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  • N vs Z nucleotide

    Dear all,
    What does a "z" means in term of nucleotides?

    I am assuming that the "n" means: any base (so it could be any base that binds those "n" spots).

    See attaced figure for "n" and "z".
    Attached Files

  • #2
    Look at Table 3, page 1387 in

    doi:10.1093/bioinformatics/btq098

    on extended IUPAC nomenclature code

    Comment


    • #3
      Originally posted by Joann View Post
      Look at Table 3, page 1387 in

      doi:10.1093/bioinformatics/btq098

      on extended IUPAC nomenclature code
      Ok thanks.

      But this brings me to my next question: whats the idea/point behind having those "z" nucleotides and the "n" ones?
      Why not just "n" for all of them?

      Isnt it better to have all "n" nucleotides , so it can bind any nucleotide?

      Comment


      • #4
        You could explore that question further with the authors of the article. Don't forget to consider posting results of discussion here.

        Comment


        • #5
          Originally posted by Joann View Post
          You could explore that question further with the authors of the article. Don't forget to consider posting results of discussion here.
          answer I got: only one from 1024 possible types of oligonucleotides is suitable for ligation. Both "XY-dinucleotide" and degenerate part should be complementary to the template for the succesfull ligation, universal bases are not specific

          I still find it weird, why they just dont use universal bases in general (for the 6 others nucleotides and not just 3).. rather then doing that, they make 1024 possible types of oligonucleotide...

          I suppose its to make them more specific because otherwise you would get more wrongly hybridised pieces.

          Comment


          • #6
            If you think about it, using a DNA polymerase is like doing a single base (1 mer) ligation.

            --
            Phillip

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