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Separation of similar in size DNA fragments

Separation of similar in size DNA fragments - Basic Lab Protocols and Techniques

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Old 11-21-2007, 05:26 AM
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Unhappy Separation of similar in size DNA fragments



Hello
One of my experiment requires separation of small fragments of size 255, 231 and 24bp in one gel. Which gel I should use agarose or acrylamide?
I have tried 3% agarose even after long run in TBE buffer. Separation is visible but not convincing. I have also tried 10% acrylamide (Acrylamide 29:1, 1X TBE, Water, APS and TEMED). Still bands are fuzzy and not well separated?
Can any body help me on this, If you suggest higher than three percent agarose then give me tips as well on how to prepare this gel.
Thanks
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Old 11-26-2007, 04:18 PM
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Default Re: Separation of similar in size DNA fragments

Here's a table for using acrylamide gels to separate small DNA Fragments.

Acrylamide (%)--------Fragment sizes separated (bases)
20 to 30----------------2 to 8
15 to 20----------------8 to 25
13.5 to 15--------------25 to 35
10 to 13.5--------------35 to 45
8 to 10-----------------45 to 70
6 to 8------------------70 to 300

Use the table and try acrylamide again.

Last edited by danfive; 11-26-2007 at 04:28 PM.
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