HNHC: a triple resonance experiment for correlating the H2, N1(N3) and C2 resonances in adenine nucleobases of <Superscript>13</Superscript>C-, <Superscript>15</Superscript>N-labeled RNA oligonucleotides

A novel NMR pulse sequence has been developed that correlates the H2 resonances with the C2 and the N1 (N3) resonances in adenine nucleobases of ¹³C, ¹⁵N labeled oligonucleotides. The pulse scheme of the new 3D-HNHC experiment is composed of a ²J-¹⁵N-HSQC and a ¹J-¹³C-HSQC and utilizes large ²J(H2, N1(N3)) and ¹J(H2, C2) couplings. The experiment was applied to a medium-size ¹³C, ¹⁵N-labeled 36mer RNA. It is useful to resolve assignment ambiguities occurring especially in larger RNA molecules due to resonance overlap in the ¹H-dimension. Therefore, the missing link in correlating the imino H3 resonances of the uracils across the AU base pair to the H8 resonances of the adenines via the novel pulse sequence and the TROSY relayed HCCH-COSY (Simon et al. in J Biomol NMR 20:173–176 2001) is provided. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Sequential correlation of anomeric ribose protons and intervening phosphorus in RNA oligonucleotides by a 1H,13C,31P triple resonance experiment: HCP-CCH-TOCSY

Summary A three-dimensional ¹H,¹³C,³¹P triple resonance experiment, HCP-CCH-TOCSY, is presented which provides unambiguous through-bond correlation of all ¹H ribose protons on the 5′ and 3′ sides of the intervening phosphorus along the backbone bonding network in ¹³C-labeled RNA oligonucleotides. The correlation of the complete ribose spin system to the intervening phosphorus is obtained by adding a C,C-TOCSY coherence transfer step to the triple resonance HCP experiment. The C,C-TOCSY transfer step, which utilizes the large and relatively uniform ¹J(C,C) coupling constant (∼40 Hz for ribose carbons), efficiently correlates the phosphorus-coupled carbons observed in the HCP correlation experiment (i.e., C4′ and C5′ in the 5′ direction and C4′ and C3′ in the 3′ direction) to all other carbons in the ribose spin system. Of the additional correlations observed in the HCP-CCH-TOCSY, that to the relatively well-resolved anomeric H1′, C1′ resonance pairs provides the greatest gain in terms of facilitating assignment. The gain in spectral resolution afforded by chemical shift labeling with the anomeric resonances should provide a more robust pathway for sequential assignment over the intervening phosphorus in larger RNA oligonucleotides. The HCP-CCH-TOCSY experiment is demonstrated on a uniformly ¹³C,¹⁵N-labeled 19-nucleotide RNA stem-loop, derived from the antisense RNA I molecule found in the ColE1 plasmid replication control system.     

Triple resonance experiments for the simultaneous correlation of H6/H5 and exchangeable protons of pyrimidine nucleotides in 13C,15N-labeled RNA applicable to larger RNA molecules

Triple-resonance two-dimensional H6/H5(C4N)H and C6/C5(C4N)H experiments are described that provide through-bond H6/H5 or C6/C5 to imino/amino correlations in pyrimidine bases in ¹³C,¹⁵N-labeled RNA. The experiments simultaneously transfer H6/H5 magnetization by an INEPT step to the C6/C5 nuclei and by homonuclear CC- and heteronuclear CN-TOCSY steps via the intervening C4 nucleus to the N3/N4 nuclei and then by a reverse INEPT step to the imino/amino hydrogens. The sensitivity of these experiments is high as demonstrated using a 30-nucleotide pyrimidine rich RNA at a concentration of 0.9 mM at temperatures of 10°C and 25°C. This indicates the general applicability of the experiments and the possibility to obtain correlations for imino resonances in non-canonical regions of the target RNA.     

