12: - $\frac{0.46E6 ng}{x \mu L}$ = $\frac{100 ng}{1 \mu L}$ of primer in water = 4600 μL of water + $\frac{0.46E6 ng}{x \mu L}$ = $\frac{100 ng}{1 \mu L}$ of primer in water = 4600 μL of water * There is limited space in the plastic container (1 mL). Instead of dissolving 0.46E6 ng of the primer in 4600 μL of water, the entire primer was dissolved in 1 mL water. * There is limited space in the plastic container (1 mL). Instead of dissolving 0.46E6 ng of the primer in 4600 μL of water, the entire primer was dissolved in 1 mL water. * Using M1V1 = M2V2, the volume taken from the solution of 0.46E6 ng in 1 mL of water was calculated to be 217.39 μL. This was transferred to a new tube and filled up with water to a total volume of 1 mL. * Using M1V1 = M2V2, the volume taken from the solution of 0.46E6 ng in 1 mL of water was calculated to be 217.39 μL. This was transferred to a new tube and filled up with water to a total volume of 1 mL. + V1 = $\frac{100 ng/ \mu L * 1000 \mu L}{0.46E3 ng/ \mu L}$ = 217.39 μL of the dissolved primer in water V1 = $\frac{100 ng/ \mu L * 1000 \mu L}{0.46E3 ng/ \mu L}$ = 217.39 μL of the dissolved primer in water - * + * The procedure listed in [[AU Biomaterials Design Lab:Protocols/PCR Mutation Protocol|PCR Mutation protocol]] was strictly followed. After the addition of all reagents, the sample was placed in the thermocycler. The amplified DNA was contained in a sterilized, 1.5 microcentrifuge tube. + + ==Continuation of Chemiluminescence== + * The luminol prepared from the previous chemiluminescence laboratory period had a pH of 7 to 8. Reviewing a [http://openwetware.org/wiki/Image:PHofluminol.pdf journal article] of Xiaoyu, it was determined that the optimal pH of luminol was 12.5. As a result, it was decided to prepare a new solution of luminol at a pH of 10 to 11. + * A weight of .0112 g of luminol was added to 6 mL of water. The buffer composed of a direct addition of .0737 g of sodium carbonate and .4358 g of sodium bicarbonate. + * Using a pH meter, the electrode detected the pH at 8.73. As suggested by Dr. Hartings, a solution of sodium carbonate was made to increase the pH of the solution. + * Several adjustments were made in increasing the pH. A total weight of 1.91 g of sodium carbonate dissolved in 15 mL of water was added to the 6 mL solution of luminol. The final pH for luminol was 10.55. + * The molarity of sodium carbonate (MW 105.9784 g/mol) added was calculated: + + $\frac{1.91 g}{15 mL}$ × $\frac{1 mol}{105.9784 g}$ = $\frac{0.00120 mol}{mL}$ × $\frac{1 mL}{1E(-3) L}$ = $\frac{1.20 mol}{L}$ = 1.20 M of sodium carbonate + + + * The concentration of luminol has been diluted by the addition of 15 mL of water. + + + Molarity of diluted luminol = $\frac{10 mM * 6 mL}{21 mL}$ = 2.85714 mM of luminol + + + * Since there was limited amounts of the solid form of luminol, it was decided to take 6 mL of the 2.86 mM luminol stock solution and then add the appropriate amount of luminol to the 6 mL volume. The molarity of the 6 mL solution was very minute; the molarity was approximated as 2 mM. By making this assumption, .00106 g of luminol would make a 1 mM solution in 6 mL of water; this amount was multiplied by 8. The product was 0.00848 g of luminol was needed to be added into the 2 mM solution of luminol to increase the molarity to 10 mM. The amount was weighed and added to the 6 mL 2.86 mM solution of luminol. + + * Due to time constraints, the chemiluminescence of the luminol at pH 10.55 was tested on a lab bench with the room lights turned off. The reaction produced a neon blue glow that lasted for more than 3 minutes. No photograph was taken since the apparatus of the camera was not suited for the fluorescence activity. + + * The volume of each reagent added to the cuvette are listed below. + + {| {{table}} + | align="center" style="background:#f0f0f0;"|'''' + | align="center" style="background:#f0f0f0;"|''HRP'' + | align="center" style="background:#f0f0f0;"|''4-iodophenol'' + | align="center" style="background:#f0f0f0;"|''luminol'' + | align="center" style="background:#f0f0f0;"|''H2O2'' + | align="center" style="background:#f0f0f0;"|''H2O'' + |- + | Molarity of stock solutions||2.3 μM||18 mM||10 mM||1.7 mM||neutral + |- + | Volume||33 μL||27 μL||450 μL||88 μL||902 μL + |- + + +

