Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics

Conformational preferences of guanine-containing threose nucleic acid building blocks in B3LYP studies

In this paper, detailed and systematic gas-phase B3LYP conformational studies of four monomers of threose nucleic acid (TNA) with guanine attached at the C1' atom and bearing different substituents (OH, OP(=O)OH2 and OCH3) in the C2' and C3' positions of the α-l-threofuranose moiety are presented. All exocyclic single-bond (χ, ε and γ) rotations, as well as the ν0-ν4 endocyclic torsion angles, were taken into consideration. Three (threoguanosines TG1-TG3) or two (TG4) energy minima were found for the rotation about the χ torsion angle. The syn orientation (the A rotamer family) is strongly privileged in geometries TG1 and TG2, whereas the anti orientation (the C rotamer family) and the syn orientation are observed to be in equilibrium (with populations of 56% and 44%, respectively) for TG3. In the case of TG4, the high-anti orientation (the B rotamer family) turned out to be by far the most favourable, with the contribution exceeding 90% in equilibrium. Such a preference can be attributed to the inability of H-bonding between sugar and nucleobase and possibly because of the steric strains. The low-energy conformers of TG1-TG4 occupy the northeastern (P ∼ 40°) and/or southern (P ∼ 210°) parts of the pseudorotational wheel, which fits the A- and B-type DNA helices quite well. Additionally, in the case of TG4, some relatively stable geometries have the furanoid ring in conformation lying on the northwestern part of the pseudorotational wheel (P ∼ 288°).

The Structure of DNA Fragments: Quantum-Chemical Modelling

In this review, we analyze and systematize our computational studies of the nucleic acid duplex formations and thermodynamic stability under the different factors of investigation. The proposed structural models of mini-helix contains N nucleobase pairs (N = 3-5); QM structural data suggest that the helical conformations of mini-helix adopt geometrical parameters comparable to those of natural A- and B-DNA forms under specific conditions as micro hydration and charge compensation. The gas-phase models adopt non regular conformations between the helical form and a ladder form.. The natural helical shape of DNA mini-helix is stabilized by the presence of counterions or by explicit micro-hydration of the major and minor groves. The presence of aqueous solution is shown as a minor factor for the helical shape formation. The studies are performed at the level of density functional theory.

Polarizable force field for RNA based on the classical drude oscillator

RNA molecules are highly dynamic and capable of adopting a wide range of complex, folded structures. The factors driving the folding and dynamics of these structures are dependent on a balance of base pairing, hydration, base stacking, ion interactions, and the conformational sampling of the 2'-hydroxyl group in the ribose sugar. The representation of these features is a challenge for empirical force fields used in molecular dynamics simulations. Toward meeting this challenge, the inclusion of explicit electronic polarization is important in accurately modeling RNA structure. In this work, we present a polarizable force field for RNA based on the classical Drude oscillator model, which represents electronic degrees of freedom via negatively charged particles attached to their parent atoms by harmonic springs. Beginning with parametrization against quantum mechanical base stacking interaction energy and conformational energy data, we have extended the Drude-2017 nucleic acid force field to include RNA. The conformational sampling of a range of RNA sequences were used to validate the force field, including canonical A-form RNA duplexes, stem-loops, and complex tertiary folds that bind multiple Mg2+ ions. Overall, the Drude-2017 RNA force field reproduces important properties of these structures, including the conformational sampling of the 2'-hydroxyl and key interactions with Mg2+ ions. © 2018 Wiley Periodicals, Inc.

Atomic charges for conformationally rich molecules obtained through a modified principal component regression

A modification of the principal component regression model is proposed for obtaining a fixed set of atomic charges (referred to as dipole-derived charges) optimized for reproducing the dipole moment of a conformationally rich molecule, i.e., a molecule with multiple local minima on the potential energy surface. The method does not require any adjustable parameters and requires the geometries of conformers, their dipole moments and atomic polar tensor (APT) charges as the only input data. The fixed atomic charges generated by the method not only reproduce the molecular dipole moment in all the conformers accurately, but are also numerically close to the APT charges, thereby ensuring accurate reproduction of the dipole moment variations caused by small geometrical distortions (e.g., by vibrations) of the conformers. The proposed method has been applied to canonical 2'-deoxyribonucleotides, the model DNA monomers, and the dipole-derived charges have been shown to outperform both the averaged APT and RESP charges in reproducing the dipole moments of large sets of conformers, thus demonstrating a potential usefulness of the dipole-derived charges as a 'reference point' for modeling polarization effects in conformationally rich molecules.

