Preparation of Specifically Deuterated RNA for NMR Studies Using a Combination of Chemical and Enzymatic Synthesis

The synthesis of deuterionucleosides

The synthesis of deuterionucleosides for site-specific incorporation into oligo-DNA or -RAA is herein reviewed for NMR or biological studies. The review covers the following aspects: (i) deuteration of the aglycone; (ii) single-site chemical deuteration of the sugar residues; (iii) multiple-site chemical deuteration of the sugar residues; (iv) enzymatic synthesis of deuterated nucleosides or nucleotides; and (v) synthesis of labelled nucleosides with multiple isotopes

The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins

During the past thirty years, deuterium labeling has been used to improve the resolution and sensitivity of protein NMR spectra used in a wide variety of applications. Most recently, the combination of triple resonance experiments and 2H, 13C, 15N labeled samples has been critical to the solution structure determination of several proteins with molecular weights on the order of 30 kDa. Here we review the developments in isotopic labeling strategies, NMR pulse sequences, and structure-determination protocols that have facilitated this advance and hold promise for future NMR-based structural studies of even larger systems. As well, we detail recent progress in the use of solution 2H NMR methods to probe the dynamics of protein sidechains.

3D C(CC)H TOCSY experiment for assigning protons and carbons in uniformly 13C- and selectively 2H-labeled RNA

We have prepared RNAs uniformly 13C-labeled in the ribose ring and with the H3',H4',H5'/H5" protons specifically replaced with deuterons (3',4',5'/5"-2H-13C, termed d4-13C ribose), which offers the advantage of spectral simplification without sacrifice of sensitivity for the remaining protons. A 3D C(CC)H TOCSY experiment that uses a combination of cross-polarization transfer and deuterium decoupling improves the transfer of magnetization around the ribose ring and facilitates assignment of all ribose carbons and H1' and H2' protons in a 30-nucleotide RNA from HIV-2. These and other combinations of labeling and pulse sequence methodology should prove invaluable for the study of large RNAs, RNA-ligand, and RNA-protein complexes.

Solution NMR spectroscopy beyond 25 kDa

Improvements in NMR instrumentation, higher magnetic field strengths, novel NMR experiments and new deuterium-labeling strategies have significantly increased the scope of structural problems that can now be addressed by solution NMR methods. To date, a number of structures of proteins of 30 kDa have been solved using multidimensional 15N,13C,2H NMR techniques, and this molecular weight limit will probably be surpassed in the near future.

Comparison of H5 and H8 relaxation rates of a 2H/13C/15N labeled RNA oligonucleotide with selective protonation at C5 and C8

Uniformly 13C/15N enriched ribonucleotide monophosphates have been prepared with extensive deuterium enrichment of the non-exchangeable positions. The purine C8 and pyrimidine C5 base positions were selectively protonated prior to incorporation of the individual nucleotide triphosphates into an RNA oligonucleotide. The longitudinal and transverse relaxation rates of the H8 and H5 resonances of this deuterated molecule were compared with the relaxation rates of the corresponding protonated, 13C/15N enriched RNA molecule. Deuteration disrupts the efficiency of 1H-1H dipolar relaxation and reduces the longitudinal and transverse magnetization relaxation rates on average to 25% and 68%, respectively, of the values measured for the non-deuterated RNA molecule. Importantly, the longitudinal relaxation rates remain sufficiently rapid (> 1s[-1]) to permit the use of short recovery delays in multidimensional NMR experiments without significant loss of sensitivity.