Problem with annealing single stranded oligos

[studentadl]

Hi all,

 

Desperately need help here.. I am currently trying to anneal two complementary single stranded oligos. They are about 44bp long and the tm is about 57C. I initially just heated the oligos in annealing buffer (10mM Tris-HCL pH8 + 1mM EDTA + 50 mM NaCL) to about 98 degrees and let it cool to room temp gradually. But when i ran them on TBE gel (4-12% gradient) i found that alot of it are still forming single strand. These oligos are AT rich so i assumed the hairpin structure is the problem, although when i ran it through oligoanalyzer program the energy is still highly favourable for double stranded annealing rather than self dimer.

 

I since tried varying different salt concentration in the buffer, as well as using pcr machine with various programs and this annoying single strand still showed up on the bottom. Worse, when i tried to anneal longer oligos (just an extended sequence of the operator oligos i mentioned above) it doesn't seem that these longer oligos anneal at all!

 

i am wondering if it is possible that the gel that i used managed to give me this funny results or was that just wishful thinking? surely annealing oligos are not supposed to be this hard. HELP!!!