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

(Difference between revisions)
 Revision as of 14:37, 16 July 2013 (view source) (→DNA/AuNP Data Analysis)← Previous diff Revision as of 14:43, 16 July 2013 (view source) (→DNA/AuNP Data Analysis)Next diff → Line 57: Line 57: 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 the percent DNA hybridized in each sample''' + '''Calculating the percentage of DNA hybridized in each sample''' *based on # of moles of DNA available to attach *based on # of moles of DNA available to attach Line 66: Line 66: % hybridized = (6.40x10-11/5.3555575 x 10-10 moles DNA)x100% = 11.95% % 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%

## Revision as of 14:43, 16 July 2013

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

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

Calculating the percentage of DNA hybridized in each sample

• based on # of moles of DNA available to attach

Sample A1

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%