I am trying to design some DNA probes.
Even three base pairs in the stem should be enough to form quite stable hairpin, but of course all depends on the kind of base pairs (GC pair stabilizes more than AT), loop size, and composition of solution (especially salt concentration).
Here are some details that might be helpful:
http://onlinelibrary.wiley.com/doi/10.1002/%28SICI%291097-0282%2819991005%2950:4%3C425::AID-BIP8%3E3.0.CO;2-B/abstract
Thank you Anna !
In addition to the salt concentration, any chelating agents will make a difference
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