Threocytidines: Insight into the Conformational Preferences of Artificial Threose Nucleic Acid (TNA) Building Blocks in B3LYP Studies

A systematic DFT conformational studies of four building blocks of TNA with cytosine attached to the C1' atom of the α-L-threofuranose moiety are presented. Structures bearing 2'-OR and 3'-OR substituents, where R represents H, CH₃ and phosphate groups, were used in the studies using a B3LYP functional in the gas phase. The χ angle (C2-N1-C1'-O4'), the ν₀-ν₄ endocyclic torsion angles and the exocyclic torsion angles ε (X-O2'-C2'-C1') and γ (X-O3'-C3'-C2') geometry parameter variations were taken into consideration. Three energy minima, high-anti, anti and syn, were found for the rotation about the C1'-N1 bond. The high-anti orientation of the base with respect to the sugar moiety, turned out to be preferred, regardless of the substituents at the C2' and C3' positions. Other orientations are at least 1.65 kcal/mol higher in Gibbs free energy than the high-anti one. It has been shown that intramolecular H-bonds and the anomeric effect of phosphate groups strongly affect the conformational preferences of the studied compounds. Further, the structure of substituents attached to the sugar moiety influence the pucker of the furanoid ring. The furanoid ring in the global minima of the compound with two OH groups (TC1) in the 2' and 3' positions, and the compound having a 3'-phosphate group (TC2), adopt roughly the same conformation located at the southern range of the pseudorotation wheel, and thus are close to those found in the B type DNA helix. The low-energy high-anti rotamers of the geometry with the phosphate group attached to the sugar ring in the 2' position (TC3) and the geometry with two methoxyl groups (TC4) have their furanoid rings in conformations resembling those found in A DNA and RNA helices (the northern range of the pseudorotation wheel).

Additive CHARMM force field for naturally occurring modified ribonucleotides

More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all‐atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers

Empirical force field parameters consistent with the CHARMM additive and classical Drude based polarizable force fields are presented for linear and cyclic ethers. Initiation of the optimization process involved validation of the aliphatic parameters based on linear alkanes and cyclic alkanes. Results showed the transfer to cyclohexane to yield satisfactory agreement with target data; however, in the case of cyclopentane direct transfer of the Lennard-Jones parameters was not sufficient due to ring strain, requiring additional optimization of these parameters for this molecule. Parameters for the ethers were then developed starting with the available aliphatic parameters, with the nonbond parameters for the oxygens optimized to reproduce both gas- and condensed-phase properties. Nonbond parameters for the polarizable model include the use of an anisotropic electrostatic model on the oxygens. Parameter optimization emphasized the development of transferable parameters between the ethers of a given class. The ether models are shown to be in satisfactory agreement with both pure solvent and aqueous solvation properties, and the resulting parameters are transferable to test molecules. The presented force field will allow for simulation studies of ethers in condensed phase and provides a basis for ongoing developments in both additive and polarizable force fields for biological molecules.

Nucleic acid reactivity: challenges for next-generation semiempirical quantum models

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next-generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self-consistent density-functional tight-binding semiempirical models are evaluated against high-level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density-functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d-PhoT model is the most robust at predicting proton affinities. AM1/d-PhoT and DFTB3-3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear-scaling "modified divide-and-conquer" model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next-generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions.

Current status of protein force fields for molecular dynamics simulations

The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields.

Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods

Neglect of diatomic differential overlap (NDDO) and self-consistent density-functional tight-binding (SCC-DFTB) semiempirical models commonly employed in combined quantum mechanical/molecular mechanical simulations fail to adequately describe the deoxyribose and ribose sugar ring puckers. This failure limits the application of these methods to RNA and DNA systems. In this work, we provide benchmark ab initio gas-phase two-dimensional potential energy scans of the RNA and DNA sugar puckering. The benchmark calculations are compared with semiempirical models. Pucker corrections are introduced into the semiempirical models via B-spline interpolation of the potential energy difference surface relative to the benchmark data. The corrected semiempirical models are shown to well reproduce the ab initio puckering profiles. Furthermore, we demonstrate that the uncorrected semiempirical models do not usually produce a transition state between the A-form and B-form sugar puckers, but the ab initio transition state is reproduced when the B-spline correction is used.

Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin

All atom molecular dynamics simulations have been used to explore the atomic detail mechanism of guanidinium induced unfolding of the protein ubiquitin.

Concentration-dependent like-charge pairing of guanidinium ions and effect of guanidinium chloride on the structure and dynamics of water from all-atom molecular dynamics simulation

An all-atom molecular dynamics simulation shows concentration-dependent like-charge ion pairing of the guanidinium ion in an aqueous solution of guanidinium chloride. We have observed two types of like-charge ion pairing for guanidinium ions, namely, stacked ion pairs and solvent-separated ion pairs. Interestingly, both of these like-charge ion-pair formations are dependent on the concentration of guanidinium chloride in water. The probability of stacked like-charge ion-pair formation decreases, whereas, the probability of solvent-separated like-charge pairing increases as the concentration of guanidinium chloride increases, which is shown from radial distribution functions and is confirmed from the energy calculations. Besides like-charge ion-pair formation, we also investigated guanidinium chloride induced changes in water structure. Hydrogen-bond analysis indicates that guanidinium chloride does not alter the strict-hydrogen-bonding patterns of water, whereas, it breaks the bend-hydrogen bond and the non-hydrogen-bonding patterns. Tetrahedral order, nearest neighbor orientation, and distance distribution of water molecules around a probe water molecule show the extent of water structure distortion.

The conformation of a ribose derivative in aqueous solution: a neutron-scattering and molecular dynamics study

The structure of aqueous solutions of methyl β-D-ribofuranoside was investigated by coupling molecular dynamics (MD) simulations and neutron scattering measurements with isotopic substitution. Using a sample of the sugar isotopically-labeled at a single unique position, neutron scattering structure factors and radial distribution functions can be compared with MD simulations constrained to different conformations to determine which conformer best fits the experimental results. Three different simulations were performed with the methyl ether group of the sugar unconstrained and constrained in each of its staggered orientations. The results of the unconstrained simulation showed that the methyl ester group occupied predominantly the 300° position, which is in agreement with the diffraction experimental results. This result suggests that the molecular mechanics force field used in the simulation adequately describes the conformation of the 1-methyl ether group in the methyl β-D-ribofuranoside.

Modeling the conformational preference of the carbon-bonded covalent adduct formed upon exposure of 2'-deoxyguanosine to ochratoxin A

The conformational flexibility of the C8-linked guanine adduct formed from attachment of ochratoxin A (OTA) was analyzed using a systematic computational approach and models ranging from the nucleobase to the adducted DNA helix. A focus was placed on the influence of the C8-modification of 2'-deoxyguanosine (dG) on the preferred relative arrangement of the nucleobase and the C8-substituent and, more importantly, the anti/syn conformational preference with respect to the glycosidic bond. Although OTA is twisted with respect to the base in the nucleobase model, addition of the deoxyribose sugar induces a further twist and restricts rotation about the C-C linkage due to close contacts between OTA and the sugar. The nucleoside model preferentially adpots a syn orientation (by 10-20 kJ mol(-1) depending on the OTA conformation) due to the presence of an O5'-H···N3 interaction. However, when this hydrogen bond is eliminated, which better mimics the DNA environment, a small (<5 kJ mol(-1)) anti/syn energy difference is predicted. Inclusion of the 5'-monophosphate group leads to an up to 20 kJ mol(-1) preference for the syn (nucleotide) conformation due to stabilizing base-phosphate interactions involving the amino group of guanine. Nevertheless, MD simulations and free energy analysis predict that both syn- and anti-conformations of OTB-dG are equally stable in helices when paired opposite cytosine. These results indicate that the adduct will likely adopt a syn conformation in an isolated nucleoside and nucleotide, while a mixture of syn and anti conformations will be observed in DNA duplexes. Since the syn conformation could stabilize base mismatches upon DNA replication or Z-DNA structures with varied biological outcomes, future computational and experimental work should elucidate the consequences of the conformational preference of this potentially harmful DNA lesion.

