Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs

A density functional theory study on interactions in water-bridged dimeric complexes of lignin

Lignin is the main plant cell wall component responsible for recalcitrance in the process of lignocellulosic biomass conversion into biofuels. The recalcitrance and insolubility of lignin in different reaction media are due in part to the hydrogen bonds and π interactions that hold syringyl (S) and guaiacyl (G) units together and promote the formation of stable water-bridged dimeric complexes (WBDCs): S⋯G and S⋯S, in native lignin. The current understanding of how each type of interaction influences the stability of these complexes within lignin native cell walls is still limited. Here, we found by DFT calculations that hydrogen bonding is more dominant than π-stacking interaction between aromatic rings of WBDCs. Although there is a stronger interaction of hydrogen bonds between subunits and water and higher π-stacking interaction in the S⋯S complex compared to the S⋯G complex, the former complex is less thermodynamically stable than the latter due to the entropic contribution coming from the methoxy substituents in the S-unit. Our results demonstrate that the methoxylation degree of lignin units does not significantly influence the structural geometries of WBDCs; if anything, an enhanced dispersion interaction between ring aromatics results in quasi-sandwich geometries as found in "coiled" lignin structures in the xylem tissue of wood. In the same way as that with ionic liquids, polar solvents can dissolve S-lignin by favorable interactions with the aliphatic hydroxyl group in the α-position as the key site or the aromatic hydroxyl group as the secondary site.

Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes

mRNA translation is a fundamental process for life. Selection of the translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for mRNA decoding. Studies in vertebrate mRNAs discovered that a purine at -3 and a G at +4 (where A of the AUG initiator codon is numbered + 1), promote TIS recognition. However, the TIS context in other eukaryotes has been poorly experimentally analyzed. We analyzed in vitro the influence of the -3, -2, -1 and + 4 positions of the TIS context in rabbit, Drosophila, wheat, and yeast. We observed that -3A conferred the best translational efficiency across these species. However, we found variability at the + 4 position for optimal translation. In addition, the Kozak motif that was defined from mammalian cells was only weakly predictive for wheat and essentially non-predictive for yeast. We discovered eight conserved sequences that significantly disfavored translation. Due to the big differences in translational efficiency observed among weak TIS context sequences, we define a novel category that we termed 'barren AUG context sequences (BACS)', which represent sequences disfavoring translation. Analysis of mRNA-ribosomal complexes structures provided insights into the function of BACS. The gene ontology of the BACS-containing mRNAs is presented.

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.

High-Order Quantum-Mechanical Analysis of Hydrogen Bonding in Hachimoji and Natural DNA Base Pairs

High-order quantum chemistry is applied to hydrogen-bonded natural DNA nucleobase pairs [adenine:thymine (A:T) and guanine:cytosine (G:C)] and non-natural Hachimoji nucleobase pairs [isoguanine:1-methylcytosine (B:S) and 2-aminoimidazo[1,2a][1,3,5]triazin-4(1H)-one:6-amino-5-nitropyridin-2-one (P:Z)] to see how the intermolecular interaction energies and their energetic components (electrostatics, exchange-repulsion, induction/polarization, and London dispersion interactions) vary among the base pairs. We examined the Hoogsteen (HG) geometries in addition to the traditional Watson-Crick (WC) geometries. Coupled-cluster theory through perturbative triples [CCSD(T)] extrapolated to the complete basis set (CBS) limit and high-order symmetry-adapted perturbation theory (SAPT) at the SAPT2+(3)(CCD)δMP2/aug-cc-pVTZ level are used to estimate highly accurate noncovalent interaction energies. Electrostatic interactions are the most attractive component of the interaction energies, but the sum of induction/polarization and London dispersion is nearly as large, for all base pairs and geometries considered. Interestingly, the non-natural Hachimoji base pairs interact more strongly than the corresponding natural base pairs, by -21.8 (B:S) and -0.3 (P:Z) kcal mol^-1 in the WC geometries, according to CCSD(T)/CBS. This is consistent with the H-bond distances being generally shorter in the non-natural base pairs. The natural base pairs are energetically more stabilized in their Hoogsteen geometries than in their WC geometries. The Hoogsteen geometry makes the A:T base pair slightly more stable, by -0.8 kcal mol^-1, and it greatly stabilizes the G:C⁺ base pair, by -15.3 kcal mol^-1. The G:C⁺ stabilization is mainly due to the fact that C has typically added a proton when found in Hoogsteen geometries. By contrast, Hoogsteen geometries are substantially less favorable than WC geometries for non-natural Hachimoji base pairs, by 17.3 (B:S) and 13.8 (P:Z) kcal mol^-1.

