On again off again PCR

[Tara Paton]

Hi,

I'm doing PCR of selected pieces of an avian mitochondrial
genome and am having trouble with some of the amplifications since the 
primers I'm using are not the best match for my template.  Attempts at
amplifying these fragments have failed miserably although some have
worked in the past (ie they are not imposible). Are there any
suggestions of strategies I can use to improve the frequency of
success?  I'm currently using the profile:  94 (45 sec)- 50 (45 sec) -
72 (1.5 min) and the fragment lengths are no longer than 1.2 kb.  These
amps have worked in the past (barely) but I need a better strategy than
pure luck!

Thanks for your time,
Tara Paton