We find that RNA runs about like DNA, but a little easier. I'd use 3-hydroxy
picolinic acid (sat'd solution in water) and some added ammonium tartrate.
Desalting to get rid of Na and K is important; my preference is to use
cation exchange resin beads that are loaded with NH4+. As Mike Knierman
noted, even with added ammonium salt in the matrix, one can gat alkali
metal adducts. As for conditions, both negative and positive modes seem
to work about the same. I'd set the other conditions the same as for a
protein of about the same mass as your oligo.
Arnie Falick
PE Biosystems