Estimating the Vertical Ionization Potential of Single-Stranded DNA Molecules

The electronic properties of DNA molecules, defined by the sequence-dependent ionization potentials of nucleobases, enable long-range charge transport along the DNA stacks. This has been linked to a range of key physiological processes in the cells and to the triggering of nucleobase substitutions, some of which may cause diseases. To gain molecular-level understanding of the sequence dependence of these phenomena, we estimated the vertical ionization potential (vIP) of all possible nucleobase stacks in B-conformation, containing one to four Gua, Ade, Thy, Cyt, or methylated Cyt. To do this, we used quantum chemistry calculations and more precisely the second-order Møller-Plesset perturbation theory (MP2) and three double-hybrid density functional theory methods, combined with several basis sets for describing atomic orbitals. The calculated vIP of single nucleobases were compared to experimental data and those of nucleobase pairs, triplets, and quadruplets, to observed mutability frequencies in the human genome, reported to be correlated with vIP values. This comparison selected MP2 with the 6-31G* basis set as the best of the tested calculation levels. These results were exploited to set up a recursive model, called vIPer, which estimates the vIP of all possible single-stranded DNA sequences of any length based on the calculated vIPs of overlapping quadruplets. vIPer's vIP values correlate well with oxidation potentials measured by cyclic voltammetry and activities obtained through photoinduced DNA cleavage experiments, further validating our approach. vIPer is freely available on the github.com/3BioCompBio/vIPer repository.

Structural and Energetic Features of Base-Base Stacking Contacts in RNA

Nucleobase π-π stacking is one of the crucial organizing interactions within three-dimensional (3D) RNA architectures. Characterizing the structural variability of these contacts in RNA crystal structures will help delineate their subtleties and their role in determining function. This analysis of different stacking geometries found in RNA X-ray crystal structures is the largest such survey to date; coupled with quantum-mechanical calculations on typical representatives of each possible stacking arrangement, we determined the distribution of stacking interaction energies. A total of 1,735,481 stacking contacts, spanning 359 of the 384 theoretically possible distinct stacking geometries, were identified. Our analysis reveals preferential occurrences of specific consecutive stacking arrangements in certain regions of RNA architectures. Quantum chemical calculations suggest that 88 of the 359 contacts possess intrinsically stable stacking geometries, whereas the remaining stacks require the RNA backbone or surrounding macromolecular environment to force their formation and maintain their stability. Our systematic analysis of π-π stacks in RNA highlights trends in the occurrence and localization of these noncovalent interactions and may help better understand the structural intricacies of functional RNA-based molecular architectures.

Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA

The Hoogsteen (HG) base pairing conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed in previous studies. However, the mechanism of the conformational transition is not well understood. A detailed understanding of the process of WC to HG base pair transition can provide a deeper understanding of DNA repair and recognition. In an earlier study, we explored the free energy landscape for this process using extensive computer simulation with the CHARMM36 force field. In this work, we study the impact of force field models in describing the WC to HG base pairing transition using meta-eABF enhanced sampling, quasi-harmonic entropy calculation, and nonbonded energy analysis. The secondary structures of both base pairing forms and the topology of the free energy landscapes were consistent over different force field models, although the relative free energy, entropy, and the interaction energies tend to vary. The relative stability of the WC and HG conformations is dictated by a delicate balance between the enthalpic stabilization and the reduced entropy of the structurally rigid HG structure. These findings highlight the impact that subtleties in force field models can have on accurately modeling DNA base pair dynamics and should stimulate further computational investigations into other dynamically important motions in DNA.

Computer Aided Development of Nucleic Acid Applications in Nanotechnologies

Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.

Quantum machine learning corrects classical forcefields: Stretching DNA base pairs in explicit solvent

In order to improve the accuracy of molecular dynamics simulations, classical forcefields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. As an example application, a potential-energy surface is generalized for a small DNA duplex, taking into account explicit solvation and long-range electron exchange-correlation effects. A long-standing problem in molecular science is that experimental studies of the structural and thermodynamic behavior of DNA under tension are not well confirmed by simulation; study of the potential energy vs extension taking into account a novel correction shows that leading classical DNA models have excessive stiffness with respect to stretching. This discrepancy is found to be common across multiple forcefields. The quantum correction is in qualitative agreement with the experimental thermodynamics for larger DNA double helices, providing a candidate explanation for the general and long-standing discrepancy between single molecule stretching experiments and classical calculations of DNA stretching. The new dataset of quantum calculations should facilitate multiple types of nucleic acid simulation, and the associated Kernel Modified Molecular Dynamics method (KMMD) is applicable to biomolecular simulations in general. KMMD is made available as part of the AMBER22 simulation software.

Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations

RNA modulation via small molecules is a novel approach in pharmacotherapies, where the determination of the structural properties of RNA motifs is considered a promising way to develop drugs capable of targeting RNA structures to control diseases. However, due to the complexity and dynamic nature of RNA molecules, the determination of RNA structures using experimental approaches is not always feasible, and computational models employing force fields can provide important insight. The quality of the force field will determine how well the predictions are compared to experimental observables. Stacking in nucleic acids is one such structural property, originating mainly from London dispersion forces, which are quantum mechanical and are included in molecular mechanics force fields through nonbonded interactions. Geometric descriptions are utilized to decide if two residues are stacked and hence to calculate the stacking free energies for RNA dinucleoside monophosphates (DNMPs) through statistical mechanics for comparison with experimental thermodynamics data. Here, we benchmark four different stacking definitions using molecular dynamics (MD) trajectories for 16 RNA DNMPs produced by two different force fields (RNA-IL and ff99OL3) and show that our stacking definition better correlates with the experimental thermodynamics data. While predictions within an accuracy of 0.2 kcal/mol at 300 K were observed in RNA CC, CU, UC, AG, GA, and GG, stacked states of purine-pyrimidine and pyrimidine-purine DNMPs, respectively, were typically underpredicted and overpredicted. Additionally, population distributions of RNA UU DNMPs were poorly predicted by both force fields, implying a requirement for further force field revisions. We further discuss the differences predicted by each RNA force field. Finally, we show that discrete path sampling (DPS) calculations can provide valuable information and complement the MD simulations. We propose the use of experimental thermodynamics data for RNA DNMPs as benchmarks for testing RNA force fields.