Correlation of nucleotide base and sugar protons in a 15N-labeled HIV-1 RNA oligonucleotide by 1H-15N HSQC experiments

Summary The advent of methods for preparing ¹⁵N- and ¹³C-labeled RNA oligonucleotides holds promise for extending the size of RNA molecules that can be studies by NMR spectroscopy. A practical limitation is the expense of the ¹³C label. It may therefore sometimes be desirable to prepare a relatively inexpensive ¹⁵N-labeled sample only. Here we show that the two-bond ¹H-¹⁵N HSQC experiment can be used on ¹⁵N-labeled RNA to correlate the intranucleotide H1 and H8,H6,H5 resonances indirectly through the shared glycosidic nitrogen. The nonrefocused version of a standard HSQC experiment for 2D proton-detected ¹H-¹⁵N chemical-shift correlation is applied in order to minimize the sensitivity loss due to the relatively fast spin-spin relaxation of RNA oligonucleotides. The experiment is applied to the 30-nucleotide RNA RBE3 which contains the high-affinity binding site of the RRE (rev response element) for the Rev protein of HIV. The results indicate that this simple experiment allows a straightforward identification of the base proton resonances CH5, CH6, UH5, UH6, purine H8, and AH2 as well as the intranucleotide H1 and H8,H6,H5 connectivities. When combined with a NOESY experiment, complete sequential assignments can be obtained.     

Estimates of methyl 13C and 1H CSA values (Δσ) in proteins from cross-correlated spin relaxation

Simple pulse schemes are presented for the measurement of methyl ¹³C and ¹H CSA values from ¹H–¹³C dipole/¹³C CSA and ¹H–¹³C dipole/¹H CSA cross-correlated relaxation. The methodology is applied to protein L and malate synthase G. Average ¹³C CSA values are considerably smaller for Ile than Leu/Val (17 vs 25 ppm) and are in good agreement with previous solid state NMR studies of powders of amino acids and dipeptides and in reasonable agreement with quantum-chemical DFT calculations of methyl carbon CSA values in peptide fragments. Small averaged ¹H CSA values on the order of 1 ppm are measured, consistent with a solid state NMR determination of the methyl group ¹H CSA in dimethylmalonic acid.     

Determination of the rotational dynamics and pH dependence of the hydrogen exchange rates of the arginine guanidino group using NMR spectroscopy

Summary An improved version of the constant-time HSQC experiment is presented that gives uniform sensitivity over the complete ¹³C bandwidth in ¹³C−¹H correlation experiments without creating artifacts in the methyl and aromatic regions of the spectra. The improvement is achieved by replacing the refocussing ¹³C 180° pulse in the evolution time by a combination of a full-power (22 kHz) hyperbolic secant 180° pulse that inverts and refocusses the entire ¹³C window, immediately followed by a selective 180° pulse on the CO region. Further improvement in signal-to-noise in the aromatic and methyl regions, although less spectacular, is obtained by replacing the other two 180° ¹³C pulses in the INEPT parts of the pulse sequence by full-power hyperbolic secant pulses. Results of simulations and experimental data are presented that demonstrate the excellent performance of the hyperbolic secant pulse for broadband inversion and show that refocussing of transverse magnetization occurs over the same bandwidth, albeit with a ¹³C signal phase that depends quadratically on offset. A further modification, in which one of the selective pulses on the CO region is omitted, is also presented. Implications for other 2D and 3D experiments performed at high fields, where uniform ¹³C inversion and refocussing is desirable, are discussed.     

[3H]Adenine is a suitable radioligand for the labeling of G protein-coupled adenine receptors but shows high affinity to bacterial contaminations in buffer solutions

[³H]Adenine has previously been used to label the newly discovered G protein-coupled murine adenine receptors. Recent reports have questioned the suitability of [³H]adenine for adenine receptor binding studies because of curious results, e.g. high specific binding even in the absence of mammalian protein. In this study, we showed that specific [³H]adenine binding to various mammalian membrane preparations increased linearly with protein concentration. Furthermore, we found that Tris-buffer solutions typically used for radioligand binding studies (50 mM, pH 7.4) that have not been freshly prepared but stored at 4°C for some time may contain bacterial contaminations that exhibit high affinity binding for [³H]adenine. Specific binding is abolished by heating the contaminated buffer or filtering it through 0.2-μm filters. Three different, aerobic, gram-negative bacteria were isolated from a contaminated buffer solution and identified as Achromobacter xylosoxidans, A. denitrificans, and Acinetobacter lwoffii. A. xylosoxidans, a common bacterium that can cause nosocomial infections, showed a particularly high affinity for [³H]adenine in the low nanomolar range. Structure–activity relationships revealed that hypoxanthine also bound with high affinity to A. xylosoxidans, whereas other nucleobases (uracil, xanthine) and nucleosides (adenosine, uridine) did not. The nature of the labeled site in bacteria is not known, but preliminary results indicate that it may be a high-affinity purine transporter. We conclude that [³H]adenine is a well-suitable radioligand for adenine receptor binding studies but that bacterial contamination of the employed buffer solutions must be avoided. Anke C. Schiedel and Heiko Meyer contributed equally to this work.     

