User:Allison K. Alix/Notebook/Thesis Research/2013/10/09

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To Do

  • There is concern about whether or not the fluorescence we are observing is from the MB bound to the DNA. MB only samples which were at the same concentration as the MB in the Au@SiO2-DNA/MB samples still showed some fluorescence, even though theoretically it should be very low, due to the fact that the beacon is closed. To test whether or not the DNA and MB are bound, we are preparing solutions with varying DNA:MB ratios.

Preparing new Au@SiO2-DNA/MB solutions

  • These will be stock solutions with which the dilutions will be made from

1) 1:3 DNA:MB

Original [DNA] = 910nM

Original [MB] = 7610nM

MB should be 2730nM

  • Added 20uL 7610nM MB to 25uL Au@Si/DNA solution


MB = 3.182uM

DNA = 404uM

(This is actually a 1:8 ratio....)

2) 1:1

Added 3.3uL 7.61uM MB to 25uL Au@Si/DNA solution

[MB] = 887nM

[DNA] = 803nM

3) 3:1 DNA:MB

Added 1uL MB to 25uL Au@Si/DNA solution

[MB] = 292.7nM

[DNA] = 875nM

Dilutions for DNA:MB samples


Dilution Factor [Au@SiO2] [DNA] [MB]
None (stock) 3.06nM 404nM 3182nM
5X 612pM 80.8nM 636.4nM
10X 306pM 40.4nM 318.2M
100X 30.6pM 4.04nM 31.82nM
1000X 3.06pM 404pM 3.182nM
10000X 306fM 40.4pM 318.2pM


Dilution Factor [Au@SiO2] [DNA] [MB]
None (stock) 4.88nM 803nM 887nM
5X 975pM 160.6nM 177.4nM
10X 488pM 80.3nM 88.7M
100X 48.8pM 8.03nM 8.87nM
1000X 4.88pM 803pM 887pM
10000X 488fM 80.3pM 88.7pM


Dilution Factor [Au@SiO2] [DNA] [MB]
None (stock) 5.31nM 875nM 292.7nM
5X 1.062nM 175nM 58.54nM
10X 531pM 87.5nM 29.3M
100X 53.1pM 8.75nM 2.93nM
1000X 5.31pM 875pM 293pM
10000X 531fM 87.5pM 29.3pM

Calculations for preparing diltuions

  • Need 20uL for each dilution
Dilution Factor Solution to make dilution from Volume of solution Volume of PBS
5X stock 4uL 16uL
10X stock 3uL 27uL
100X 10X 3uL 27uL
1000X 100X 3uL 27uL
10000X 1000X 3uL 27uL