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.

Refined procedures for accurate determination of solution structures of nucleic acids by two dimensional nuclear magnetic resonance spectroscopy.

New procedures have been described for accurate determination of solution structures of nucleic acids. These are two fold; new two dimensional nuclear magnetic resonance techniques and better approaches for interpretation of nuclear magnetic resonance data for structure determination purposes. The significant development in two dimensional nuclear magnetic resonance techniques for this purpose are ω1 -scaling and recording of pure phase spectra. Use of ω1-scaled correlated and nuclear Overhauser effect spectra for estimation of interproton distances and 1H-1H coupling constants has been described. Computer simulation procedures for exact determination of structure have been described. Experimental spectra demonstrating the application of new procedures have been presented.