IGEM:Harvard/2006/DNA nanostructures/Protocols

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See also iGEM Harvard 2006 protocols

Aptamer-decorated Nanostructure Binding Assay Potential protocol for a 2 μL incubation reaction (revised with Dr. Shih's suggestions)

• In a 0.2 mL PCR tube, mix:
  • 0.5 μL of 4x (not 5x) Bock's selection buffer
  • 1.0 μL of 2 μM aptamers (final concentration: 1.0 μM = 2 pmol)
  • 0.5 μL of 2 μM thrombin (final concentration: 0.5 μM = 1 pmol)
• OR in a 0.2 mL PCR tube, mix:
  • 0.5 μL of 4x (not 5x) Bock's selection buffer
  • 0.5 μL of 2 μM aptamers (final concentration: 0.5 μM = 1 pmol)
  • 1.0 μL of 2 μM thrombin (final concentration: 1.0 μM = 2 pmol)
• Alternative mix: Liu uses 10 pmol of DNA (1 μL of 10 μM) and varies thrombin amount from 2 pmol (1 μL of 0.2x thrombin working stock) to 100 pmol (1 μL of 10x thrombin working stock)
• Incubate at room temperature for 30 min.
• Load onto a non-denaturing polyacrylamide gel (10% to 20% gradient) at 4[[:Category:{{{1}}}|{{{1}}}]]
  • Run at 130 V for approximately 90 min.
  • Liu runs at 25 mA for 48 h.