Dear Diana,

Assuming your sequence is designed to form a hairpin, you should not encounter any problems folding to the desired conformation. In the case of competing alternate structures, lower DNA and salt concentrations favor the hairpin over intermolecular forms as demonstrated experimentally by Marky et al., 1983 (Biopolymers , 22: 1247).

http://onlinelibrary.wiley.com/doi/10.1002/bip.360220416/abstract

Regarding specific annealing conditions, you might refer to the article authored by Shockett and Schatz, 1999 (Mol. Cell. Biol., 19: 4159), which employs heating at 95 ºC and rapid cooling to favor hairpin formation over intermolecular association as paraphrased on page 4160: "Hairpin oligonucleotides were denatured at 95 °C and quick cooled on ice to favor intramolecular hairpin annealing rather than intermolecular association".

http://mcb.asm.org/content/19/6/4159.full.pdf+html

I hope this information is useful when conducting your experiments.

Best Regards,

Conceição

The cooling needs to be slowly (e.g. at room temperature), that annealing and folding of the spatial structure can take plase.

best GAD

Dear Diana,

Assuming your sequence is designed to form a hairpin, you should not encounter any problems folding to the desired conformation. In the case of competing alternate structures, lower DNA and salt concentrations favor the hairpin over intermolecular forms as demonstrated experimentally by Marky et al., 1983 (Biopolymers , 22: 1247).

http://onlinelibrary.wiley.com/doi/10.1002/bip.360220416/abstract

Regarding specific annealing conditions, you might refer to the article authored by Shockett and Schatz, 1999 (Mol. Cell. Biol., 19: 4159), which employs heating at 95 ºC and rapid cooling to favor hairpin formation over intermolecular association as paraphrased on page 4160: "Hairpin oligonucleotides were denatured at 95 °C and quick cooled on ice to favor intramolecular hairpin annealing rather than intermolecular association".

http://mcb.asm.org/content/19/6/4159.full.pdf+html

I hope this information is useful when conducting your experiments.

Best Regards,

Conceição

Most publications described the process as "slowly cool down for more than an hour", I also want to know how to make it slow enough. Have you solved this problem yet?