Affinity and Correlation in DNA

A statistical analysis of important DNA sequences and related proteins has been performed to study the relationships between monomers, and some general considerations about these macromolecules can be provided from the results. First, the most important relationship between sites in all the DNA sequences examined is that between two consecutive base pairs. This is an indication of an energetic stabilization due to the stacking interaction of these couples of base pairs. Secondly, the difference between human chromosome sequences and their coding parts is relevant both in the relationships between sites and in some specific compositional rules, such as the second Chargaff rule. Third, the evidence of the relationship in two successive triplets of DNA coding sequences generates a relationship between two successive amino acids in the proteins. This is obviously impossible if all the relationships between the sites are statistical evidence and do not involve causes; therefore, in this article, due to stacking interactions and this relationship in coding sequences, we will divide the concept of the relationship between sites into two concepts: affinity and correlation, the first with physical causes and the second without. Finally, from the statistical analyses carried out, it will emerge that the human genome is uniform, with the only significant exception being the Y chromosome.

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids

The lone-pair···π (lp···π) (deoxy)ribose···nucleobase stacking is a recurring interaction in Z-DNA and RNAs that is characterized by sub-van der Waals lp···π contacts (<3.0 Å). It is a part of the structural signature of CpG Z-step motifs in Z-DNA and r(UNCG) tetraloops that are known to behave poorly in molecular dynamics (MD) simulations. Although the exact origin of the MD simulation issues remains unclear, a significant part of the problem might be due to an imbalanced description of nonbonded interactions, including the characteristic lp···π stacking. To gain insights into the links between lp···π stacking and MD, we present an in-depth comparison between accurate large-basis-set double-hybrid Kohn-Sham density functional theory calculations DSD-BLYP-D3/ma-def2-QZVPP (DHDF-D3) and data obtained with the nonbonded potential of the AMBER force field (AFF) for NpN Z-steps (N = G, A, C, and U). Among other differences, we found that the AFF overestimates the DHDF-D3 lp···π distances by ∼0.1-0.2 Å, while the deviation between the DHDF-D3 and AFF descriptions sharply increases in the short-range region of the interaction. Based on atom-in-molecule polarizabilities and symmetry-adapted perturbation theory analysis, we inferred that the DHDF-D3 versus AFF differences partly originate in identical nucleobase carbon atom Lennard-Jones (LJ) parameters despite the presence/absence of connected electron-withdrawing groups that lead to different effective volumes or vdW radii. Thus, to precisely model the very short CpG lp···π contact distances, we recommend revision of the nucleobase atom LJ parameters. Additionally, we suggest that the large discrepancy between DHDF-D3 and AFF short-range repulsive part of the interaction energy potential may significantly contribute to the poor performances of MD simulations of nucleic acid systems containing Z-steps. Understanding where, and if possible why, the point-charge-type effective potentials reach their limits is vital for developing next-generation FFs and for addressing specific issues in contemporary MD simulations.

Role of Stacking Interactions in the Stability of Primitive Genetics: A Quantum Chemical View

The origin of genetic material on earth is an age-old, entangled mystery that lacks a unanimous explanation. Recent studies have suggested that noncanonical bases such as barbituric acid (BA), melamine (MM), cyanuric acid (CA), and 2,4,6-triaminopyrimidine (TAP) may have undergone molecular selection within the "prebiotic soup" to spontaneously form supramolecular assemblies, which then covalently assembled into an RNA-like polymer (preRNA). However, information on the role of intrinsic interactions of these candidate heterocycles in their molecular selection as the components of preRNA, and the subsequent transition from preRNA to RNA, is currently missing in the literature. To fill this gap in our knowledge on the origin and evolution of primitive genetics, the present work employs density functional theory (B3LYP-D3) to evaluate and compare the stacking propensities of dimers containing prebiotic noncanonical (BA, MM, CA, and TAP) and/or canonical RNA bases (A, C, G, and U). Our detailed analysis of the variation in stacking strength with respect to four characteristic geometrical parameters between the monomers [i.e., the vertical distance, the angle of rotation, and (two) displacements in the x and y directions] reveals that stacking between nonidentical bases is preferred over identical bases for both prebiotic-prebiotic and canonical-canonical dimers. This not only underscores the similarity between the fundamental chemical properties of preRNA and RNA constituents but also supports the likelihood of the evolution of modern (RNA) genetics from primitive (preRNA) genetics. Furthermore, greater average stacking stabilization of canonical dimers than that of dimers containing one canonical and one preRNA nucleobase (by ∼5 kJ mol^-1) or dimers solely containing preRNA nucleobases (by ∼12 kJ mol^-1) indicates that enhanced stacking is an important factor that may have spurred the evolution of preRNA to an intermediate informational polymer to RNA. More importantly, our study identifies the central roles of CA, BA, and TAP in stacking stabilization within the preRNA and of BA in stacking interactions within the intermediate polymers and suggests that these heterocycles may have played distinct roles in various stages during the evolution from preRNA to RNA. Overall, our results highlight the significance of stacking interactions in the selection of nucleobase components of preRNA.

Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction

DNA synthesis by polymerases is essential for life. Deprotonation of the nucleophile 3'-OH is thought to be the obligatory first step in the DNA synthesis reaction. We have examined each entity surrounding the nucleophile 3'-OH in the reaction catalyzed by human DNA polymerase (Pol) η and delineated the deprotonation process by combining mutagenesis with steady-state kinetics, high-resolution structures of in crystallo reactions, and molecular dynamics simulations. The conserved S113 residue, which forms a hydrogen bond with the primer 3'-OH in the ground state, stabilizes the primer end in the active site. Mutation of S113 to alanine destabilizes primer binding and reduces the catalytic efficiency. Displacement of a water molecule that is hydrogen bonded to the 3'-OH using the 2'-OH of a ribonucleotide or 2'-F has little effect on catalysis. Moreover, combining the S113A mutation with 2'-F replacement, which removes two potential hydrogen acceptors of the 3'-OH, does not reduce the catalytic efficiency. We conclude that the proton can leave the O3' via alternative paths, supporting the hypothesis that binding of the third Mg²⁺ initiates the reaction by breaking the α-β phosphodiester bond of an incoming deoxyribonucleoside triphosphate (dNTP).

W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model

Representation of electrostatic interactions by a Coulombic pairwise potential between atom-centered partial charges is a fundamental and crucial part of empirical force fields used in classical molecular dynamics simulations. The broad success of the AMBER force-field family originates mainly from the restrained electrostatic potential (RESP) charge model, which derives partial charges to reproduce the electrostatic field around the molecules. However, the description of the electrostatic potential around molecules by standard RESP may be biased for some types of molecules. In this study, we modified the RESP charge derivation model to improve its description of the electrostatic potential around molecules and thus electrostatic interactions in the force field. In particular, we reoptimized the atomic radii for definition of the grid points around the molecule, redesigned the restraining scheme, and included extra point (EP) charges. The RESP fitting was significantly improved for aromatic heterocyclic molecules. Thus, the suggested W-RESP(-EP) charge derivation model shows some potential for improving the performance of the nucleic acid force fields, for which the poor description of nonbonded interactions, such as the underestimated stability of base pairing, is well-established. We also report some preliminary simulation tests (around 1 ms of simulation data) on A-RNA duplexes, tetranucleotides, and tetraloops. The simulations reveal no adverse effects, while the description of base-pairing interactions might be improved. The new charges can thus be used in future attempts to improve the nucleic acid simulation force fields, in combination with reparametrization of the other terms.

MD simulations reveal the basis for dynamic assembly of Hfq-RNA complexes

The conserved protein Hfq is a key factor in the RNA-mediated control of gene expression in most known bacteria. The transient intermediates Hfq forms with RNA support intricate and robust regulatory networks. In Pseudomonas, Hfq recognizes repeats of adenine–purine–any nucleotide (ARN) in target mRNAs via its distal binding side, and together with the catabolite repression control (Crc) protein, assembles into a translation–repression complex. Earlier experiments yielded static, ensemble-averaged structures of the complex, but details of its interface dynamics and assembly pathway remained elusive. Using explicit solvent atomistic molecular dynamics simulations, we modeled the extensive dynamics of the Hfq–RNA interface and found implications for the assembly of the complex. We predict that syn/anti flips of the adenine nucleotides in each ARN repeat contribute to a dynamic recognition mechanism between the Hfq distal side and mRNA targets. We identify a previously unknown binding pocket that can accept any nucleotide and propose that it may serve as a ‘status quo’ staging point, providing nonspecific binding affinity, until Crc engages the Hfq–RNA binary complex. The dynamical components of the Hfq–RNA recognition can speed up screening of the pool of the surrounding RNAs, participate in rapid accommodation of the RNA on the protein surface, and facilitate competition among different RNAs. The register of Crc in the ternary assembly could be defined by the recognition of a guanine-specific base–phosphate interaction between the first and last ARN repeats of the bound RNA. This dynamic substrate recognition provides structural rationale for the stepwise assembly of multicomponent ribonucleoprotein complexes nucleated by Hfq–RNA binding.