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## PCR mutation

• In reference to the PCR Mutation protocol, 100 ng/μL of the primer was needed for the reaction. The weight of the primer in the provided container was 0.46 mg. A ratio of the weight over volume was equated to the required concentration of the primer:

0.46 mg = 0.46E6 ng

$\frac{0.46E6 ng}{x \mu L}$ = $\frac{100 ng}{1 \mu L}$ of primer in water = 4600 μL of water

• There is limited space in the plastic container (1 mL). Instead of dissolving 0.46E6 ng of the primer in 4600 μL of water, the entire primer was dissolved in 1 mL water.
• Using M1V1 = M2V2, the volume taken from the solution of 0.46E6 ng in 1 mL of water was calculated to be 217.39 μL. This was transferred to a new tube and filled up with water to a total volume of 1 mL.

V1 = $\frac{100 ng/ \mu L * 1000 \mu L}{0.46E3 ng/ \mu L}$ = 217.39 μL of the dissolved primer in water

• The procedure listed in PCR Mutation protocol was strictly followed. After the addition of all reagents, the sample was placed in the thermocycler. The amplified DNA was contained in a sterilized, 1.5 microcentrifuge tube.

## Continuation of Chemiluminescence

• The luminol prepared from the previous chemiluminescence laboratory period had a pH of 7 to 8. Reviewing a journal article of Xiaoyu, it was determined that the optimal pH of luminol was 12.5. As a result, it was decided to prepare a new solution of luminol at a pH of 10 to 11.
• A weight of .0112 g of luminol was added to 6 mL of water. The buffer composed of a direct addition of .0737 g of sodium carbonate and .4358 g of sodium bicarbonate.
• Using a pH meter, the electrode detected the pH at 8.73. As suggested by Dr. Hartings, a solution of sodium carbonate was made to increase the pH of the solution.
• Several adjustments were made in increasing the pH. A total weight of 1.91 g of sodium carbonate dissolved in 15 mL of water was added to the 6 mL solution of luminol. The final pH for luminol was 10.55.
• The molarity of sodium carbonate (MW 105.9784 g/mol) added was calculated:

$\frac{1.91 g}{15 mL}$ × $\frac{1 mol}{105.9784 g}$ = $\frac{0.00120 mol}{mL}$ × $\frac{1 mL}{1E(-3) L}$ = $\frac{1.20 mol}{L}$ = 1.20 M of sodium carbonate

• The concentration of luminol has been diluted by the addition of 15 mL of water.

Molarity of diluted luminol = $\frac{10 mM * 6 mL}{21 mL}$ = 2.85714 mM of luminol

• Since there was limited amounts of the solid form of luminol, it was decided to take 6 mL of the 2.86 mM luminol stock solution and then add the appropriate amount of luminol to the 6 mL volume. The molarity of the 6 mL solution was very minute; the molarity was approximated as 2 mM. By making this assumption, .00106 g of luminol would make a 1 mM solution in 6 mL of water; this amount was multiplied by 8. The product was 0.00848 g of luminol was needed to be added into the 2 mM solution of luminol to increase the molarity to 10 mM. The amount was weighed and added to the 6 mL 2.86 mM solution of luminol.
• Due to time constraints, the chemiluminescence of the luminol at pH 10.55 was tested on a lab bench with the room lights turned off. The reaction produced a neon blue glow that lasted for more than 3 minutes. No photograph was taken since the apparatus of the camera was not suited for the fluorescence activity.
• The volume of each reagent added to the cuvette are listed below.
 ' HRP 4-iodophenol luminol H2O2 H2O Molarity of stock solutions 2.3 μM 18 mM 10 mM 1.7 mM neutral Volume 33 μL 27 μL 450 μL 88 μL 902 μL