Dear all, can long (45nt) poly(dA), poly(dT) and poly(dC) ssDNA chain form duplexes, harpins or any other secondary structures (guadruplex, etc.)? If yes, could you, please, put some references here?
as per conventional information and hydrogen bond base pairing between AT and GC, hairpin loop will not form in stretch of 45 bases long containing all 45 bases as either A, or T or G or C.
However in one of the reference on poly A signal of AAUAAA, in HIV and SIV, when this sequence acts as polyA signal in these viruses, it fold and forms hairpin structure with uracil present in AAUAAA signal sequence.
But as your questing mentioned about all bases are only A, or only T, or only G etc. then I think that it will not form any secondary structure, it its just a single stranded DNA of Single stranded RNA and acting just as polynucleotide.
С-rich ssDNA can form a four-stranded structure called the i-tetraplex or i-motif. See the references from this review:
Kerwin, S. (2000). G-Quadruplex DNA as a Target for Drug Design. Current Pharmaceutical Design, 6(4), 441–471. doi:10.2174/1381612003400849
question is very specific whether "Can a 45 nt poly(dT) DNA chain form any secondary structures?".
That means if all the 45 bases are same, will it form secondary structure ?
Dear all,
thank you all.
There are several publications abou poly(dA) stacking. Here is one of them:http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.018302#fulltext.
Poly(dC) can form the i-motif as Anna has written: http://www.google.cz/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CCkQFjAB&url=http%3A%2F%2Fwww.researchgate.net%2Fprofile%2FJean-Francois_Riou2%2Fpublication%2F11568752_Interaction_of_an_acridine_dimer_with_DNA_quadruplex_structures%2Flinks%2F0fcfd5069fb8ee872f000000.pdf&ei=FIveVOLxFITeauD8gPgN&usg=AFQjCNHtzpnirxixjC5bNIO1nfN2HLDWhg&sig2=_bvGcG8NjdMbbO_vTs3GpA&bvm=bv.85970519,d.d2s
Nevertheless, I am more interested in the poly(dT) 45nt ssDNA...
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