Difference between revisions of "User:Allison K. Alix/Notebook/Thesis Research/2013/07/16"

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(DNA/AuNP Data Analysis)
(DNA/AuNP Data Analysis)
Line 76: Line 76:
1.42x10<sup>-10</sup>/0.001349886m<sup>2</sup> AuNP = 1.05x10<sup>-7</sup>moles DNA/m<sup>2</sup>AuNP
1.42x10<sup>-10</sup>/0.001349886m<sup>2</sup> AuNP = 1.05x10<sup>-7</sup>moles DNA/m<sup>2</sup>AuNP
'''Calculating the percentage of DNA hybridized in each sample'''
'''Calculating the percentage of DNA hybridized in each sample'''
*based on # of moles of DNA available to attach
Sample A1
Sample A1
moles DNA = (1.827x10<sup>-7</sup>M x 350 x 10<sup>-6</sup>L) = 6.40x10<sup>-11</sup> moles
4.74x10<sup>-8</sup>moles DNA/m<sup>2</sup>AuNP/3.967x10<sup>-7</sup> moles DNA/m<sup>2</sup> AuNP = 11.95%
% hybridized = (6.40x10<sup>-11</sup>/5.3555575 x 10<sup>-10</sup> moles DNA)x100% = 11.95%
Sample B
moles DNA = 4.44x10<sup>-8</sup>M x 500 x 10<sup>-6</sup>L = 2.22x10<sup>-11</sup> moles
% hybridized = (2.22x10<sup>-11</sup> moles/5.3555575 x 10<sup>-10</sup> moles DNA)x100% = 4.14%
Sample A2
moles DNA = 1.42x10<sup>-10</sup>
% hybridized = (1.42x10<sup>-10</sup>/5.3555575 x 10<sup>-10</sup>) = 26.5%

Revision as of 11:53, 16 July 2013

Owwnotebook icon.png UV-Vis Analysis/Silica Coating Pt. 2 <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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To Do

  • Continue with Silica Coating Procedure
  • Analyze UV-Vis Data from AuNP/DNA attachment performed yesterday

Silica Coating Procedure

1) Prepare the following solutions:

  • 1mL AuNP & MHA solution/20μL TES/0.125mL NH4OH/5mL propanol
  • 1mL AuNP & MHA solution/15μL TES/0.125mL NH4OH/5mL propanol
  • 1mL AuNP & MHA solution/10μL TES/0.125mL NH4OH/5mL propanol
  • 1mL AuNP & MHA solution/5μL TES/0.125mL NH4OH/5mL propanol

2) Stir solutions for one hour to allow reaction to proceed

3) Centrifuge solutions at 4000 rpm for one hour

4) Re-suspend particles in PBS to a final concentration of 5nM?

DNA/AuNP Data Analysis

See File:2013 0715 AuNP-DNA.xlsx for AuNP/DNA spectra as well as absorbance values and molar extinction coefficients used to calculate concentrations of each in final solutions.

Calculating the surface area of 1 AuNP

Surface Area of a sphere = 4πr2, r = 5nm

4π(5x10-9m)2 = 3.14 x 10-16m2 = 314nm2

Calculating the # of AuNP in 240.7μL 29.67nM solution

29.67 x 10-9mol/L x 240 x 10-6L x 6.02x1023 AuNP/mol = 4.299 x 1012 AuNP

Calculating the Total Surface Area Available for DNA Attachment

4.299 x 1012 AuNP x 3.14x10-16m2/1 AuNP = 0.001349886 m2

Calculating the Number of Moles of DNA Available to Attach

2.225x10-6moles/L x 240.7x10-6L = 5.3555575 x 10-10 moles DNA

Calculating oligonucleotide density on each particle (theoretical)

5.3555575x10-10moles DNA/0.001349886m2 AuNP = 3.967x10-7 moles DNA/m2 AuNP (OR 39.67pmol DNA/cm2 AuNP)

Calculating oligonucleotide density on each particle (actual)

Sample A1

moles DNA = (1.827x10-7M x 350 x 10-6L) = 6.40x10-11 moles

6.40x10-11 moles/0.001349886m2 AuNP = 4.74x10-8moles DNA/m2AuNP

Sample B

moles DNA = 4.44x10-8M x 500 x 10-6L = 2.22x10-11 moles

2.22x10-11 moles/0.001349886m2 AuNP = 1.64x10-8moles DNA/m2AuNP

Sample A2

moles DNA = 1.42x10-10

1.42x10-10/0.001349886m2 AuNP = 1.05x10-7moles DNA/m2AuNP

Calculating the percentage of DNA hybridized in each sample

Sample A1

4.74x10-8moles DNA/m2AuNP/3.967x10-7 moles DNA/m2 AuNP = 11.95%