An ab Initio Study of Hydrogen Bonding Effects on the 15N and 1H Chemical Shielding Tensors in the Watson−Crick Base Pairs

Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements

Numerous biological processes and mechanisms depend on details of base pairing and hydrogen bonding in DNA. Hydrogen bonds are challenging to quantify by X-ray crystallography and cryo-EM due to difficulty of visualizing hydrogen atom locations but can be probed with site specificity by NMR spectroscopy in solution and the solid state with the latter particularly suited to large, slowly tumbling DNA complexes. Recently, we showed that low-temperature dynamic nuclear polarization (DNP) enhanced solid-state NMR is a valuable tool for distinguishing Hoogsteen base pairs (bps) from canonical Watson-Crick bps in various DNA systems under native-like conditions. Here, using a model 12-mer DNA duplex containing two central adenine-thymine (A-T) bps in either Watson-Crick or Hoogsteen confirmation, we demonstrate DNP solid-state NMR measurements of thymine N3-H3 bond lengths, which are sensitive to details of N-H···N hydrogen bonding and permit hydrogen bonds for the two bp conformers to be systematically compared within the same DNA sequence context. For this DNA duplex, effectively identical TN3-H3 bond lengths of 1.055 ± 0.011 Å and 1.060 ± 0.011 Å were found for Watson-Crick A-T and Hoogsteen A (syn)-T base pairs, respectively, relative to a reference amide bond length of 1.015 ± 0.010 Å determined for N-acetyl-valine under comparable experimental conditions. Considering that prior quantum chemical calculations which account for zero-point motions predict a somewhat longer effective peptide N-H bond length of 1.041 Å, in agreement with solution and solid-state NMR studies of peptides and proteins at ambient temperature, to facilitate direct comparisons with these earlier studies TN3-H3 bond lengths for the DNA samples can be readily scaled appropriately to yield 1.083 Å and 1.087 Å for Watson-Crick A-T and Hoogsteen A (syn)-T bps, respectively, relative to the 1.041 Å reference peptide N-H bond length. Remarkably, in the context of the model DNA duplex, these results indicate that there are no significant differences in N-H···N A-T hydrogen bonds between Watson-Crick and Hoogsteen bp conformers. More generally, high precision measurements of N-H bond lengths by low-temperature DNP solid-state NMR based methods are expected to facilitate detailed comparative analysis of hydrogen bonding for a range of DNA complexes and base pairing environments.

Accurate and Cost-Effective NMR Chemical Shift Predictions for Nucleic Acids Using a Molecules-in-Molecules Fragmentation-Based Method

We have developed, implemented, and assessed an efficient protocol for the prediction of NMR chemical shifts of large nucleic acids using our molecules-in-molecules (MIM) fragment-based quantum chemical approach. To assess the performance of our approach, MIM-NMR calculations are calibrated on a test set of three nucleic acids, where the structure is derived from solution-phase NMR studies. For DNA systems with multiple conformers, the one-layer MIM method with trimer fragments (MIM1trimer) is benchmarked to get the lowest energy structure, with an average error of only 0.80 kcal/mol with respect to unfragmented full molecule calculations. The MIMI-NMRdimer calibration with respect to unfragmented full molecule calculations shows a mean absolute deviation (MAD) of 0.06 and 0.11 ppm, respectively, for 1H and 13C nuclei, but the performance with respect to experimental NMR chemical shifts is comparable to the more expensive MIM1-NMR and MIM2-NMR methods with trimer subsystems. To compare with the experimental chemical shifts, a standard protocol is derived using DNA systems with Protein Data Bank (PDB) IDs 1SY8, 1K2K, and 1KR8. The effect of structural minimizations is employed using a hybrid mechanics/semiempirical approach and used for computations in solution with implicit and explicit-implicit solvation models in our MIM1-NMRdimer methodology. To demonstrate the applicability of our protocol, we tested it on seven nucleic acids, including structures with nonstandard residues, heteroatom substitutions (F and B atoms), and side chain mutations with a size ranging from ∼300 to 1100 atoms. The major improvement for predicted MIM1-NMRdimer calculations is obtained from structural minimizations and implicit solvation effects. A significant improvement with the explicit-implicit solvation model is observed only for two smaller nucleic acid systems (1KR8 and 7NBK), where the expensive first solvation shell is replaced by the microsolvation model, in which a single water molecule is added for each solvent-exposed amino and imino protons, along with the implicit solvation. Overall, our target accuracy of ∼0.2-0.3 ppm for 1H and ∼2-3 ppm for 13C has been achieved for large nucleic acids. The proposed MIM-NMR approach is accurate and cost-effective (linear scaling with system size), and it can aid in the structural assignments of a wide range of complex biomolecules.

