Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
- - - - -

a question about degenerate primer (NNK)

  • Please log in to reply
No replies to this topic

#1 Biogareth



  • Active Members
  • PipPipPipPipPip
  • 73 posts

Posted 13 September 2011 - 01:54 AM

Recently I made a saturation library at a specific position with NNK primer designed by Strategene software, but when I checked the quality by sequencing (see the picture below), it is not good at all because of almost wild-type nucleotides.
Because I have succeeded in some other positions with NNK primer, I compared those good primers with this bad primer, and found that the stability of the primer looks quite important, therefore, I redesigned this primer by replacing three nucleotides on both flanks (silent mutation) in order to get the higher stability.
The primer is as follows, and the replaced nucleotides were shown in red:

Do you think is it reasonable to design the primer like this?
Any suggestion is welcome!


Attached Thumbnails

  • Picture1.png

Edited by Biogareth, 13 September 2011 - 02:40 AM.

Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.