The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

Knowledge of geometrical and physico-chemical properties of the sugar-phosphate backbone substantially contributes to the comprehension of the structural dynamics, function and evolution of nucleic acids. We provide a side by side overview of structural biology/bioinformatics, quantum chemical and molecular mechanical/simulation studies of the nucleic acids backbone. We highlight main features, advantages and limitations of these techniques, with a special emphasis given to their synergy. The present status of the research is then illustrated by selected examples which include classification of DNA and RNA backbone families, benchmark structure-energy quantum chemical calculations, parameterization of the dihedral space of simulation force fields, incorporation of arsenate into DNA, sugar-phosphate backbone self-cleavage in small RNA enzymes, and intricate geometries of the backbone in recurrent RNA building blocks. Although not apparent from the current literature showing limited overlaps between the QM, simulation and bioinformatics studies of the nucleic acids backbone, there in fact should be a major cooperative interaction between these three approaches in studies of the sugar-phosphate backbone.

Structural and functional consequences of phosphate-arsenate substitutions in selected nucleotides: DNA, RNA, and ATP

A recent finding of a bacterial strain (GFAJ-1) that can rely on arsenic instead of phosphorus raised the questions of if and how arsenate can replace phosphate in biomolecules that are essential to sustain cell life. Apart from questions related to chemical stability, there are those of the structural and functional consequences of phosphate-arsenate substitutions in vital nucleotides in GFAJ1-like cells. In this study we selected three types of molecules (ATP/ADP as energy source and replication regulation; DNA-protein complexes for DNA replication and transcription initiation; and a tRNA-protein complex and ribosome for protein synthesis) to computationally probe if arsenate nucleotides can retain the structural and functional features of phosphate nucleotides. Hydrolysis of adenosine triarsenate provides 2-3 kcal/mol less energy than ATP hydrolysis. Arsenate DNA/RNA interacts with proteins slightly less strongly than phosphate DNA/RNA, mainly due to the weaker electrostatic interactions of arsenate. We observed that the weaker arsenate RNA-protein interactions may hamper rRNA assembly into a functional ribosome. We further compared the experimental EXAFS spectra of the arsenic bacteria with theoretical EXAFS spectra for arsenate DNA and rRNA. Our results demonstrate that while it is possible that dried GFAJ-1 cells contain linear arsenate DNA, the arsenate 70S ribosome does not contribute to the main arsenate depository in the GFAJ-1 cell. Our study indicates that evolution has optimized the inter-relationship between proteins and DNA/RNA, which requires overall changes at the molecular and systems biology levels when replacing phosphate by arsenate.

Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity

Canonical duplex RNA assumes only the A-form conformation at the secondary structure level while, in contrast, a wide range of noncanonical, tertiary conformations of RNA occur. Here, we show how the 2'-hydroxyl controls RNA conformational properties. Quantum mechanical calculations reveal that the orientation of the 2'-hydroxyl significantly alters the intrinsic flexibility of the phosphodiester backbone, favoring the A-form in duplex RNA when it is in the base orientation and facilitating sampling of a wide range of noncanonical, tertiary structures when it is in the O3' orientation. Influencing the orientation of the 2'-hydroxyl are interactions with the environment, as evidenced by crystallographic survey data, indicating the 2'-hydroxyl to sample more of the O3' orientation in noncanonical RNA structures. These results indicate that the 2'-hydroxyl acts as a "switch", both limiting the conformation of RNA to the A-form at the secondary structure level and allowing RNA to sample a wide range of noncanonical tertiary conformations.

