Primer design:Is it ok to omit extra bases after RE site? - (Aug/13/2005 )

Hi all:

I know it is necessary to add some extra bases around the restriction enzyme site to facilitate enzyme cutting.

But if doing so, my primer will be too long, so I want to omit 2 extra bases(CG) after the BamHI site.

So What I want to do is : Primer with BamHI site (GGATCC)

Originally suggest seq:
CG GGATCC CG+some my cloning inserts seq

Change design to:
CG GGATCC+some my cloning inserts seq

Is it ok to omit those extra bases?

Thank you for your reading!

Vincent

Hi,

So basically you just want to make your actual primer sequence 2 bases shorter? How long is it now? Is the "CG" that follows your BamHI sequence part of your primer, or just 2 random bases? You really only need extra sequence upstream of your restriction site if this is the case.

-Hank

Yes

Daniel

Longer automated DNA sequencing reads

Does adding required number of extra bases in front of the RE site work? cauze it never worked for me. I usually design pcr primers with the RE site embedded in it (without any extra bases), then clone the pcr product into the TA vector and later digest the cloned TA vector to get a clean digested fragment (pcr fragement). And it works 100%.

hi
the important beses are the ones BEFORE the RE

so Originally suggest seq:
CG GGATCC CG+some my cloning inserts seq

Change design to:
CG GGATCC+some my cloning inserts seq

both are ok.