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

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 Revision as of 14:52, 16 July 2013 (view source) (→DNA/AuNP Data Analysis)← Previous diff Current revision (15:09, 16 July 2013) (view source) (→References) (6 intermediate revisions not shown.) Line 40: Line 40: 4π(5x10-9m)2 = 3.14 x 10-16m2 = '''314nm2''' 4π(5x10-9m)2 = 3.14 x 10-16m2 = '''314nm2''' + '''Calculating the # of AuNP in 240.7μL 29.67nM solution''' '''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''' 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''' '''Calculating the Total Surface Area Available for DNA Attachment''' 4.299 x 1012 AuNP x 3.14x10-16m2/1 AuNP = '''0.001349886 m2''' 4.299 x 1012 AuNP x 3.14x10-16m2/1 AuNP = '''0.001349886 m2''' + '''Calculating the Number of Moles of DNA Available to Attach''' '''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''' 2.225x10-6moles/L x 240.7x10-6L = '''5.3555575 x 10-10 moles DNA''' + '''Calculating oligonucleotide density on each particle (theoretical)''' '''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) 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)''' '''Calculating oligonucleotide density on each particle (actual)''' Line 63: Line 68: moles DNA = (1.827x10-7M x 350 x 10-6L) = 6.40x10-11 moles 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 + 6.40x10-11 moles/0.001349886m2 AuNP = '''4.74x10-8moles DNA/m2AuNP''' Sample B Sample B Line 69: Line 74: moles DNA = 4.44x10-8M x 500 x 10-6L = 2.22x10-11 moles 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 + 2.22x10-11 moles/0.001349886m2 AuNP = '''1.64x10-8moles DNA/m2AuNP''' Sample A2 Sample A2 Line 75: Line 80: moles DNA = 1.42x10-10 moles DNA = 1.42x10-10 - 1.42x10-10/0.001349886m2 AuNP = 1.05x10-7moles DNA/m2AuNP + 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 - '''Calculating the percentage of DNA hybridized in each sample''' + 1.05x10-7moles DNA/m2AuNP/3.967x10-7 moles DNA/m2 AuNP = '''26.5%''' - *based on # of moles of DNA available to attach + ==References== - Sample A1 + [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] - moles DNA = (1.827x10-7M x 350 x 10-6L) = 6.40x10-11 moles - % hybridized = (6.40x10-11/5.3555575 x 10-10 moles DNA)x100% = 11.95% - Sample B - - moles DNA = 4.44x10-8M x 500 x 10-6L = 2.22x10-11 moles - - % hybridized = (2.22x10-11 moles/5.3555575 x 10-10 moles DNA)x100% = 4.14% - - Sample A2 - - moles DNA = 1.42x10-10 - % hybridized = (1.42x10-10/5.3555575 x 10-10) = 26.5%

## Current revision

UV-Vis Analysis/Silica Coating Pt. 2 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 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%