Delocalization-Assisted Transport through Nucleic Acids in Molecular Junctions

The flow of charge through molecules is central to the function of supramolecular machines, and charge transport in nucleic acids is implicated in molecular signaling and DNA repair. We examine the transport of electrons through nucleic acids to understand the interplay of resonant and nonresonant charge carrier transport mechanisms. This study reports STM break junction measurements of peptide nucleic acids (PNAs) with a G-block structure and contrasts the findings with previous results for DNA duplexes. The conductance of G-block PNA duplexes is much higher than that of the corresponding DNA duplexes of the same sequence; however, they do not display the strong even-odd dependence conductance oscillations found in G-block DNA. Theoretical analysis finds that the conductance oscillation magnitude in PNA is suppressed because of the increased level of electronic coupling interaction between G-blocks in PNA and the stronger PNA-electrode interaction compared to that in DNA duplexes. The strong interactions in the G-block PNA duplexes produce molecular conductances as high as 3% G₀, where G₀ is the quantum of conductance, for 5 nm duplexes.

Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study

The non-natural ethynylmethylpyridone C-nucleoside (W), a thymidine (T) analogue that can be incorporated in oligonucleotides by automated synthesis, has recently been reported to form a high fidelity base pair with adenosine (A) and to be well accommodated in B-DNA duplexes. The enhanced binding affinity for A of W, as compared to T, makes it an ideal modification for biotechnological applications, such as efficient probe hybridization for the parallel detection of multiple DNA strands. In order to complement the experimental study and rationalize the impact of the non-natural W nucleoside on the structure, stability and dynamics of DNA structures, we performed quantum mechanics (QM) calculations along with molecular dynamics (MD) simulations. Consistently with the experimental study, our QM calculations show that the A:W base pair has an increased stability as compared to the natural A:T pair, due to an additional CH-π interaction. Furthermore, we show that mispairing between W and guanine (G) causes a distortion in the planarity of the base pair, thus explaining the destabilization of DNA duplexes featuring a G:W pair. MD simulations show that incorporation of single or multiple consecutive A:W pairs in DNA duplexes causes minor changes to the intra- and inter-base geometrical parameters, while a moderate widening/shrinking of the major/minor groove of the duplexes is observed. QM calculations applied to selected stacks from the MD simulations also show an increased stacking energy for W, over T, with the neighboring bases.

On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions

The astonishing diversity in folding patterns of RNA three-dimensional (3D) structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. A systematic and comprehensive classification and annotation of these interactions is necessary for a molecular-level understanding of their roles. However, unlike in the case of base pairing, where a widely accepted nomenclature and classification scheme exists in the public domain, currently available classification schemes for base-base stacking need major enhancements to comprehensively capture the necessary features underlying the rich stacking diversity in RNA. Here, we extend the previous stacking classification based on nucleobase interacting faces by introducing a structurally intuitive geometry-cum topology-based scheme. Specifically, a stack is first classified in terms of the geometry described by the relative orientation of the glycosidic bonds, which generates eight basic stacking geometric families for heterodimeric stacks and six of those for homodimeric stacks. Further annotation in terms of the identity of the bases and the region of involvement of purines (five-membered, six-membered, or both rings) leads to the enumeration of 384 distinct RNA base stacks. Based on our classification scheme, we present an algorithm for automated identification of stacks in RNA crystal structures and analyze the stacking context in selected RNA structures. Overall, the work described here is expected to greatly facilitate the structure-based RNA research.

Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs

We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution ≤3.0 Å. Such contacts may be of either the lone pair-π (lp-π) or the OH-π type, in nature. The distribution of the distances of the water oxygen from the nucleobase plane peaks at 3.5 Å for A, G and C, and approximately at 3.1-3.2 Å for U. Quantum mechanics (QM) calculations confirm, as expected, that the optimal energy is reached at a shorter distance for the lp-π interaction as compared to the OH-π one (3.0 versus 3.5 Å). The preference of each nucleobase for either type of interaction closely correlates with its electrostatic potential map. Furthermore, QM calculations show that for all the nucleobases a favorable interaction, of either the lp-π or the OH-π type, can be established at virtually any position of the water molecule above the nucleobase skeleton, which is consistent with the uniform projection of the OW atoms over the nucleobases ring we observed in the experimental occurrences. Finally, molecular dynamics simulations of a model system for the characterization of water-nucleobase stacking contacts confirm the stability of these interactions also under dynamic conditions.

Energy, orbital and structural stacking landscape of a purine homodimer system

The multidimensional study, combining the extensive calculations of potential energy surfaces for the parallel-displaced configurations and methods such as energy decomposition and natural bond orbital analysis, has been carried out. The resulted data give an energy, orbital and structural landscapes of this biologically essential system. The balance of the two energy sources, electrostatic and dispersion, is clearly visible. The obtained results, taken as a whole, provide an insight into the hierarchy of intermolecular interactions in the purine system, together with their sources.

Impact of the Substituents on the Electronic Structure of the Four Most Stable Tautomers of Purine and Their Adenine Analogues

Substituent effects at the C2-, C8-, and N-positions of adenine and purine on the structural and π-electronic changes in their four tautomers were studied using the B97D3/aug-cc-pvdz computational level. The effect of various substituents (NO2, CN, CHO, Cl, F, H, Me, OMe, OH, and NH2) was characterized by the charge of the substituent active region (cSAR) approach and Hammett substituent constants σ. It has been found that for both adenine and purine derivatives, substituents from the C8-X position have a stronger influence on their electronic structure than from the C2-X and N-X positions. The presence of the amino group in adenine enhances the substituent effect compared to that which occurs in purine. In addition, its electronic structure is more sensitive to the effect of the substituent in 3H and 1H than in the 9H and 7H adenine tautomers. For a given substituent, a large variation in cSAR(X) values is observed, strongly dependent on the substitution position. For 7H and 9H adenine tautomers for C8-X systems, substituents reduce the aromaticity of the five-membered rings but increase the aromaticity of the six-membered rings.

