N vs Z nucleotide

[joskee]

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".

[Joann]

Look at Table 3, page 1387 in

doi:10.1093/bioinformatics/btq098

on extended IUPAC nomenclature code

[joskee]

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?

[Joann]

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

[joskee]

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.

[pmiguel]

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

--
Phillip