User:Allison K. Alix/Notebook/Thesis Research/2013/07/11

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To Do

  • DNA extraction after oxidation with DTT. Attach to AuNP and run UV-Vis measurements to determine amount of DNA attached.
  • Prepare Igor Graphs from Oligo-D FCS measurements taken by Madeleine on 7/10
  • Prepare new 1X PBS buffer and take FCS measurements.
  • Prepare new 284mM sodium citrate buffer, pH=3.0
  • Finish up timeline for Thesis Research

Calculating DNA and AuNP concentrations

  • original AuNP concentration = 19.4nM
  • final concentration of AuNP after mixing with DNA/sodium citrate = 232.4uL(19.4nM)= x(500uL) x = 9.01712nM
  • final concentration of DNA after mixing with AuNP/sodium citrate = (9.01712nM)x (75) = 0.676284uM
  • original concentration of DNA needs to be = (0.676284uM)(500uL) = x (232.4uL)

x = 1.455uM <-----this is the concentration prior to mixing with AuNP/sodium citrate

1.455uM(500uL) = x (250uL) x = 2.91uM <---this is the concentration prior to mixing with 250uL 100mM DTT in 4% TEA

Concentration of stock DNA = 5.31uM

5.31uM(x) = 2.91uM(250uL)

x = 137uL in 113uL PBS

Preparation of 1X PBS

Make 500mL 1X from 10X stock solution


x = 50mL in 450mL

Preparation of 284mM sodium citrate buffer

[Base] = sodium citrate dihydrate, FW= 294.1 g/mol

[Acid] = citric acid, FW= 210.14 g/mol

pH = pKa + log [base]/[acid]

3.0 = 3.14 + log [base]/[acid]

-0.14 = log [base]/[acid]

[base]/[acid] = 0.7244

[acid] + [base] = 284mM

[base] = 284mM - [acid]

284mM-[acid]/[acid] = 0.7244

[acid]= 0.165M

[base]= 0.119M

0.165mol/L x 0.5L x 210.14g/mol = 17.30g citric acid

0.1193mol/L x 0.5L x 294.1g/mol = 17.54g sodium citrate dihydrate

1) Add 17.3g citric acid and 17.54g sodium citrate dihydrate to ~400mL of water

2) Adjust pH to 3.0 using 1M HCl

3) Adjust volume to 500mL using milliQ water