Two polymorphic residues account for the differences in DNA binding and transcriptional activation by NF-κB proteins encoded by naturally occurring alleles in Nematostella vectensis

The NF-κB family of transcription factors is activated in response to many environmental and biological stresses, and plays a key role in innate immunity across a broad evolutionary expanse of animals. A simple NF-κB pathway is present in the sea anemone Nematostella vectensis, an important model organism in the phylum Cnidaria. Nematostella has previously been shown to have two naturally occurring NF-κB alleles (Nv-NF-κB-C and Nv-NF-κB-S) that encode proteins with different DNA-binding and transactivation abilities. We show here that polymorphic residues 67 (Cys vs. Ser) and 269 (Ala vs. Glu) play complementary roles in determining the DNA-binding activity of the NF-κB proteins encoded by these two alleles and that residue 67 is primarily responsible for the difference in their transactivation ability. Phylogenetic analysis indicates that Nv-NF-κB-S is the derived allele, consistent with its restricted geographic distribution. These results define polymorphic residues that are important for the DNA-binding and transactivating activities of two naturally occurring variants of Nv-NF-κB. The implications for the appearance of the two Nv-NF-κB alleles in natural populations of sea anemones are discussed.

Intramolecular CH···O hydrogen bonds in the AI and BI DNA-like conformers of canonical nucleosides and their Watson-Crick pairs. Quantum chemical and AIM analysis

The aim of this work is to cast some light on the H-bonds in double-stranded DNA in its AI and BI forms. For this purpose, we have performed the MP2 and DFT quantum chemical calculations of the canonical nucleoside conformers, relative to the AI and BI DNA forms, and their Watson-Crick pairs, which were regarded as the simplest models of the double-stranded DNA. Based on the atoms-in-molecules analysis (AIM), five types of the CH···O hydrogen bonds, involving bases and sugar, were detected numerically from 1 to 3 per a conformer: C2'H···O5', C1'H···O2, C6H···O5', C8H···O5', and C6H···O4'. The energy values of H-bonds occupy the range of 2.3-5.6 kcal/mol, surely exceeding the kT value (0.62 kcal/mol). The nucleoside CH···O hydrogen bonds appeared to "survive" turns of bases against the sugar, sometimes in rather large ranges of the angle values, pertinent to certain conformations, which points out to the source of the DNA lability, necessary for the conformational adaptation in processes of its functioning. The calculation of the interactions in the dA·T nucleoside pair gives evidence, that additionally to the N6H···O4 and N1···N3H canonical H-bonds, between the bases adenine and thymine the third one (C2H···O2) is formed, which, though being rather weak (about 1 kcal/mol), satisfies the AIM criteria of H-bonding and may be classified as a true H-bond. The total energy of all the CH···O nontraditional intramolecular H-bonds in DNA nucleoside pairs appeared to be commensurable with the energy of H-bonds between the bases in Watson-Crick pairs, which implies their possible important role in the DNA shaping.

Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA

The ability of a dinucleoside monophosphate to mimic the conformation of B-DNA was tested using a combination of different phosphate models (anionic, neutral, counterion), environments (gas, water), and density functionals (B3LYP, MPWB1K, M06-2X) with the 6-31G(d,p) basis set. Three sequences (5'-GX(Py)-3', where X(Py) = T, U or (Br)U) were considered, which vary in the (natural or modified) 3' pyrimidine nucleobase (X(Py)). These bases were selected due to their presence in natural DNA, structural similarity to T and/or applications in radical-initiated anti-tumour therapies. The accuracy of each of the 54 model, method and sequence combinations was judged based on the ability to reproduce key structural features of natural B-DNA, including the stacked base-base orientation and important backbone torsion angles. B3LYP yields distorted or tilted relative base-base orientations, while many computational challenges were encountered for MPWB1K. Despite wide use in computational studies of DNA, the neutral (protonated) phosphate model could not consistently predict a stacked arrangement for all sequences. In contrast, stacked base-base arrangements were obtained for all sequences with M06-2X in conjunction with both the anionic and (sodium) counterion phosphate models. However, comparison of calculated and experimental backbone conformations reveals the charge-neutralized counterion phosphate model best mimics B-DNA. Structures optimized with implicit solvent (water) are comparable to gas-phase structures, which suggests similar results should be obtained in an environment of intermediate polarity. We recommend the use of either gas-phase or water M06-2X optimizations with the counterion phosphate model to study the structure and/or reactivity of natural or modified DNA with a dinucleoside monophosphate.

