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Silica Clean up of DNA

Silica Clean-up of DNA


Silica Suspension:

add 2 g of silica to 15 ml of H2O

wash 3x by centifugation at 2000 x g for 2 min

estimate vol of silica and resuspend in 2 vol H2O

Silica Wash Solution:

50 mM NaCl, 10 mM Tris 7.5, 2.5 mM EDTA, 50% Ethanol

6 M NaI

note: light sensitive


  1. Add 5 volumes of 6M NaI to DNA solution or agarose gel slice
    • if gel slice, melt at 55 degrees for 5 minutes with occasional agitation
    • for aqueous solutions add 1/10 vol 3M NaOAc to ensure pH is less than 7
  2. Bind DNA to silica
    • add appropriate volume of silica suspension (binds approx 200 ng of DNA / ul of suspension) and mix well
    • sediment silica matrix by centrifugation (10 seconds in 'nanofuge' or brief spin at full spend in microfuge)
    • wash silica 3 times with 500 ul wash solution
    • pellet silica once more to remove any residual wash solution
    • air dry to remove any residual EtOH
  3. Elute DNA from silica
    • resuspend silica pellet in desired volume of 10 mM Tris 7.5 or TE or 1X restriction buffer for downstream digests
    • heat 5 minutes at 60 degrees
    • spin 2 min @ full speed in microcentrifuge
    • remove DNA-containing supernatant to clean tube


Notes & Misc:




compiled by Chad Rappleye

Aroian Lab Protocols