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
NEW CONCENTRATIONS:
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
1)
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
|
2)
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
|
3)
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
|
|