Transverse relaxation optimized triple-resonance NMR experiments for nucleic acids

Triple resonance HCN and HCNCH experiments are reliable methods of establishing sugar-to-base connectivity in the NMR spectra of isotopicaly labeled oligonucleotides. However, with larger molecules the sensitivity of the experiments is drastically reduced due to relaxation processes. Since the polarization transfer between ¹³C and ¹⁵N nuclei relies on rather small heteronuclear coupling constants (11–12 Hz), the long evolution periods (up to 30–40 ms) in the pulse sequences cannot be avoided. Therefore any effort to enhance sensitivity has to concentrate on manipulating the spin system in such a way that the spin–spin relaxation rates would be minimized. In the present paper we analyze the efficiency of the two known approaches of relaxation rate control, namely the use of multiple-quantum coherence (MQ) and of the relaxation interference between chemical shift anisotropy and dipolar relaxation – TROSY. Both theoretical calculations and experimental results suggest that for the sugar moiety (H1-C1-N1/9) the MQ approach is clearly preferable. For the base moiety (H6/8-C6/8-N1/9), however, the TROSY shows results superior to the MQ suppression of the dipole–dipole relaxation at moderate magnetic fields (500 MHz) and the sensitivity improvement becomes dramatically more pronounced at very high fields (800 MHz). The pulse schemes of the triple-resonance HCN experiments with sensitivity optimized performance for unambiguous assignments of intra-residual sugar-to-base connectivities combining both approaches are presented.     

Assignment of cytosine N3 resonances in nucleic acids via intrabase three-bond coupling to amino protons

Coherences were observed between ¹⁵N3 of cytosine and its trans amino proton (H42) using a modified gradient-based heteronuclear single quantum coherence (HSQC) pulse sequence optimized for three-bond proton-nitrogen couplings. The method is demonstrated with a 22-nucleotide RNA fragment of the P5abc region of a group I intron uniformly labeled with ¹⁵N. Use of intraresidue ¹⁵ N3-amino proton couplings to assign cytosine ¹⁵ N3 signals complements the recently proposed J_NN HNN COSY [Dingley, A.J. and Grzesiek, S. (1998) J. Am. Chem. Soc., 120, 8293–8297] method of identifying hydrogen-bonded base pairs in RNA.     

Three-dimensional 1H-TOCSY-relayed ct-[13C,1H]-HMQC for aromatic spin system identification in uniformly 13C-labeled proteins

Summary Three-dimensional ¹H-TOCSY-relayed ct-[¹³C,¹H]-HMQC is a novel experiment for aromatic spin system identification in uniformly ¹³C-labeled proteins, which is implemented so that it correlates the chemical shift of a given aromatic proton with those of the directly attached carbon and all vicinal protons. The ct-HMQC scheme is used both for overlay of the indirect ¹H and ¹³C chemical shift evolution periods and for the generation of ¹H-¹H antiphase magnetization to accelerate the ¹H-TOCSY magnetization transfer at short mixing times. As an illustration, data recorded for the 18 kDa protein cyclophilin A are presented. Since transverse relaxation of ¹³C-¹H zero-quantum and double-quantum coherences is to first order insensitive to ¹³C-¹H heteronuclear dipolar relaxation, the new experiment should work also for proteins with molecular weights above 20 kDa.     

HNCAN pulse sequences for sequential backbone resonance assignment across proline residues in perdeuterated proteins

A TROSY-based triple-resonance pulse scheme is described which correlates backbone ¹H and ¹⁵N chemical shifts of an amino acid residue with the ¹⁵N chemical shifts of both the sequentially preceding and following residues. The sequence employs ¹ J _NC and ² J _NC couplings in two sequential magnetization transfer steps in an `out-and-back' manner. As a result, N,N connectivities are obtained irrespective of whether the neighbouring amide nitrogens are protonated or not, which makes the experiment suitable for the assignment of proline resonances. Two different three-dimensional variants of the pulse sequence are presented which differ in sensitivity and resolution to be achieved in one of the nitrogen dimensions. The new method is demonstrated with two uniformly ²H/¹³C/¹⁵N-labelled proteins in the 30-kDa range.     

