IGEM:Harvard/2006/Folding DNA nanostructures

• working stocks
  • 44 nM scaffold (20 μL)
  • 0.99 μM each oligo
• goal
  • 10 nM scaffold
  • 100 nM each oligo
  • 20 μL reaction volume
• calculations
  • scaffold = (10 nM)/(44 nM) * 20 μL = 4.5 μL
  • oligos = (100 nM)/(990 nM) * 20 μL = 2 μL
• reaction mixture
  • 4.5 μL p7308 scaffold (44 nM)
  • 2 μL oligos (990 nM)
  • 2 μL 10x folding buffer (500 mM HEPES pH 7.5, 500 mM NaCl, 100 mM MgCl₂)
  • 11.5 μL dH₂O
• annealing protocol
  • 90[[:Category:{{{1}}}|{{{1}}}]] 5' → 65[[:Category:{{{1}}}|{{{1}}}]] 20' → 55[[:Category:{{{1}}}|{{{1}}}]] 20' → 45[[:Category:{{{1}}}|{{{1}}}]] 20' → 37[[:Category:{{{1}}}|{{{1}}}]] 30'

Gel Analysis

• Run 1% agarose gel, supplemented to 10 mM MgCl₂
• Run at low voltage (80V) for 1.5 hours

File:SMD-gel060612a.jpg

1% agarose 10 mM MgCl₂

Lane	Contents	Loading Buffer
0	1kb DNA ladder (10 μL)	10x loading dye (1.1 μL)
1	control: +scaffold -oligos (10 μL)	10x loading dye (1.1 μL)
2	control: -scaffold +oligos (10 μL)	10x loading dye (1.1 μL)
3	folded nanotubes (10 μL)	10x loading dye (1.1 μL)