Nucleic acid helix structure determination from NMR proton chemical shifts

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR

Determination of structure of RNA via NMR is complicated in large part by the lack of a precise parameterization linking the observed chemical shifts to the underlying geometric parameters. In contrast to proteins, where numerous high-resolution crystal structures serve as coordinate templates for this mapping, such models are rarely available for smaller oligonucleotides accessible via NMR, or they exhibit crystal packing and counter-ion binding artifacts that prevent their use for the chemical shifts analysis. On the other hand, NMR-determined structures of RNA often are not solved at the density of restraints required to precisely define the variable degrees of freedom. In this study we sidestep the problems of direct parameterization of the RNA chemical shifts/structure relationship and examine the effects of imposing local fragmental coordinate similarity restraints based on similarities of the experimental secondary ribose ¹³C/¹H chemical shifts instead. The effect of such chemical shift similarity (CSS) restraints on the structural accuracy is assessed via residual dipolar coupling (RDC)-based cross-validation. Improvements in the coordinate accuracy are observed for all of the six RNA constructs considered here as test cases, which argues for routine inclusion of these terms during NMR-based oligonucleotide structure determination. Such accuracy improvements are expected to facilitate derivation of the chemical shift/structure relationships for RNA.

Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation

Nucleic acid (NA) aptamers bind to their targets with high affinity and selectivity. The three-dimensional (3D) structures of aptamers play a major role in these non-covalent interactions. Here, we use a four-step approach to determine a true 3D structure of aptamers in solution using small-angle X-ray scattering (SAXS) and molecular structure restoration (MSR). The approach consists of (i) acquiring SAXS experimental data of an aptamer in solution, (ii) building a spatial distribution of the molecule's electron density using SAXS results, (iii) constructing a 3D model of the aptamer from its nucleotide primary sequence and secondary structure, and (iv) comparing and refining the modeled 3D structures with the experimental SAXS model. In the proof-of-principle we analyzed the 3D structure of RE31 aptamer to thrombin in a native free state at different temperatures and validated it by circular dichroism (CD). The resulting 3D structure of RE31 has the most energetically favorable conformation and the same elements such as a B-form duplex, non-complementary region, and two G-quartets which were previously reported by X-ray diffraction (XRD) from a single crystal. More broadly, this study demonstrates the complementary approach for constructing and adjusting the 3D structures of aptamers, DNAzymes, and ribozymes in solution, and could supply new opportunities for developing functional nucleic acids. Graphical abstract.

Chemical shift-based methods in NMR structure determination

Chemical shifts are highly sensitive probes harnessed by NMR spectroscopists and structural biologists as conformational parameters to characterize a range of biological molecules. Traditionally, assignment of chemical shifts has been a labor-intensive process requiring numerous samples and a suite of multidimensional experiments. Over the past two decades, the development of complementary computational approaches has bolstered the analysis, interpretation and utilization of chemical shifts for elucidation of high resolution protein and nucleic acid structures. Here, we review the development and application of chemical shift-based methods for structure determination with a focus on ab initio fragment assembly, comparative modeling, oligomeric systems, and automated assignment methods. Throughout our discussion, we point out practical uses, as well as advantages and caveats, of using chemical shifts in structure modeling. We additionally highlight (i) hybrid methods that employ chemical shifts with other types of NMR restraints (residual dipolar couplings, paramagnetic relaxation enhancements and pseudocontact shifts) that allow for improved accuracy and resolution of generated 3D structures, (ii) the utilization of chemical shifts to model the structures of sparsely populated excited states, and (iii) modeling of sidechain conformations. Finally, we briefly discuss the advantages of contemporary methods that employ sparse NMR data recorded using site-specific isotope labeling schemes for chemical shift-driven structure determination of larger molecules. With this review, we aim to emphasize the accessibility and versatility of chemical shifts for structure determination of challenging biological systems, and to point out emerging areas of development that lead us towards the next generation of tools.

Capturing Excited States in the Fast-Intermediate Exchange Limit in Biological Systems Using 1 H NMR Spectroscopy

Changes in molecular structure are essential for the function of biomolecules. Characterization of these structural fluctuations can illuminate alternative states and help in correlating structure to function. NMR relaxation dispersion (RD) is currently the only method for detecting these alternative, high-energy states. In this study, we present a versatile ¹ H R_1ρ RD experiment that not only extends the exchange timescales at least three times beyond the rate limits of ¹³ C/¹⁵ N R_1ρ and ten times for CPMG experiments, but also makes use of easily accessible probes, thus allowing a general description of biologically important excited states. This technique can be used to extract chemical shifts for the structural characterization of excited states and to elucidate complex excited states.

Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR and (13)C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and (1)H and (13)C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA (1)H and (13)C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.