3D 13C/1H NMR-based assignments for side-chain resonances of Lactobacillus casei dihydrofolate reductase. Evidence for similarities between the solution and crystal structures of the enzyme

Summary ¹³C-based three-dimensional ¹H–¹H correlation experiments have been used to determine essentially complete ¹³C and ¹H resonance assignments for the amino acid side chains of uniformly ¹³C/¹⁵N labelled L. casei dihydrofolate reductase in a complex with the drug methotrexate. Excellent agreement is observed between these assignments and an earlier set of partial assignments made on the basis of correlating nuclear Overhauser effect and crystal structure data, indicating that the tertiary structure of the enzyme is similar in solution and in the crystal state.To whom correspondence should be addressed.     

Direct measurement of 1H-1H dipolar couplings in proteins: A complement to traditional NOE measurements

An intensity-based constant-time COSY (CT-COSY) method is described for measuring ¹H-¹H residual dipolar couplings of proteins in weakly aligned media. For small proteins, the overall sensitivity of this experiment is comparable to the NOESY experiment. In cases where the ¹H-¹H distances are defined by secondary structure, such as ¹H-¹H^N and ¹H^N-¹H^N sequential distances in -helices and -sheets, these measurements provide useful orientational constraints for protein structure determination. This experiment can also be used to provide distance information similar to that obtained from NOE connectivities once the angular dependence is removed. Because the measurements are direct and non-coherent processes, such as spin diffusion, do not enter, the measurements can be more reliable. The 1/r ³ distance dependence of directly observed dipolar couplings, as compared with the 1/r ⁶ distance dependence of NOEs, also can provide longer range distance information at favorable angles. A simple 3D, ¹⁵N resolved version of the pulse sequence extends the method to provide the improved resolution required for application to larger biomolecules.     

Laboratory Calibrations of the [3H]Adenine Technique for Measuring Rates of RNA and DNA Synthesis in Marine Microorganisms

The nucleic acid synthesis rates of several marine phytoplankton and bacteria grown in chemostat and batch cultures were measured by using [³H]adenine. The [³H]adenine synthesis rates showed excellent agreement with the known rates of synthesis estimated from chemical RNA and DNA data. Under certain conditions, RNA turnover and ATP pool compartmentalization produce inaccuracies in synthesis measurements made with [³H]adenine. However, accurate measurements of the rates of microbial RNA and DNA synthesis can be made in any environmental situation provided a few simple precautions are observed. First, time course experiments are recommended. Second, experiments should be conducted for periods long enough to avoid problems arising from disequilibria of internal ATP pools. Finally, exogenous [³H]adenine should remain in the medium over the length of the time course.     

13C spin relaxation measurements in RNA: Sensitivity and resolution improvement using spin-state selective correlation experiments

A set of new NMR pulse sequences has been designed for the measurement of ¹³C relaxation rate constants in RNA and DNA bases: the spin-lattice relaxation rate constant R(C_z), the spin-spin relaxation rate constant R(C₊), and the CSA-dipolar cross-correlated relaxation rate constant . The use of spin-state selective correlation techniques provides increased sensitivity and spectral resolution. Sensitivity optimised C-C filters are included in the pulse schemes for the suppression of signals originating from undesired carbon isotopomers. The experiments are applied to a 15% ¹³C-labelled 33-mer RNA–theophylline complex. The measured ratios indicate that ¹³C CSA tensors do not vary significantly for the same type of carbon (C₂, C₆, C₈), but that they differ from one type to another. In addition, conformational exchange effects in the RNA bases are detected as a change in the relaxation decay of the narrow ¹³C doublet component when varying the spacing of a CPMG pulse train. This new approach allows the detection of small exchange effects with a higher precision compared to conventional techniques.     