Evaluation of 15N-detected H-N correlation experiments on increasingly large RNAs

Recently, ¹⁵N-detected multidimensional NMR experiments have been introduced for the investigation of proteins. Utilization of the slow transverse relaxation of nitrogen nuclei in a ¹⁵N-TROSY experiment allowed recording of high quality spectra for high molecular weight proteins, even in the absence of deuteration. Here, we demonstrate the applicability of three ¹⁵N-detected H-N correlation experiments (TROSY, BEST-TROSY and HSQC) to RNA. With the newly established ¹⁵N-detected BEST-TROSY experiment, which proves to be the most sensitive ¹⁵N-detected H-N correlation experiment, spectra for five RNA molecules ranging in size from 5 to 100 kDa were recorded. These spectra yielded high resolution in the ¹⁵N-dimension even for larger RNAs since the increase in line width with molecular weight is more pronounced in the ¹H- than in the ¹⁵N-dimension. Further, we could experimentally validate the difference in relaxation behavior of imino groups in AU and GC base pairs. Additionally, we showed that ¹⁵N-detected experiments theoretically should benefit from sensitivity and resolution advantages at higher static fields but that the latter is obscured by exchange dynamics within the RNAs.

Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes

NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r²) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization.

15N CHEMICAL SHIFT CALCULATIONS AND NATURAL BONDING ORBITAL ANALYSES OF (BENZAMIDE)n = 1 - 6 CLUSTERS

A DFT/B3LYP study was performed to calculate 15 N chemical shielding tensors in ( benzamide )n = 1-6 clusters. We found that N–H⋯O hydrogen bonds around the benzamide molecule in crystalline lattice have significant influences on the 15 N chemical shielding tensors. For ( benzamide )n clusters, the n-dependent trend in 15 N chemical shielding appears to be correlated with cooperative effects in R [N–H⋯O ] bond distance. Natural bonding orbital (NBO) analysis was used to rationalize the chemical shielding results in terms of [Formula: see text] charge delocalization effects in the benzamide clusters. This suggests that 15 N chemical shielding measurements can provide a useful probe of electron delocalization phenomena in both gaseous and condensed media.

Dynamics of large elongated RNA by NMR carbon relaxation

We present an NMR strategy for characterizing picosecond-to-nanosecond internal motions in uniformly 13C/15N-labeled RNAs that combines measurements of R1, R1rho, and heteronuclear 13C{1H} NOEs for protonated base (C2, C5, C6, and C8) and sugar (C1') carbons with a domain elongation strategy for decoupling internal from overall motions and residual dipolar coupling (RDC) measurements for determining the average RNA global conformation and orientation of the principal axis of the axially symmetric rotational diffusion. TROSY-detected pulse sequences are presented for the accurate measurement of nucleobase carbon R1 and R1rho rates in large RNAs. The relaxation data is analyzed using a model free formalism which takes into account the very high anisotropy of overall rotational diffusion (Dratio approximately 4.7), asymmetry of the nucleobase CSAs and noncollinearity of C-C, C-H dipolar and CSA interactions under the assumption that all interaction tensors for a given carbon experience identical isotropic internal motions. The approach is demonstrated and validated on an elongated HIV-1 TAR RNA (taum approximately 18 ns) both in free form and bound to the ligand argininamide (ARG). Results show that, while ARG binding reduces the amplitude of collective helix motions and local mobility at the binding pocket, it leads to a drastic increase in the local mobility of "spacer" bulge residues linking the two helices which undergo virtually unrestricted internal motions (S2 approximately 0.2) in the ARG bound state. Our results establish the ability to quantitatively study the dynamics of RNAs which are significantly larger and more anisotropic than customarily studied by NMR carbon relaxation.

