User:Madeleine Y. Bee/Notebook/Single Molecule Fluorescence/2013/06/28: Difference between revisions

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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Meeting,</span>
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Meeting and FCS Measurements</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
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===Notes from Meeting===
===Notes from Meeting===
*Find averages and standard deviation of inconsistent DNA/ThT spectra for calibration curve
*Find averages and standard deviation of inconsistent DNA/ThT spectra for calibration curve
**Fit Gaussian to inconsistent spectra
**Fit Gaussian for inconsistent spectra (use Igor Pro program)
*Check literature for AuNP@SiO2 shift and silica-shell radius calculations
*Check literature for AuNP@SiO2 shift and silica-shell radius calculations
*Label axes for FCS data
*Label axes for FCS data
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*FCS: increase time as concentration decreases
*FCS: increase time as concentration decreases
*Repeat old AuNP procedure with solutions from new procedure
*Repeat old AuNP procedure with solutions from new procedure
===FCS Measurements===
===FCS Measurements===
*Prepare Samples
*Prepare Samples
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**100, 80, 60, 20pM  Oligo D  
**100, 80, 60, 20pM  Oligo D  
**10, 1, 5nM, 500, 100, 50, 25pM DNA/MB samples
**10, 1, 5nM, 500, 100, 50, 25pM DNA/MB samples
====Results====
====Results and Notes====
Calibration graphs:<br.>
[[Image:FCS_data_2013_0628_calibration_graphs.PNG]]<br.>
<br.>
*Oligo D samples were run for 300s, the 60pM and 80pM samples are still inconsistent with the trend of the other concentrations
*The first round of MB/DNA samples were run for 300s, results had lots of noise and inconsistencies
*The second round of MB/DNA samples were run for 700s to eliminate noise, only the 25pM sample lied outside the trend of the other concentrations
*Future work:
**Always align laser with 10000x diluted green fluorescent beads, include spectra for comparison
**Create more samples for MB/DNA with 100pM intervals from 1nM to 100pM, and a 75pM sample
**Create more samples for Oligo D at 50, 30, and 10pM concentrations
**Make samples by serial dilutions after hybridization (?)
**For pM concentrations increase time to 700s to eliminate noise from spectra
***Increase time even further for concentrations lower than 25pM (?)
**Attach AuNPs in proper ratio at successfully run concentrations of MB/DNA




Revision as of 13:25, 28 June 2013

Meeting and FCS Measurements <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>

June 28, 2013

Notes from Meeting

  • Find averages and standard deviation of inconsistent DNA/ThT spectra for calibration curve
    • Fit Gaussian for inconsistent spectra (use Igor Pro program)
  • Check literature for AuNP@SiO2 shift and silica-shell radius calculations
  • Label axes for FCS data
  • FCS spectra for fluorescent beads in prezi
  • FCS: increase time as concentration decreases
  • Repeat old AuNP procedure with solutions from new procedure

FCS Measurements

  • Prepare Samples
    • 10000x diluted green fluorescent beads
    • 100, 80, 60, 20pM Oligo D
    • 10, 1, 5nM, 500, 100, 50, 25pM DNA/MB samples

Results and Notes

Calibration graphs:<br.> <br.> <br.>

  • Oligo D samples were run for 300s, the 60pM and 80pM samples are still inconsistent with the trend of the other concentrations
  • The first round of MB/DNA samples were run for 300s, results had lots of noise and inconsistencies
  • The second round of MB/DNA samples were run for 700s to eliminate noise, only the 25pM sample lied outside the trend of the other concentrations
  • Future work:
    • Always align laser with 10000x diluted green fluorescent beads, include spectra for comparison
    • Create more samples for MB/DNA with 100pM intervals from 1nM to 100pM, and a 75pM sample
    • Create more samples for Oligo D at 50, 30, and 10pM concentrations
    • Make samples by serial dilutions after hybridization (?)
    • For pM concentrations increase time to 700s to eliminate noise from spectra
      • Increase time even further for concentrations lower than 25pM (?)
    • Attach AuNPs in proper ratio at successfully run concentrations of MB/DNA



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