H+-dependent efflux of Ca2+ from heart mitochondria

A rapid loss of accumulated Ca²⁺ is produced by addition of H⁺ to isolated heart mitochondria. The H⁺-dependent Ca⁺ efflux requires that either (a) the NAD(P)H pool of the mitochondrion be oxidized, or (b) the endogenous adenine nucleotides be depleted. The loss of Ca²⁺ is accompanied by swelling and loss of endogenous Mg^2–. The rate of H⁺-dependent Ca²⁺ efflux depends on the amount of Ca²⁺ and P_i taken up and the extent of the pH drop imposed. In the absence of ruthenium red the H⁺-induced Ca²⁺-efflux is partially offset by a spontaneous re-accumulation of released Ca²⁺. The H⁺-induced Ca²⁺ efflux is inhibited when the P_i transporter is blocked withN-ethylmaleimide, is strongly opposed by oligomycin and exogenous adenine nucleotides (particularly ADP), and inhibited by nupercaine. The H⁺-dependent Ca²⁺ efflux is decreased markedly when Na⁺ replaces the K⁺ of the suspending medium or when the exogenous K⁺/H⁺ exchanger nigericin is present. These results suggest that the H⁺-dependent loss of accumulated Ca²⁺ results from relatively nonspecific changes in membrane permeability and is not a reflection of a Ca²⁺/H⁺ exchange reaction.     

Through-bond correlation of adenine H2 and H8 protons in unlabeled DNA fragments by HMBC spectroscopy

Summary A new application of the HMBC experiment is presented that provides a useful means to discriminate between H2 and H8 proton resonances, to assign the base proton resonances to the various residue types and, most importantly, to correlate the H2 and H8 protons for adenine or inosine residues in natural abundance ¹³C fragments. The utility of this experiment is demonstrated for an unlabeled DNA 20-mer. Thanks to the obtained results, preliminary conclusions could be drawn regarding the molecular conformations of the non-canonical G/I-A base pairs in the hairpin formed by this fragment.     

Cross-correlated spin relaxation effects in methyl <Superscript>1</Superscript>H CPMG-based relaxation dispersion experiments: Complications and a simple solution

Artifacts associated with the measurement of methyl ¹H single quantum CPMG-based relaxation dispersion profiles are described. These artifacts arise due to the combination of cross-correlated spin relaxation effects involving intra-methyl ¹H–¹H dipolar interactions and imperfections in ¹H refocusing pulses that are applied during CPMG intervals that quantify the effects of chemical exchange on measured transverse relaxation rates. As a result substantial errors in extracted exchange parameters can be obtained. A simple work-around is presented where the ¹H chemical shift difference between the exchanging states is extracted from a combination of ¹³C single quantum and ¹³C–¹H multiple quantum dispersion profiles. The approach is demonstrated with an application to a folding/unfolding reaction involving a G48M mutant Fyn SH3 domain.     

Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments

A fast, robust and reliable strategy for automated sequential resonance assignment for uniformly [¹³C, ¹⁵N]-labeled RNA via its phosphodiester backbone is presented. It is based on a series of high-dimensional through-bond APSY experiments: a 5D HCP-CCH COSY, a 4D H1′C1′CH TOCSY for ribose resonances, a 5D HCNCH for ribose-to-base connection, a 4D H6C6C5H5 TOCSY for pyrimidine resonances, and a 4D H8C8(C)C2H2 TOCSY for adenine resonances. The utilized pulse sequences are partially novel, and optimized to enable long evolution times in all dimensions. The highly precise APSY peak lists derived with these experiments could be used directly for reliable automated resonance assignment with the FLYA algorithm. This approach resulted in 98 % assignment completeness for all ¹³C–¹H, ¹⁵N1/9 and ³¹P resonances of a stem-loop with 14 nucleotides.     

Transverse relaxation optimized HCN experiment for nucleic acids: Combining the advantages of TROSY and MQ spin evolution

A three-dimensional MQ-TROSY-HCN pulse sequence is presented which provides intra-base and sugar-to-base correlations for ¹³C, ¹⁵N labeled nucleic acids (RNA, DNA). The experiment simultaneously exploits the favorable relaxation properties of ¹H-¹³C multiple quantum coherence for sugar carbons and of ¹³C TROSY-type spin evolution for base carbons. MQ-TROSY-HCN thus combines the advantages of MQ-HCN for sugar-to-base and TROSY-HCN for intra-base correlations in a single experiment. In addition, two slightly different implementations of the MQ-TROSY-HCN experiment ensure optimal performance for small and larger oligonucleotides, respectively. The advantages of the MQ-TROSY-HCN experiment compared to the best previous implementations of HCN are demonstrated for a 33 nucleotide RNA aptamer.