I want to design a really rigid DNA hairpin. My ideal requirement is a hairpin which can be thought as a rigid wall such that if another organic molecule is attached to the hairpin, then the molecule has minimum randomness resulting from the flexibility of the hairpin. I've seen papers with 4T loops. But from my experience I know it has some flexibility. Can I have less number of bases (like 1 or 2) to form a hairpin?
I think the most rigid hairpins (RNA) are the tetraloops like ANYA, CUYG, GNRA, UMAC and UNCG. I am not sure if they also apply to DNA.
Thanks Martin for your answer. What's the Y/N? Is it an arbitrary base? I saw, in the papers for DNA as well they use T4 loops, but I doubt they are felixible.
That is the aberration for multiple possible nucleotides, here is a link: https://en.wikipedia.org/wiki/Nucleic_acid_notation
I think the flexibility depends on the sequence, I just looked into some old lectures and found a link to this paper: http://pubs.acs.org/doi/pdf/10.1021/bi026479k
They also reported Triloops I don't know if you can go even smaller and how flexible each loop is later one.
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