Name |
Company |
Catalog Number |
Comments |
3-aminopropyltriethoxysilane (APTS) |
Sigma Aldrich |
440140-100ML |
Store in dessicator box |
5 Minute Epoxy |
Devcon |
20845 |
use for sealing the microfluidic device |
acetone |
Pharmco |
329000ACS |
use for cleaning coverslips |
bath sonicator |
Fisher Scientific |
CPXH Model 2800 |
catalog number 15-337-410 |
Beaker, glass, 100 mL |
|
|
|
Benchtop centrifuge |
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|
|
Biotin-PEG-Succinimidyl Valerate (MW 5,000) |
Laysan Bio |
BIO-SVA-5K |
Succinimidyl valerate has a longer half-life than succinimidyl carbonate |
biotinylated oligonucleotide |
Integrated DNA Technologies |
custom - see protocol for design considerations |
Request 5' Biotin modification and HPLC purification |
Bovine Serum Albumin (BSA) |
VWR |
0903-5G |
prepare a 10 mg/mL solution (aq) and heat to 95 °C before using |
Centri-Spin-10 Size Exclusion Spin Columns |
Princeton Separations |
CS-100 or CS-101 |
used to purify thiolated oligonucleotides after reducing the disulfide bond |
Centrifuge tubes 1.5. mL |
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|
|
Coverslips, 1-inch square glass |
|
|
|
coverslip holders |
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|
|
diamond point wheel |
Dremel |
7134 |
use for drilling holes in quartz flow cell topper |
dithiothreitol (DTT) |
Thermo Scientific |
A39255 |
No-Weigh Format, 7.7 mg/vial |
drill press rotary tool workstation stand |
Dremel |
220-01 |
facilitates quartz drilling |
EcoRV (REase used to generate example data) |
New England Biolabs |
R0195T or R0195M |
Use 100,000 units/mL stock to avoid adding excess glycerol Check REBASE for suppliers of other REases |
ethanol |
various |
CAS 64-17-5 |
denatured or 95% are acceptable, use for cleaning coverslips |
Ethylenediaminetetraacetic acid (EDTA) |
Sigma Aldrich |
EDS |
BioUltra, anhydrous, store in dessicator box |
Flea Micro Spinbar |
Fisherbrand |
14-513-65 |
3 mm x 10 mm size to fit beneath coverslip rack |
fluorescein |
Acros Organics |
17324 |
use to make experimental buffers |
gravity convection oven |
Binder |
9010-0131 |
|
handheld rotary multitool |
Dremel |
8220 |
use for drilling holes in quartz flow cell topper |
ImagEM X2 EM-CCD Camera |
Hamamatsu |
C9100-23B |
air cooling is adequate for this experiment, use HCImage software or similar to control |
Imaging spacer, double-sided, adhesive |
|
|
|
Jar, glass with screw cap, (approximately 50 mm diameter by 50 mm high) |
|
|
|
magnesium chloride hexahydrate |
Fisher Bioreagents |
BP214-500 |
use to make experimental buffer with magnesium |
MATLAB software |
|
|
Data analysis |
metal tweezers |
Fisher Brand |
16-100-110 |
|
methoxy-PEG-Succinimidyl Valerate (MW 5,000) |
Laysan Bio |
M-SVA-5K |
Both PEGs should have the same NHS ester so that the rate of reaction is consistent |
microcentrifuge |
Eppendorf |
5424 |
|
multiposition magnetic stirrer |
VWR |
12621-022 |
|
N-cyclohexyl-2-aminoethanesulfonic acid (CHES) |
Acros Organics |
AC20818 |
CAS 103-47-9, use to make CHES buffer |
orbital shaker and heater for microcentrifuge tubes |
Q Instruments |
1808-0506 |
with 1808-1061 adaptor for 24 x 2.0 mL or 15 x 0.5 mL tubes |
Parafilm |
|
|
|
PE60 Polyethylene tubing (inner diameter 0.76 mm, outer diameter 1.22 mm) |
Intramedic |
6258917 |
22 G blunt needles are a good fit for this tubing size |
Phosphate-Buffered Saline (PBS) 10x |
Sigma Aldrich |
P7059 |
Use at 1x strength |
potassium hydroxide |
VWR Chemicals BDH |
BDH9262 |
use a 1 M solution to clean coverslips |
Qdot 655 ITK Amino (PEG) Quantum Dots |
Invitrogen |
Q21521MP |
|
Quartz Slide, 1 inch square, 1 mm thick |
Electron Microscopy Sciences |
72250-10 |
holes must be drilled in the corners for inlet and outlet tubing insertion |
reinforced plastic tweezers |
Rubis |
K35a |
use for handling coverslips and building microfluidic device |
SecureSeal Adhesive Sheets |
Grace Biolabs |
SA-S-1L |
cut to form spacer for microfluidic device |
Single channel syringe pump for microfluidics |
New Era Pump Systems |
NE-1002X-US |
fitted with a 50 mL syringe and a 22 G blunt needle |
Slide-a-Lyzer MINI Dialysis Devices, 10 kDa MWCO, 0.1 mL |
Thermo Scientific |
69570 or 69572 |
used for buffer exchange during quantum dot coupling to DNA |
sodium bicarbonate |
EMD Millipore |
SX0320 |
use to make buffer for surface functionalization; 100 mM, pH 8 |
sodium chloride |
Macron |
7581-12 |
use to make experimental buffers |
Sodium phosphate dibasic solution (BioUltra, 0.5 M in water) |
Sigma Aldrich |
94046 |
use to make 100 mM sodium phosphate buffer |
Sodium phosphate monobasic solution (BioUltra, 5M in water) |
Sigma Aldrich |
74092 |
use to adjust pH of 100 mM sodium phosphate buffer |
Streptavidin from Streptomyces avidinii |
Sigma Aldrich |
S4762 |
dissolve at 1 mg/mL and store 25 mL aliqouts at -20 ? |
Sulfosuccinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (sulfo-SMCC) |
Thermo Scientific |
A39268 |
No-Weigh Format, 2 mg/vial |
Syringe fitted with blunt 21 G needle |
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|
|
Syringe pump |
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|
|
thiolated oligonucleotide |
Integrated DNA Technologies |
custom - see protocol for design considerations |
Request 5' Thiol Modifier C6 S-S and HPLC purificaiton |
TIRF imaging system with 488 nm laser illumination |
various |
|
custom built |
Tris -HCl |
Research Products International |
T60050 |
use to make experimental buffers |
Tris base |
JT Baker |
4101 |
use to make experimental buffers |
Tween-20 |
Sigma |
P7949 |
use to make blocking buffer |
Ultrapure water |
|
|
|
vortex mixer |
VWR |
10153-842 |
|
Wash-N-Dry Coverslip Rack |
Electron Microscopy Sciences |
70366-16 |
used for surface functionalization of coverslips |