Synthetic oligonucleotides

[Ron Caspi]

Hi everybody

This is a dumb question, but I might as well ask it:
I need to design oligonucleotides, that will be used mainly as primers
for cycle sequencing. 
I have a program that can analyze the oligos (vectorNTI), and provide
thermodynamic data about the stability of possible dimers and hairpin
loops. My problem is - what are acceptable numbers: for example, if
the program anticipates a dimer with dG of 0.4Kcal/mol, is this
acceptabe for my purpose, or not?
And what if I use these oligos for radioactive probing, what are the
limits in that case?

Thank you for any input on this issue

Ron

______________________________________________________
Ron Caspi
Scripps Institution of Oceanography            Phone (619) 534-0638
La Jolla  CA  92093-0202                          Fax     (619) 534-7313