Nucleic acid NMR is the use of nuclear magnetic resonance spectroscopy to obtain information about the structure and dynamics of nucleic acid molecules, such as DNA or RNA. It is useful for molecules of up to 100 nucleotides, and as of 2003, nearly half of all known RNA structures had been determined by NMR spectroscopy. NMR has advantages over X-ray crystallography, which is the other method for high-resolution nucleic acid structure determination, in that the molecules are being observed in their natural solution state rather than in a crystal lattice that may affect the molecule's structural properties. It is also possible to investigate dynamics with NMR. This comes at the cost of slightly less accurate and detailed structures than crystallography. Nucleic acid NMR uses techniques similar to those of protein NMR, but has several differences. Nucleic acids have a smaller percentage of hydrogen atoms, which are the atoms usually observed in NMR, and because nucleic acid double helices are stiff and roughly linear, they do not fold back on themselves to give "long-range" correlations. Nucleic acids also tend to have resonances distributed over a smaller range than proteins, making the spectra potentially more crowded and difficult to interpret.
Experimental methods Two-dimensional NMR methods are almost always used with nucleic acids. These include correlation spectroscopy (COSY) and total coherence transfer spectroscopy (TOCSY) to detect through-bond nuclear couplings, and nuclear Overhauser effect spectroscopy (NOESY) to detect couplings between nuclei that are close to each other in space. The types of NMR usually done with nucleic acids are 1H NMR, 13C NMR, 15N NMR, and 31P NMR. 19F NMR is also useful if nonnatural nucleotides such as 2'-fluoro-2'-deoxyadenosine are incorporated into the nucleic acid strand, as natural nucleic acids do not contain any fluorine atoms. 1H and 31P have near 100% natural abundance, while 13C and 15N have low natural abundances. For these latter two nuclei, there is the capability of isotopically enriching desired atoms within the molecules, either uniformly or in a site-specific manner. Nucleotides uniformly enriched in 13C and/or 15N can be obtained through biochemical methods, by performing polymerase chain reaction or in vitro transcription using dNTPs or NTPs derived from bacteria grown in an isotopically enriched environment. Site-specific isotope enrichment must be done through chemical synthesis of the labeled nucleoside phosphoramidite monomer and of the full strand; however these are difficult and expensive to synthesize. Because nucleic acids have a relatively large number of protons which are solvent-exchangeable, nucleic acid NMR is generally not done in D2O solvent as is common with other types of NMR. This is because the deuterium in the solvent would replace the exchangeable protons and extinguish their signal. H2O is used as a solvent, and other methods are used to eliminate the strong solvent signal, such as saturating the solvent signal before the normal pulse sequence ("presaturation"), which works best a low temperature to prevent exchange of the saturated solvent protons with the nucleic acid protons; or exciting only resonances of interest ("selective excitation"), which has the additional, potentially undesired effect of distorting the peak amplitudes.
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