I have tried mixing them in 1x Annealing Buffer (10 mM Tris, pH 7.5–8.0, 50 mM NaCl, 1 mM EDTA) at 10uM final concentration for both the forward and the reverse and then putting them at 97ºC for 10-15 min and cooling down slowly either on a thermomixer or on a thermal cycler with a decrease of 1 degree/minute after the 97ºC step. I let them reach 25ºC before storing them at 4ºC. So far when I run the single strand DNA (either forward or reverse sequence) and the "annealed" mixture in a 1% agarose gel the "annealed" sample is migrating more (lower) and produces a smear (possible DNA degradation?)