Structural features of a 3' splice site in influenza a

Influenza A is an RNA virus with a genome of eight negative sense segments. Segment 7 mRNA contains a 3′ splice site for alternative splicing to encode the essential M2 protein. On the basis of sequence alignment and chemical mapping experiments, the secondary structure surrounding the 3′ splice site has an internal loop, adenine bulge, and hairpin loop when it is in the hairpin conformation that exposes the 3′ splice site. We report structural features of a three-dimensional model of the hairpin derived from nuclear magnetic resonance spectra and simulated annealing with restrained molecular dynamics. Additional insight was provided by modeling based on ¹H chemical shifts. The internal loop containing the 3′ splice site has a dynamic guanosine and a stable imino (cis Watson–Crick/Watson–Crick) GA pair. The adenine bulge also appears to be dynamic with the A either stacked in the stem or forming a base triple with a Watson–Crick GC pair. The hairpin loop is a GAAA tetraloop closed by an AC pair.

NMR proton chemical shift prediction of C·C mismatches in B-DNA

Accurate prediction of DNA chemical shifts facilitates resonance assignment and allows recognition of different conformational features. Based on the nearest neighbor model and base pair replacement approach, we have determined a set of triplet chemical shift values and correction factors for predicting the proton chemical shifts of B-DNA containing an internal C·C mismatch. Our results provide a reliable chemical shift prediction with an accuracy of 0.07 ppm for non-labile protons and 0.09 ppm for labile protons. In addition, we have also shown that the correction factors for C·C mismatches can be used interchangeably with those for T·T mismatches. As a result, we have generalized a set of correction factors for predicting the flanking residue chemical shifts of pyrimidine·pyrimidine mismatches.

Development and application of aromatic [(13)C, (1)H] SOFAST-HMQC NMR experiment for nucleic acids

Higher sensitivity of NMR spectrometers and novel isotopic labeling schemes have ushered the development of rapid data acquisition methodologies, improving the time resolution with which NMR data can be acquired. For nucleic acids, longitudinal relaxation optimization in conjunction with Ernst angle excitation (SOFAST-HMQC) for imino protons, in addition to rendering rapid pulsing, has been demonstrated to yield significant improvements in sensitivity per unit time. Extending such methodology to other spins offers a viable prospect to measure additional chemical shifts, thereby broadening their utilization for various applications. Here, we introduce the 2D [(13)C, (1)H] aromatic SOFAST-HMQC that results in overall sensitivity gain of 1.4- to 1.7-fold relative to the conventional HMQC and can also be extended to yield long-range heteronuclear chemical shifts such as the adenine imino nitrogens N1, N3, N7 and N9. The applications of these experiments range from monitoring real-time biochemical processes, drug/ligand screening, and to collecting data at very low sample concentration and/or in cases where isotopic enrichment cannot be achieved.

Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts

Structured noncoding RNAs underlie fundamental cellular processes, but determining their three-dimensional structures remains challenging. We demonstrate that integrating ¹H NMR chemical shift data with Rosetta de novo modeling can be used to consistently determine high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 'blind' targets, chemical-shift Rosetta for RNA (CS-Rosetta-RNA) recovered experimental structures with high accuracy (0.6-2.0 Å all-heavy-atom r.m.s. deviation) in 18 cases.

Prediction of RNA 1H and 13C chemical shifts: a structure based approach

The use of NMR-derived chemical shifts in protein structure determination and prediction has received much attention, and, as such, many methods have been developed to predict protein chemical shifts from three-dimensional (3D) coordinates. In contrast, little attention has been paid to predicting chemical shifts from RNA coordinates. Using the random forest machine learning approach, we developed RAMSEY, which is capable of predicting both (1)H and protonated (13)C chemical shifts from RNA coordinates. In this report, we introduce RAMSEY, assess its accuracy, and demonstrate the sensitivity of RAMSEY-predicted chemical shifts to RNA 3D structure.

NMR proton chemical shift prediction of T·T mismatches in B-DNA duplexes

A proton chemical shift prediction scheme for B-DNA duplexes containing a T·T mismatch has been established. The scheme employs a set of T·T mismatch triplet chemical shift values, 5'- and 3'-correction factors extracted from reference sequences, and also the B-DNA chemical shift values predicted by Altona et al. The prediction scheme was tested by eight B-DNA duplexes containing T·T mismatches. Based on 560 sets of predicted and experimental proton chemical shift values, the overall prediction accuracy for non-labile protons was determined to be 0.07 ppm with an excellent correlation coefficient of 0.9996. In addition, the prediction accuracy for 96 sets of labile protons was found to be 0.22 ppm with a correlation coefficient of 0.9961. The prediction scheme developed herein can facilitate resonance assignments of B-DNA duplexes containing T·T mismatches and be generalized for the chemical shift prediction of other DNA mismatches. Our chemical shift data will also be useful for establishing structure-chemical shift information in B-DNA containing mismatches.