Understand the Specific Regio- and Enantioselectivity of Fluostatin Conjugation in the Post-Biosynthesis

Fluostatins, benzofluorene-containing aromatic polyketides in the atypical angucycline family, conjugate into dimeric and even trimeric compounds in the post-biosynthesis. The formation of the C-C bond involves a non-enzymatic stereospecific coupling reaction. In this work, the unusual regio- and enantioselectivities were rationalized by density functional theory calculations with the M06-2X (SMD, water)/6-311 + G(d,p)//6-31G(d) method. These DFT calculations reproduce the lowest energy C1-(R)-C10'-(S) coupling pathway observed in a nonenzymatic reaction. Bonding of the reactive carbon atoms (C1 and C10') of the two reactant molecules maximizes the HOMO-LUMO interactions and Fukui function involving the highest occupied molecular orbital (HOMO) of nucleophile p-QM and lowest unoccupied molecular orbital (LUMO) of electrophile FST2- anion. In particular, the significant π-π stacking interactions of the low-energy pre-reaction state are retained in the lowest energy pathway for C-C coupling. The distortion/interaction-activation strain analysis indicates that the transition state (TScp-I) of the lowest energy pathway involves the highest stabilizing interactions and small distortion among all possible C-C coupling reactions. One of the two chiral centers generated in this step is lost upon aromatization of the phenol ring in the final difluostatin products. Thus, the π-π stacking interactions between the fluostatin 6-5-6 aromatic ring system play a critical role in the stereoselectivity of the nonenzymatic fluostatin conjugation.

Stacking geometry between two sheared Watson-Crick basepairs: Computational chemistry and bioinformatics based prediction

BACKGROUND

Molecular modeling of RNA double helices is possible using most probable values of basepair parameters obtained from crystal structure database. The A:A w:wC non-canonical basepair, involving Watson-Crick edges of two Adenines in cis orientation, appears quite frequently in database. Bimodal distribution of its Shear, due to two different H-bonding schemes, introduces the confusion in assigning most the probable value. Its effect is pronounced when the A:A w:wC basepair stacks on Sheared wobble G:U W:WC basepairs.

METHODS

We employed molecular dynamics simulations of three possible double helices with GAG, UAG and GAU sequence motifs at their centers and quantum chemical calculation for non-canonical A:A w:wC basepair stacked on G:U W:WC basepair.

RESULTS

We noticed stable structures of GAG motif with specifically negative Shear of the A:A basepair but stabilities of the other motifs were not found with A:A w:wC basepairing. Hybrid DFT-D and MP2 stacking energy analyses on dinucleotide step sequences, A:A w:wC::G:U W:WC and A:A w:wC::U:G W:WC reveal that viable orientation of A:A::G:U prefers one of the H-bonding modes with negative Shear, supported by crystal structure database. The A:A::U:G dinucleotide, however, prefers structure with only positive Shear.

CONCLUSIONS

The quantum chemical calculations explain why MD simulations of GAG sequence motif only appear stable. In the cases of the GAU and UAG motifs "tug of war" situation between positive and negative Shears of A:A w:wC basepair induces conformational plasticity.

GENERAL SIGNIFICANCE

We have projected comprehensive reason behind the promiscuous nature of A:A w:wC basepair which brings occasional structural plasticity.

Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking

Nucleobase stacking interactions are crucial for the stability of nucleic acids. This study investigates base stacking energies of the cytosine homodimer in different configurations, including intermolecular separation plots, detailed twist dependence, and displaced structures. Highly accurate ab initio quantum chemical single point energies using an energy function based on MP2 complete basis set extrapolation ([6 → 7]ZaPa-NR) and a CCSD(T)/cc-pVTZ-F12 high-level correction are presented as new reference data, providing the most accurate stacking energies of nucleobase dimers currently available. Accurate SAPT2+(3)δMP2 energy decomposition is used to obtain detailed insights into the nature of base stacking interactions at varying vertical distances and twist values. The ab initio symmetry adapted perturbation theory (SAPT) energy decomposition suggests that the base stacking originates from an intricate interplay between dispersion attraction, short-range exchange-repulsion, and Coulomb interaction. The interpretation of the SAPT data is a complex issue as key energy terms vary substantially in the region of optimal (low energy) base stacking geometries. Thus, attempts to highlight one leading stabilizing SAPT base stacking term may be misleading and the outcome strongly depends on the used geometries within the range of geometries sampled in nucleic acids upon thermal fluctuations. Modern dispersion-corrected density functional theory (among them DSD-BLYP-D3, ωB97M-V, and ωB97M-D3BJ) is benchmarked and often reaches up to spectroscopic accuracy (below 1 kJ/mol). The classical AMBER force field is benchmarked with multiple different sets of point-charges (e.g. HF, DFT, and MP2-based) and is found to produce reasonable agreement with the benchmark data.

