The differences in the T2 relaxation rates of the protons in the partially-deuteriated and fully protonated sugar residues in a large oligo-DNA ('NMR-window') gives complementary structural information

Selective incorporation of the stereospeciflcally deuterlated sugar moieties (<97 atom % 2H enhancements at H2′, H2″, H3′ and H5′/5′ sites, ∑85 atom % 2H enhancement at H4′ and ∑20 atom % 2H enhancement at H1′) in DNA and RNA by the ‘NMR-window’ approach has been shown to solve the problem of the resonance overlap [refs. 1, 2 & 3]. Such specific deuterium labelling gives much improved resolution and sensitivity of the residual sugar proton (i.e. H1′ or H4′) vicinal to the deuteriated centers (ref. 3). The T<inf>2</inf> relaxation time of the residual protons also increases considerably in the partially-deuteriated (shown by underline) sugar residues in dlnucleotldes [d(CpG), d(GpC), d(ApT, d(TpA)], trlnucleotide r(A2′p5′A2′p5′A) and 20-mer DNA duplex 5′d(C1G2C3G4C5G6C7G8A9A10T11T12C13G14C15G16C17G18 C19G20)<inf>2</inf>3′. The protons with shorter T<inf>2</inf> can be filtered away using a number of different NMR experiments such as ROESY, MINSY or HAL. The NOE intensity of the cross-peaks in these experiments includes only straight pathway from H1′ to aromatic proton (I-I and 1-1 + 1) without any spin-diffusion. The volumes of these NOE cross-peaks could be measured with high accuracy as their intensity is 3 to 4 times larger than the corresponding peaks in the fully protonated residues in the normal NOESY spectra. The structural informations thus obtainable from the residual protons in the partially-deuteriated part of the duplex and the fully protonated part in the ‘NMR window’ can indeed complement each other.