Estimating Strengths of Individual Hydrogen Bonds in RNA Base Pairs: Toward a Consensus between Different Computational Approaches

Ab initio Modeling of Hydrogen Bonding of Remdesivir and Adenosine with Uridine

Remdesivir (RDV) emerged as an effective drug against the SARS-CoV-2 virus pandemic. One of the crucial steps in the mechanism of action of RDV is its incorporation into the growing RNA strand. RDV, an adenosine analogue, forms Watson-Crick (WC) type hydrogen bonds with uridine in the complementary strand and the strength of this interaction will control efficacy of RDV. While there is a plethora of structural and energetic information available about WC H-bonds in natural base pairs, the interaction of RDV with uridine has not been studied yet at the atomic level. In this article, we aim to bridge this gap, to understand RDV and its hydrogen bonding interactions, by employing density functional theory (DFT) at the M06-2X/cc-pVDZ level. The interaction energy, QTAIM analysis, NBO and SAPT2 are performed for RDV, adenosine, and their complex with uridine to gain insights into the nature of hydrogen bonding. The computations show that RDV has similar geometry, energetic, molecular orbitals, and aromaticity as adenosine, suggesting that RDV is an effective adenosine analogue. The important geometrical parameters, such as bond distances and red-shift in the stretching vibrational modes of adenosine, RDV and uridine identify two WC-type H-bonds. The relative strength of these two H-bonds is computed using QTAIM parameters and the computed hydrogen bond energy. Finally, the SAPT2 study is performed at the minima and at non-equilibrium base pair distances to understand the dominant intermolecular physical force. This study, based on a thorough analysis of a variety of computations, suggests that both adenosine and RDV have similar structure, energetic, and hydrogen bonding behaviour.

Exploring the adaptability of the secondary structure of mRNA to temperature in intertidal snails based on SHAPE experiments

RNA-based thermal regulation is an important strategy for organisms to cope with temperature changes. Inhabiting the intertidal rocky shore, a key interface of the ocean, atmosphere and terrestrial environments, intertidal species have developed variable thermal adaptation mechanisms; however, adaptions at the RNA level remain largely uninvestigated. To examine the relationship between mRNA structural stability and species distribution, in the present study, the secondary structure of cytosolic malate dehydrogenase (cMDH) mRNA of Echinolittorina malaccana, Echinolittorina radiata and Littorina brevicula was determined using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), and the change in folding free energy of formation (ΔGfold) was calculated. The results showed that ΔGfold increased as the temperature increased. The difference in ΔGfold (ΔΔGfold) between two specific temperatures (25 versus 0°C, 37 versus 0°C and 57 versus 0°C) differed among the three species, and the ΔΔGfold value of E. malaccana was significantly lower than those of E. radiata and L. brevicula. The number of stems of cMDH mRNA of the snails decreased with increasing temperature, and the breakpoint temperature of E. malaccana was the highest among these. The number of loops was also reduced with increasing temperature, while the length of the loop structure increased accordingly. Consequently, these structural changes can potentially affect the translational efficiency of mRNA. These results imply that there were interspecific differences in the thermal stability of RNA secondary structures in intertidal snails, and these differences may be related to snail distribution.

A study of the valence photoelectron spectrum of uracil and mixed water-uracil clusters

The valence ionization of uracil and mixed water-uracil clusters has been studied experimentally and by ab initio calculations. In both measurements, the spectrum onset shows a red shift with respect to the uracil molecule, with the mixed cluster characterized by peculiar features unexplained by the sum of independent contributions of the water or uracil aggregation. To interpret and assign all the contributions, we performed a series of multi-level calculations, starting from an exploration of several cluster structures using automated conformer-search algorithms based on a tight-binding approach. Ionization energies have been assessed on smaller clusters via a comparison between accurate wavefunction-based approaches and cost-effective DFT-based simulations, the latter of which were applied to clusters up to 12 uracil and 36 water molecules. The results confirm that (i) the bottom-up approach based on a multilevel method [Mattioli et al. Phys. Chem. Chem. Phys. 23, 1859 (2021)] to the structure of neutral clusters of unknown experimental composition converges to precise structure-property relationships and (ii) the coexistence of pure and mixed clusters in the water-uracil samples. A natural bond orbital (NBO) analysis performed on a subset of clusters highlighted the special role of H-bonds in the formation of the aggregates. The NBO analysis yields second-order perturbative energy between the H-bond donor and acceptor orbitals correlated with the calculated ionization energies. This sheds light on the role of the oxygen lone-pairs of the uracil CO group in the formation of strong H-bonds, with a stronger directionality in mixed clusters, giving a quantitative explanation for the formation of core-shell structures.