Association of Nucleobases in Hydrated Ionic Liquid from Biased Molecular Dynamics Simulations

We employed metadynamics-based classical molecular dynamics simulations to methylated adenine-thymine (mA-mT) and guanine-cytosine (mG-mC) base pairs to see favorable conformations in various concentrations of hydrated 1-ethyl, 3-methyl imidazolium acetate. We investigated various stacked and hydrogen-bonded conformations of association of base pairs through appropriately chosen collective variables. Stacked conformations more favored in water for both base pairs, whereas Watson-Crick (WC) hydrogen-bonding conformations are favored in pure and hydrated ionic liquids (ILs) except for 0.75 mol fraction IL. We observe that EMIm cations surround the base pairs in WC conformations creating a kind of hydrophobic cavity and protect the hydrogen bonds between base pairs. However, the five-membered heteroaromatic rings of cations stack with the nucleobases in the cation-base-cation (π-π-π) model, which resembles the base-base-base stacking in a DNA duplex. Interestingly, from additional simulations of 0.5 mol fraction hydrated choline dihydrogen phosphate IL, we observe that the stacked conformations become more favored than the WC conformation due to the absence of π-bonds in cations. The calculated values of relative solubility of base pairs in pure and hydrated ionic liquids compared to those in pure water correlate well with the free energy values of WC and stacked conformations.

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.

Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs

The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4' atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We identified 2015 ribose-base stacking interactions in a high-resolution set of non-redundant RNA crystal structures. They are widespread in structured RNA molecules and are located in structural motifs other than regular stems. Over 50% of them involve an adenine, as we found ribose-adenine contacts to be recurring elements in A-minor motifs. Fewer than 50% of the interactions involve a ribose and a base of neighboring residues, while approximately 30% of them involve a ribose and a nucleobase at least four residues apart. Some of them establish inter-domain or inter-molecular contacts and often implicate functionally relevant nucleotides. In vacuo ribose-nucleobase stacking interaction energies were calculated by quantum mechanics methods. Finally, we found that lone pair-π stacking interactions also occur between ribose and aromatic amino acids in RNA-protein complexes.

What Hinders Electron Transfer Dissociation (ETD) of DNA Cations?

Radical activation methods, such as electron transfer dissociation (ETD), produce structural information complementary to collision-induced dissociation. Herein, electron transfer dissociation of 3-fold protonated DNA hexamers was studied to gain insight into the fragmentation mechanism. The fragmentation patterns of a large set of DNA hexamers confirm cytosine as the primary target of electron transfer. The reported data reveal backbone cleavage by internal electron transfer from the nucleobase to the phosphate linker leading either to a•/w or d/z• ion pairs. This reaction pathway contrasts with previous findings on the dissociation processes after electron capture by DNA cations, suggesting multiple, parallel dissociation channels. However, all these channels merely result in partial fragmentation of the precursor ion because the charge-reduced DNA radical cations are quite stable. Two hypotheses are put forward to explain the low dissociation yield of DNA radical cations: it is either attributed to non-covalent interactions between complementary fragments or to the stabilization of the unpaired electron in stacked nucleobases. MS³ experiments suggest that the charge-reduced species is the intact oligonucleotide. Moreover, introducing abasic sites significantly increases the dissociation yield of DNA cations. Consequently, the stabilization of the unpaired electron by π-π-stacking provides an appropriate rationale for the high intensity of DNA radical cations after electron transfer. Graphical Abstract.

Noncovalent Interactions in the Catechol Dimer

Noncovalent interactions play a significant role in a wide variety of biological processes and bio-inspired species. It is, therefore, important to have at hand suitable computational methods for their investigation. In this paper, we report on the contribution of dispersion and hydrogen bonds in both stacked and T-shaped catechol dimers, with the aim of delineating the respective role of these classes of interactions in determining the most stable structure. By using second-order Møller⁻Plesset (MP2) calculations with a small basis set, specifically optimized for these species, we have explored a number of significant sections of the interaction potential energy surface and found the most stable structures for the dimer, in good agreement with the highly accurate, but computationally more expensive coupled cluster single and double excitation and the perturbative triples (CCSD(T))/CBS) method.

Multireflection propagation of conformational kinks in a two-component model of DNA as the transfer mode of the transcriptional replication fork

The propagation, or movement, of a conformational kink along a linear structure can occur in capture, transfer, or multireflection modes. Here we use a model for two-component bistable polymer molecules with energetically non-equivalent stable states to model the propagation of the DNA transcription bubble via movement of a non-linear longitudinal stretching region along the DNA chain. We show that under certain conditions the longitudinal excitation can act as a reflector for a conformational kink and, furthermore, that conformational switching may propagate in a multireflection mode alongside conformational kink transition and conformational kink trapping.

