IGEM:Harvard/2006/Folding DNA nanostructures

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Contents

Six-helix bundles

  • 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

Our structures

  • 4.5 μL p7308 scaffold (44 nM)
  • 8 μL oligos (250 nM)
  • 2 μL 10x folding buffer (500 mM HEPES pH 7.5, 500 mM NaCl, 100 mM MgCl2)
  • 5.5 μL dH2O

Annealing protocols

Don't use higher than 50 μL volumes in any one tube, because thermal cycling is unreliable otherwise

  • 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'

or

  • start at 80[[:Category:{{{1}}}|{{{1}}}]], decrement 1[[:Category:{{{1}}}|{{{1}}}]] every 2 min. for 60 cycles.

Gel Analysis

  • Run 2% agarose gel, supplemented to 10 mM MgCl2
  • Also supplement 1x TBE to 11 mM MgCl2
  • Run at low voltage (80V) for 1 hour (longer if necessary)
Image:SMD-gel060612a.jpg
1% agarose 10 mM MgCl2
Lane Contents Loading Buffer
01kb DNA ladder (10 μL)10x loading dye (1.1 μL)
1control: +scaffold -oligos (10 μL)10x loading dye (1.1 μL)
2control: -scaffold +oligos (10 μL)10x loading dye (1.1 μL)
3folded nanotubes (10 μL)10x loading dye (1.1 μL)
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