List of Materials and Equipment Needed for In vitro Selection (or SELEX)

If you are new to in vitro selection (or SELEX) or you are interested in the process of isolating Functional Nucleic acids, then you must be wondering if your lab is capable equipped with the basic instruments needed to perform these experiments. Below, we break down the general materials and equipment required to from start to finish!

1. Equipment

  1. Standard Calibrated Pipette SetVolumes from 1 uL - 1000 uL 
  2. VortexerFor mixing solutions in microcentrifuge tubes
  3. Benchtop minicentrifugeFor quick collection of samples 
  4. Magnetic RackWill be used if the target molecule is immobilized on magnetic beads
  5. Dry Block HeatersAble to hold 1.5 mL microcentrifuge tubes
  6. -20°C FreezerRequired for storing samples and for precipitation of DNA experiments
  7. Refrigerated CentrifugeRotor able to hold 1.5 mL microcentrifuge tubes and generate greater than 14,000 x g of force
  8. Speed Vacuum (Optional)Can be used to speed of drying of DNA pellets and removal of trace ethanol
  9. Fluorometer - Equipped with a ~488 nm laser and emission filters ~520 nm
  10. Thermocycler - Needed for amplification of library using Polymerase Chain Reaction
  11. Gel Imaging System - Equipped with a 488 nm laser or 470 nm blue LED or broad blue excitation
  12. High-voltage Electrophoresis Power Supply - Able to reach at least 1500 Volts
  13. Agarose Gel Electrophoresis setup - Agarose trays, housing, combs etc. 
  14. Polyacrylamide Gel Electrophoresis setup - Polyacrylamide housing, combs, plates etc.
  15. Blue Light Transilluminator - With an amber filter unit (orange panel) 
  16. Rotators or mixers - Gentle mixers for reactions and DNA elution from gels

2. Consumable Materials

  1. An optimally designed Library with primers for enrichment - Aptamers (N30, N40, N50) or ANDzymes (N30, N40, N50)
  2. 3 M Sodium Acetate Buffer (pH 5.2) - Used for precipitation of Nucleic Acids
  3. 2x TBE-Urea Loading Buffer - Used for disrupting nucleic acid secondary structure prior to loading on a denaturing PAGE
  4. Selection Buffer - Buffering solutions used to isolate Aptamers or ANDzymes
  5. DNA Elution Buffer - Needed to recover nucleic acids from agarose or polyacrylamide gels
  6. 10x Tris-Borate-EDTA buffer (TBE) - Standard running buffer for both agarose and polyacrylamide gel electrophoresis
  7. Centrifugal Columns - Clean and efficient removal of gels from nucleic acids
  8. Glycogen - Required for recovering low concentration of nucleic acids
  9. Microcentrifuge tubes (1.5 mL, 0.5 mL) - Tight seal caps are HIGHLY recommended as samples are regularly heated to high temperatures
  10. PCR tubes (0.2 mL) - PCR 8-tube strips are recommended
  11. Deoxyribonucleoside triphosphates (dNTPs) - Standard dNTPs for Polymerase Chain Reaction
  12. Taq Polymerase Enzyme - Our recommendation is to use OneTaq from New England Biolabs
  13. Agarose - Standard reagent for separation of dsDNA 
  14. Sybr Safe - Can be purchased from ThermoScientific and is used with agarose to image dsDNA
  15. Low-range DNA ladder - Any standard low-range DNA ladder used in Agarose gel
  16. 10% denaturing Urea Polyacrylamide Solution - Denaturing urea polyacrylamide gel electrophoresis will be used to isolate highly pure libraries after enrichment
  17. Tetramethylethylenediamine (TEMED) - Required for polymerization of acrylamide/bisacrylamide 
  18. 10% Ammonium persulfate solution - Required for polymerization of acrylamide/bisacrylamide 
  19. Razor blades - Required to excise gel bands from polyacrylamide gels (or other sharp blades can be used)
  20. Magnetic Beads - Required for aptamer selection whereby the target if interest is immobilized onto the magnetic beads
  21. Anhydrous or denatured Ethanol - Needed for precipitation of nucleic acids
  22. DNase-, RNase-free water - Ensure all water sources are free from nuclease contamination