Dissociation of the Watson-Crick base pairs in vacuum and in aqueous solution: a first-principles molecular dynamics study

The damage of the DNA structure can affect the correct functioning of the cellular processes. This work investigates the required forces to dissociate the Watson-Crick (WC) base pairs AT into A and T, and GC into G and C. The WC base pairs are immersed in water under realistic conditions of temperature, volume, and density that reproduce the main characteristics of a biological system. The simulations are based on first-principles molecular dynamics combined with steering atomic forces. In addition to the force intensities, the charge transfers between the nucleic acid bases, energy variations, and temperature fluctuations in the cleavage moments are reported. With the purpose of evaluating the effects of the aqueous medium, simulations of the WC base pairs in vacuum are included. The results considering the solvated medium are consistent with the experimental measurements, and show the importance of the aqueous solution to regulate the structural modifications of the nucleic acid bases. The investigation contributes with a novel molecular model in molecular simulations, and to better understand the biological processes where the DNA compounds play an active role in life forms.Communicated by Ramaswamy H. Sarma.

Fentanyl Assay Derived from Intermolecular Interaction-Enabled Small Molecule Recognition (iMSR) with Differential Impedance Analysis for Point-of-Care Testing

Rapid and effective differentiation and quantification of a small molecule drug, such as fentanyl, in bodily fluids are major challenges for diagnosis and personal medication. However, the current toxicology methods used to measure drug concentration and metabolites require laboratory-based testing, which is not an efficient or cost-effective way to treat patients in a timely manner. Here, we show an assay for monitoring fentanyl levels by combining the intermolecular interaction-enabled small molecule recognition (iMSR) with differential impedance analysis of conjugated polymers. The differential interactions with the designed anchor interface were transduced through the perturbance of the electric status of the flexible conducting polymer. This assay showed excellent fentanyl selectivity against common interferences, as well as in variable body fluids through either testing strips or skin patches. Directly using the patient blood, the sensor provided 1%-5% of the average deviation compared to the "gold" standard method LC-MS results in the medically relevant fentanyl range of 20-90 nM. The superior sensing properties, in conjunction with mechanical flexibility and compatibility, enabled point-of-care detection and provided a promising avenue for applications beyond the scope of biomarker detection.

Carbohydrate Metabolism in Bacteria: Alternative Specificities in ADP-Glucose Pyrophosphorylases Open Novel Metabolic Scenarios and Biotechnological Tools

We explored the ability of ADP-glucose pyrophosphorylase (ADP-Glc PPase) from different bacteria to use glucosamine (GlcN) metabolites as a substrate or allosteric effectors. The enzyme from the actinobacteria Kocuria rhizophila exhibited marked and distinctive sensitivity to allosteric activation by GlcN-6P when producing ADP-Glc from glucose-1-phosphate (Glc-1P) and ATP. This behavior is also seen in the enzyme from Rhodococcus spp., the only one known so far to portray this activation. GlcN-6P had a more modest effect on the enzyme from other Actinobacteria (Streptomyces coelicolor), Firmicutes (Ruminococcus albus), and Proteobacteria (Agrobacterium tumefaciens) groups. In addition, we studied the catalytic capacity of ADP-Glc PPases from the different sources using GlcN-1P as a substrate when assayed in the presence of their respective allosteric activators. In all cases, the catalytic efficiency of Glc-1P was 1-2 orders of magnitude higher than GlcN-1P, except for the unregulated heterotetrameric protein (GlgC/GgD) from Geobacillus stearothermophilus. The Glc-1P substrate preference is explained using a model of ADP-Glc PPase from A. tumefaciens based on the crystallographic structure of the enzyme from potato tuber. The substrate-binding domain localizes near the N-terminal of an α-helix, which has a partial positive charge, thus favoring the interaction with a hydroxyl rather than a charged primary amine group. Results support the scenario where the ability of ADP-Glc PPases to use GlcN-1P as an alternative occurred during evolution despite the enzyme being selected to use Glc-1P and ATP for α-glucans synthesis. As an associated consequence in such a process, certain bacteria could have improved their ability to metabolize GlcN. The work also provides insights in designing molecular tools for producing oligo and polysaccharides with amino moieties.

The life and death of RNA across temperatures

Temperature is an environmental condition that has a pervasive effect on cells along with all the molecules and reactions in them. The mechanisms by which prototypical RNA molecules sense and withstand heat have been identified mostly in bacteria and archaea. The relevance of these phenomena is, however, broader, and similar mechanisms have been recently found throughout the tree of life, from sex determination in reptiles to adaptation of viral RNA polymerases, to genetic disorders in humans. We illustrate the temperature dependence of RNA metabolism with examples from the synthesis to the degradation of mRNAs, and review recently emerged questions. Are cells exposed to greater temperature variations and gradients than previously surmised? How do cells reconcile the conflicting thermal stability requirements of primary and tertiary structures of RNAs? To what extent do enzymes contribute to the temperature compensation of the reaction rates in mRNA turnover by lowering the energy barrier of the catalyzed reactions? We conclude with the ecological, forensic applications of the temperature-dependence of RNA degradation and the biotechnological aspects of mRNA vaccine production.

Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity

RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.

Variable temperature FTIR spectra of polycrystalline purine nucleobases and estimating strengths of individual hydrogen bonds

In the first part of this work, we report the FTIR spectra of pure NH and isotopically substituted ND (10-15% D and 80-90% D) polycrystalline hypoxanthine, xanthine, adenine and guanine recorded in the 400-4000 cm^-1 range, as a function of temperature (10-300 K). We provide assignments of the stretching and out-of-plane bending amine (NH₂) and imine (NH) bands to the distinct H-bonds present in the crystal, based on the temperature sensitivity and isotopic exchange behavior. Empirical correlations between spectral and thermodynamic or structural parameters enabled us to estimate the energies and lengths of H-bonds in the studied nucleobase crystals and to correlate them with literature data. The empirical H-bonding energies are compared with H-bonding and stacking energies computed for hypoxanthine. In the second part, strategies for using the empirical correlations together with information extracted from quantum mechanical data (in particular from the Bader's quantum theory of atoms in molecules, QTAIM) for the evaluation of hydrogen bonding properties are discussed, and their advantages and drawbacks pointed out. The justification for a cooperative use of quantum-mechanical calculations with empirical spectra-energy correlations is discussed.

Assessment of O-H⋯O and O-H⋯S intramolecular hydrogen bond energies in some substituted pyrimidines using quantum chemistry methods

Resonance-assisted hydrogen bond (RAHB) theory was studied in some substituted pyrimidines in which encompass O-H⋯Y unit (Y= O and S). Alteration of substituents (R ₁, R₂, R₃ = H, C₂H, C₂F) on pyrimidine ring changes properties of electron charge density at this ring and influences indirectly on strength of intramolecular hydrogen bond (IHB) interactions in the mentioned structures. Then, IHB energies were estimated using cis-trans method (CTM), related rotamers method (RRM), Espinosa' method (EM), and a viewpoint based on properties of electron charge densities at ring critical point (RCP) of RAHB ring. Moreover, the estimated IHB energies with these methods were compared with those obtained using modified Espinosa' method (MEM), Iogansen's relationship, and chemical shift-based method to find more consistent method with the proposed viewpoint based on RCP characteristics. The linear correlations between the all estimated IHB energies and some hydrogen bonding descriptors such as geometrical, spectroscopic, topological, and molecular orbital factors were examined. Results indicated that the IHB energies that obtained by way of MEM and Iogansen's relationship have better correlations with hydrogen bonding descriptors. Also, there are good consistencies between results of these two methods with viewpoint based on properties of RCPs. Therefore, IHB energies can suitably estimate using properties of RCPs in heterocyclic molecular systems especially in cases that rotation around C-C/CC bonds makes additional interactions in isomers and influences on accuracy of calculated IHB energies using approaches such as CTM and RRM.

Do weak interactions affect the biological behavior of DNA? A DFT study of CpG island-like chains

The origin, stability, and contribution to the formation of noncovalent interactions, such as hydrogen bonds and π - π stacking, have been already widely discussed. However, there are few discussions about the relevance of these weak interactions in DNA performance. In this work, we seek to shed light on the effect of hydrogen bonds and π - π stacking interactions on the biological behavior of DNA through the description of these intermolecular forces in CpG island-like (GC-rich) chains. Furthermore, we made some comparisons with TATA box-like (TA-rich) chains in order to describe hydrogen bond and π - π stacking interactions as a function of the DNA sequence. For hydrogen bonds, we found that there is not a significant effect related to the number of base pairs. Whereas for π - π stacking interactions, the energy tended to decrease as the number of base pairs increased. We observed anticooperative effects for both hydrogen bonds and π - π stacking interactions. These results are in contrast with those of TATA box-like chains since cooperative and additive effects were found for both hydrogen bonds and π - π stacking, respectively. Based on the chemical hardness and density of states, we can conclude that proteins may interact easier with GC-rich chains. We conclude that regardless of the chain length, a protein could interact more easily with these genomics regions because the π - π stacking energies did not increase as a function of the number of base pairs, making, for the first time, a first approximation of the influence of noncovalent interaction on DNA behavior. We did all this work by means of DFT framework included in the DMol³ code (M06-L/DNP). Graphical Abstract Cartoon representation of how nocovalent interactions affect the interaction of DNA with a protein, i.e., how hydrogen bond and π - π stacking interactions influence the biological behavior of DNA.

