NMR structural characterisation of a hairpin DNA with two-base loop: solution conformation of d-GGTACIAGTACC.

An inosine-adenosine mismatched base-pair oligonucleotide, d-GGTACIAGTACC has been studied by 1H and 31P NMR spectroscopy. Almost complete 1H and 31P resonance assignments of the oligomer at 0.90 mM concentration and 310 K have been achieved. NMR results demonstrate that the oligomer adopts a hairpin conformation, which has a structure with two purines I6 and A7 forming a two-base loop on a B-DNA stem. Stacking is continued on the 5'-side of the loop, with the I6 stacked upon C5. The base A7, on the 3'-side of the loop stacks partially with I6. All the bases are in anti conformation with respect to their respective sugar moiety.