User:Allison K. Alix/Notebook/Thesis Research/2013/07/16

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(DNA/AuNP Data Analysis)
Current revision (15:09, 16 July 2013) (view source)
(References)
 
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4π(5x10<sup>-9</sup>m)<sup>2</sup> = 3.14 x 10<sup>-16</sup>m<sup>2</sup> = '''314nm<sup>2</sup>'''
4π(5x10<sup>-9</sup>m)<sup>2</sup> = 3.14 x 10<sup>-16</sup>m<sup>2</sup> = '''314nm<sup>2</sup>'''
 +
'''Calculating the # of AuNP in 240.7μL 29.67nM solution'''
'''Calculating the # of AuNP in 240.7μL 29.67nM solution'''
29.67 x 10<sup>-9</sup>mol/L x 240 x 10<sup>-6</sup>L x 6.02x10<sup>23</sup> AuNP/mol = '''4.299 x 10<sup>12</sup> AuNP'''
29.67 x 10<sup>-9</sup>mol/L x 240 x 10<sup>-6</sup>L x 6.02x10<sup>23</sup> AuNP/mol = '''4.299 x 10<sup>12</sup> AuNP'''
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'''Calculating the Total Surface Area Available for DNA Attachment'''
'''Calculating the Total Surface Area Available for DNA Attachment'''
4.299 x 10<sup>12</sup> AuNP x 3.14x10<sup>-16</sup>m<sup>2</sup>/1 AuNP = '''0.001349886 m<sup>2</sup>'''
4.299 x 10<sup>12</sup> AuNP x 3.14x10<sup>-16</sup>m<sup>2</sup>/1 AuNP = '''0.001349886 m<sup>2</sup>'''
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'''Calculating the Number of Moles of DNA Available to Attach'''
'''Calculating the Number of Moles of DNA Available to Attach'''
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2.225x10<sup>-6</sup>moles/L x 240.7x10<sup>-6</sup>L = '''5.3555575 x 10<sup>-10</sup> moles DNA'''
2.225x10<sup>-6</sup>moles/L x 240.7x10<sup>-6</sup>L = '''5.3555575 x 10<sup>-10</sup> moles DNA'''
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'''Calculating oligonucleotide density on each particle'''
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'''Calculating oligonucleotide density on each particle (theoretical)'''
5.3555575x10<sup>-10</sup>moles DNA/0.001349886m<sup>2</sup> AuNP = '''3.967x10<sup>-7</sup> moles DNA/m<sup>2</sup> AuNP''' (OR 39.67pmol DNA/cm<sup>2</sup> AuNP)
5.3555575x10<sup>-10</sup>moles DNA/0.001349886m<sup>2</sup> AuNP = '''3.967x10<sup>-7</sup> moles DNA/m<sup>2</sup> AuNP''' (OR 39.67pmol DNA/cm<sup>2</sup> AuNP)
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'''Calculating the percent DNA hybridized in each sample'''
 
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*based on # of moles of DNA available to attach
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'''Calculating oligonucleotide density on each particle (actual)'''
Sample A1
Sample A1
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[DNA]= 1.827x10<sup>=7</sup>
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moles DNA = (1.827x10<sup>-7</sup>M x 350 x 10<sup>-6</sup>L) = 6.40x10<sup>-11</sup> moles
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6.40x10<sup>-11</sup> moles/0.001349886m<sup>2</sup> AuNP = '''4.74x10<sup>-8</sup>moles DNA/m<sup>2</sup>AuNP'''
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Sample B
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moles DNA = 4.44x10<sup>-8</sup>M x 500 x 10<sup>-6</sup>L = 2.22x10<sup>-11</sup> moles
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2.22x10<sup>-11</sup> moles/0.001349886m<sup>2</sup> AuNP = '''1.64x10<sup>-8</sup>moles DNA/m<sup>2</sup>AuNP'''
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Sample A2
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moles DNA = 1.42x10<sup>-10</sup>
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1.42x10<sup>-10</sup>/0.001349886m<sup>2</sup> AuNP = '''1.05x10<sup>-7</sup>moles DNA/m<sup>2</sup>AuNP'''
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 +
 
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'''Calculating the percentage of DNA hybridized in each sample'''
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 +
Sample A1
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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%'''
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Sample B
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1.64x10<sup>-8</sup>moles DNA/m<sup>2</sup>AuNP/3.967x10<sup>-7</sup> moles DNA/m<sup>2</sup> AuNP = '''4.12%'''
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Sample A2
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1.05x10<sup>-7</sup>moles DNA/m<sup>2</sup>AuNP/3.967x10<sup>-7</sup> moles DNA/m<sup>2</sup> AuNP = '''26.5%'''
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==References==
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[https://www.cs.duke.edu/~reif/temp/IN.VITRO.EVO/OTHER/DNA%20AuNP/Taton%20Protocol.pdf], [http://pubs.acs.org/doi/pdf/10.1021/ac0006627]
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Current revision

UV-Vis Analysis/Silica Coating Pt. 2 Main project page
Previous entry      Next entry

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 Image: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%

Sample B

1.64x10-8moles DNA/m2AuNP/3.967x10-7 moles DNA/m2 AuNP = 4.12%

Sample A2

1.05x10-7moles DNA/m2AuNP/3.967x10-7 moles DNA/m2 AuNP = 26.5%

References

[1], [2]









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