Stepping Library-Based Post-SELEX Strategy Approaching to the Minimized Aptamer in SPR

When evolved from SELEX (systematic evolution of ligands by exponential enrichment), aptamers are generally about 70-130 nucleotides in length and needed to be effectively truncated for further diagnosis or therapeutic uses. Post-SELEX optimization is then aroused to simplify the aptamer sequence and improve the affinity property. In this work, we report a new post-SELEX strategy based on a stepping library for the first time. With a hypothesis that one nucleobase can influence the whole binding affinity through its adjacent base stacking and potential steric hydrogen bonding interaction, we designed a stepping library composed of all probable nucleotide truncation directions. We employed an aptamer 807-39nt toward EPO-α as a model, and surface plasmon resonance (SPR) as an efficient screening and evaluation method to optimize all label-free sequences in the library. We have successfully picked out In27 as the minimized aptamer from a mini library of only 35 sequences. Aptamer In27 has a sole loop, without the original stem portion of the initial aptamer, but retains the whole binding affinity. We have also defined the key nucleotide contribution by site mutagenesis with natural bases, and finally produced a degenerated sequence with higher or the same good affinities. Furthermore, we explored different binding behaviors between aptamer In27 and other recognition molecule such as agglutinin, monoclonal antibody, or receptor by competition or binding assays. Our work provides a new and efficient post-SELEX optimization strategy, as well as a minimized aptamer In27 with an explicit degenerated sequence and a defined binding behavior. That would enhance their great potential in future diagnosis and therapy.

Stacking interactions involving non-Watson–Crick basepairs: dispersion corrected density functional theory studies

Stacking interactions between a non Watson–Crick G:A S:HT basepair and C:G basepair is predicted in terms of roll, twist and slide basepair step parameters using DFT-D augmented with coarse-grain energy penalty for sugar–phosphate backbone.

Non-linear longitudinal compression effect on dynamics of the transcription bubble in DNA

The dependence of the dynamics of transcription bubble on the parameters of non-linear longitudinal compression is presented on the base of simple model of soliton-like conformational switchings in two-component bistable polymer molecules with energetically non-equivalent stable states. It has been shown that under certain conditions the longitudinal compression may be a trap for a conformational switching.

Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix

Triple-stranded RNA was first deduced to form in vitro more than 50 years ago and has since been implicated in RNA catalysis, stability, and small molecule binding. Despite the emerging biological significance of RNA triple helices, it remains unclear how their nucleotide composition contributes to their thermodynamic stability and cellular function. To investigate these properties, we used in vitro RNA electrophoretic mobility shift assays (EMSAs) and in vivo intronless β-globin reporter assays to measure the relative contribution of 20 RNA base triples (N•A-U, N•G-C, N•C-G, N•U-A, and N•G-U) to triple-helical stability. These triples replaced a single internal U•A-U within the known structure of the triple-helical RNA stability element of human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), which contains 10 major-groove base triples. In addition to the canonical C•G-C triple, the noncanonical base triples U•G-C, U•G-U, C•C-G, and U•C-G exhibited at least 30% stability relative to the wild-type U•A-U base triple in both assays. Of these triples, only U•A-U, C•G-C, and U•G-C, when tested as four successive triples, formed stabilizing structures that allowed accumulation of the intronless β-globin reporter. Overall, we find that Hoogsteen-position pyrimidines support triple helix stability and function and that thermodynamic stability, based on EMSA results, is necessary but not sufficient for stabilization activity of the MALAT1 triple helix in cells. These results suggest that additional RNA triple helices containing noncanonical triples likely exist in nature.

Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations

Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and the possible role of delocalized electrons in stacked aromatic π systems, leading to some confusion about the issue. The recent advance of computer hardware and software finally allowed the application of state of the art quantum-mechanical approaches with inclusion of electron correlation effects to study aromatic base stacking, now providing an ultimitate qualitative description of the phenomenon. Base stacking is determined by an interplay of the three most commonly encountered molecular interactions: dispersion attraction, electrostatic interaction, and short-range repulsion. Unusual (aromatic- stacking specific) energy contributions were in fact not evidenced and are not necessary to describe stacking. The currently used simple empirical potential form, relying on atom-centered constant point charges and Lennard-Jones van der Waals terms, is entirely able to reproduce the essential features of base stacking. Thus, we can conclude that base stacking is in principle one of the best described interactions in current molecular modeling and it allows to study base stacking in DNA using large-scale classical molecular dynamics simulations. Neglect of cooperativity of stacking appears to be the most serious approximation of the currently used force field form. This review summarizes recent developments in the field. It is written for an audience that is not necessarily expert in computational quantum chemistry and follows up on our previous contribution (Sponer et. al., J. Biomol. Struct. Dyn. 14, 117, (1997)). First, the applied methodology, its accuracy, and the physical nature of base stacking is briefly overviewed, including a comment on the accuracy of other molecular orbital methods and force fields. Then, base stacking is contrasted with hydrogen bonding, the other dominant force in nucleic acid structure. The sequence dependence and cooperativity of base stacking is commented on, and finally a brief introduction into recent progress in large-scale molecular dynamics simulations of nucleic acids is provided. Using four stranded DNA assemblies as an example, we demonstrate the efficacy of current molecular dynamics techniques that utilize refined and verified force fields in the study of stacking in nucleic acid molecules.