Effect of Alkali Metal Cations on Length and Strength of Hydrogen Bonds in DNA Base Pairs

For many years, non-covalently bonded complexes of nucleobases have attracted considerable interest. However, there is a lack of information about the nature of hydrogen bonding between nucleobases when the bonding is affected by metal coordination to one of the nucleobases, and how the individual hydrogen bonds and aromaticity of nucleobases respond to the presence of the metal cation. Here we report a DFT computational study of nucleobase pairs interacting with alkali metal cations. The metal cations contribute to the stabilization of the base pairs to varying degrees depending on their position. The energy decomposition analysis revealed that the nature of bonding between nucleobases does not change much upon metal coordination. The effect of the cations on individual hydrogen bonds were described by changes in VDD charges on frontier atoms, H-bond length, bond energy from NBO analysis, and the delocalization index from QTAIM calculations. The aromaticity changes were determined by a HOMA index.

On the Interaction between Superatom Al12Be and DNA Nucleobases/Base Pairs: Bonding Nature and Potential Applications in O2 Activation and CO Oxidation

The interaction between quasi-chalcogen superatom Al₁₂Be and DNA nucleobases/base pairs has been explored by searching for the most stable Al₁₂Be-X (X = DNA bases and base pairs) complexes. Our results reveal that Al₁₂Be prefers to combine with guanine by two Al-O and Al-N bonds rather than the other DNA bases, no matter in free state or base pair. The formed Al-N and Al-O bonds between Al₁₂Be and DNA bases proved to be strong polar covalent bonds by the Wiberg bond index, nature bond orbitals, atoms in molecules theory, localized molecular orbitals, and electron localization functions analyses. More importantly, it is found that the formed global minimum of Al₁₂Be-G has the ability to activate an oxygen molecule into a peroxide dianion ¹O₂ ^2-, which can further catalyze the CO oxidation via the Eley-Rideal mechanism with a small energy barrier of 7.78 kcal/mol. We hope that this study could not only provide an in-depth understanding on the intermolecular interaction between metallic superatoms and DNA at the molecular level but also attract more interest in designing and synthesizing superatom-based heterogeneous catalysts with DNA/nucleobases as basic building blocks.

Structural Patterns and Stabilities of Hydrogen-Bonded Pairs Involving Ribonucleotide Bases and Arginine, Glutamic Acid, or Glutamine Residues of Proteins from Quantum Mechanical Calculations

Ribonucleotide:protein interactions play crucial roles in a number of biological processes. Unlike the RNA:protein interface where van der Waals contacts are prevalent, the recognition of a single ribonucleotide such as ATP by a protein occurs predominantly through hydrogen-bonding interactions. As a first step toward understanding the role of hydrogen bonding in ribonucleotide:protein recognition, the present work employs density functional theory to provide a detailed quantum-mechanical analysis of the structural and energetic characteristics of 18 unique hydrogen-bonded pairs involving the nucleobase/nucleoside moiety of four canonical ribonucleotides and the side chains of three polar amino-acid residues (arginine, glutamine, and glutamic acid) of proteins. In addition, we model five new pairs that are till now not observed in crystallographically identified ribonucleotide:protein complexes but may be identified in complexes crystallized in the future. We critically examine the characteristics of each pair in its ribonucleotide:protein crystal structure occurrence and (gas phase and water phase) optimized intrinsic structure. We further evaluated the interaction energy of each pair and characterized the associated hydrogen bonds using a number of quantum mechanics-based relationships including natural bond orbital analysis, quantum theory atoms in molecules analysis, Iogansen relationships, Nikolaienko-Bulavin-Hovorun relationships, and noncovalent interaction-reduced density gradient analysis. Our analyses reveal rich variability in hydrogen bonds in the crystallographic as well as intrinsic structure of each pair, which includes conventional O/N-H···N/O and C-H···O hydrogen bonds as well as donor/acceptor-bifurcated hydrogen bonds. Further, we identify five combinations of nucleobase and amino acid moieties; each of which exhibits at least two alternate (i.e., multimodal) structures that interact through the same nucleobase edge. In fact, one such pair exhibits four multimodal structures; one of which possesses unconventional "amino-acceptor" hydrogen bonding with comparable (-9.4 kcal mol^-1) strength to the corresponding conventional (i.e., amino:donor) structure (-9.2 kcal mol^-1). This points to the importance of amino-acceptor hydrogen bonds in RNA:protein interactions and suggests that such interactions must be considered in the future while studying the dynamics in the context of molecular recognition. Overall, our study provides preliminary insights into the intrinsic features of ribonucleotide:amino acid interactions, which may help frame a clearer picture of the molecular basis of RNA:protein recognition and further appreciate the role of such contacts in biology.