An investigation of hydrogen-bonding effects on the nitrogen and hydrogen electric field gradient and chemical shielding tensors in the 9-methyladenine real crystalline structure: a density functional theory study

Hydrogen-bonding effects in the real crystalline structure of 9-methyladenine, 9-MA, were studied using calculated electric field gradient, EFG, and chemical shielding, CS, tensors for nitrogen and hydrogen nuclei via density functional theory. The calculations were carried out at the B3LYP and B3PW91 levels with the 6-311++G basis set via the Gaussian 98 package. Nuclear quadrupole coupling constants, C(Q), and asymmetry parameters, eta(Q), are reported for (14)N and (2)H. The chemical shielding anisotropy, Deltasigma, and chemical shielding isotropy, sigma(iso), are also reported for (15)N and (1)H. The difference between the calculated parameters of the monomer and heptameric layer-like cluster 9-MA shows how much H-bonding interactions affect the EFG and CS tensors of each nucleus. This result indicates that N(10) (imino nitrogen) has a major role in H-bonding interactions, whereas that of N(9) is negligible. There is good agreement between the present calculated parameters and reported experimental data. Although some discrepancies were observed, this could be attributed to the different conditions which were applied for calculation and the experiments.

JNH Values Show that N1···N3 Hydrogen Bonds Are Stronger in dsRNA A:U than dsDNA A:T Base Pairs

Here, we show that 1JNH values are on average 0.4 Hz less negative for double-stranded RNA A:U than for DNA A:T base pairs, which, according to existing theory, suggests that RNA N1...N3 hydrogen bond distances are about 0.02 A shorter than those of DNA. Also, there is a statistically relevant trend between 1JNH and 2hDelta13C2 values, which supports the original hypothesis that 2hDelta13C2 values are also sensitive to hydrogen bond distances. Finally, a context dependence is observed for these values, which suggests that hydrogen-bonding and base-stacking interactions are coupled.

Determination of 13C CSA tensors: extension of the model-independent approach to an RNA kissing complex undergoing anisotropic rotational diffusion in solution

Chemical shift anisotropy (CSA) tensor parameters have been determined for the protonated carbons of the purine bases in an RNA kissing complex in solution by extending the model-independent approach [Fushman, D., Cowburn, D. (1998) J. Am. Chem. Soc. 120, 7109-7110]. A strategy for determining CSA tensor parameters of heteronuclei in isolated X-H two-spin systems (X = 13C or 15N) in molecules undergoing anisotropic rotational diffusion is presented. The original method relies on the fact that the ratio kappa2=R2 auto/R2 cross of the transverse auto- and cross-correlated relaxation rates involving the X CSA and the X-H dipolar interaction is independent of parameters related to molecular motion, provided rotational diffusion is isotropic. However, if the overall motion is anisotropic kappa2 depends on the anisotropy D(parallel)/D (perpendicular) of rotational diffusion. In this paper, the field dependence of both kappa2 and its longitudinal counterpart kappa1=R1 auto/R1 cross are determined. For anisotropic rotational diffusion, our calculations show that the average kappa(av) = 1/2 (kappa1+kappa2), of the ratios is largely independent of the anisotropy parameter D(parallel)/D (perpendicular). The field dependence of the average ratio kappa(av) may thus be utilized to determine CSA tensor parameters by a generalized model-independent approach in the case of molecules with an overall motion described by an axially symmetric rotational diffusion tensor.

Dynamics of circular hydrogen bond array in calix[4]arene in a nonpolar solvent: A nuclear magnetic resonance study

Hydroxyl groups on the lower rim of calix[4]arene form a circular array of four equivalent hydrogen bonds. The rate constants of reversal of the array in the temperature range of 221-304 K were determined by means of the NMR measurements of quaternary (13)C nuclear spin transverse relaxation dependence on the effective radio frequency field. The flip-flop rate constants are in the range of 1.4 x 10(2)-4.2 x 10(4) s(-1), the activation enthalpy is 36.8 kJ/mol, the activation entropy is -36 J mol(-1) K(-1). This process was found uncorrelated with conformational transition cone-inverted cone, which is about thousand times slower. Molecular tumbling of calix[4]arene measured using (13)C spin relaxation was found isotropic with correlation times lying in the range of 0.1-3 ns and with the activation energy of 21 kJ/mol. In order to assess relaxation of (13)C aromatic nuclei, their principal components of chemical shift tensor were calculated using the density functional theory approach.

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modern QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard base pairs, mismatched base pairs, thio-base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C [bond] H...O interbase contacts, sugar-base stacking, intrinsically nonplanar base pairs, out-of-plane hydrogen bonds, and amino-acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations. These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation-pi interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed.

NMR methodology for the study of nucleic acids

During the past few years, NMR methodology for the study of nucleic acids has benefited from new developments that greatly improved state-of-the-art technology for the precise determination of three-dimensional structures. Substantial progress has been made in designing experimental protocols for the measurement of residual dipolar couplings, in sensitivity optimization of triple-resonance experiments and in detection of hydrogen bonds and in developing computational methods for structure refinement using NMR restraints.