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA

Here, we present an update of the CHARMM27 all-atom additive force field for nucleic acids that improves the treatment of RNA molecules. The original CHARMM27 force field parameters exhibit enhanced Watson-Crick base pair opening which is not consistent with experiment, whereas analysis of molecular dynamics (MD) simulations show the 2'-hydroxyl moiety to almost exclusively sample the O3' orientation. Quantum mechanical (QM) studies of RNA related model compounds indicate the energy minimum associated with the O3' orientation to be too favorable, consistent with the MD results. Optimization of the dihedral parameters dictating the energy of the 2'-hydroxyl proton targeting the QM data yielded several parameter sets, which sample both the base and O3' orientations of the 2'-hydroxyl to varying degrees. Selection of the final dihedral parameters was based on reproduction of hydration behavior as related to a survey of crystallographic data and better agreement with experimental NMR J-coupling values. Application of the model, designated CHARMM36, to a collection of canonical and noncanonical RNA molecules reveals overall improved agreement with a range of experimental observables as compared to CHARMM27. The results also indicate the sensitivity of the conformational heterogeneity of RNA to the orientation of the 2'-hydroxyl moiety and support a model whereby the 2'-hydroxyl can enhance the probability of conformational transitions in RNA.

Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations

Deoxyribonucleic acid (DNA) is composed of five major elements carbon, hydrogen, nitrogen, oxygen, and phosphorus. The substitution of any of these elements in DNA would be anticipated to have major biological implications. However, recent studies have suggested that the substitution of arsenic into DNA (As-DNA) in bacteria may be possible. To help evaluate this possibility, ab initio quantum mechanical calculations are used to show that arsenodiester and phosphodiester linkages have similar geometric and conformational properties. Based on these results, it is suggested that the As-DNA will have similar conformational properties to phosphorus-based DNA, including the maintenance of base stacking.

Selection of G-quadruplex folding topology with LNA-modified human telomeric sequences in K+ solution

G-rich nucleic acid oligomers can form G-quadruplexes built by G-tetrads stacked upon each other. Depending on the nucleotide sequence, G-quadruplexes fold mainly with two topologies: parallel, in which all G-tracts are oriented parallel to each other, or antiparallel, in which one or more G-tracts are oriented antiparallel to the other G-tracts. In the former topology, all glycosidic bond angles conform to anti conformations, while in the latter topology they adopt both syn and anti conformations. It is of interest to understand the molecular forces that govern G-quadruplex folding. Here, we approach this problem by examining the impact of LNA (locked nucleic acid) modifications on the folding topology of the dimeric model system of the human telomere sequence. In solution, this DNA G-quadruplex forms a mixture of G-quadruplexes with antiparallel and parallel topologies. Using CD and NMR spectroscopies, we show that LNA incorporations can modulate this equilibrium in a rational manner and we establish a relationship between incorporation of LNA nucleotides in syn and/or anti positions and the shift of the equilibrium to obtain exclusively the parallel G-quadruplex. The change in topology is driven by a combination of the C3'-endo puckering of LNA nucleotides and their preference for the anti glycosidic conformation. In addition, the parallel LNA-modified G-quadruplexes are thermally stabilised by about 11 °C relative to their DNA counterparts.

Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?

In this feature article, we provide a side-by-side introduction for two research fields: quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics. Our main aim is to demonstrate that these research areas, while largely separated in contemporary literature, have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids. We identify research questions amenable to the combined application of modern ab initio methods and bioinformatics analysis of experimental structures while also assessing the limitations of these approaches. The ultimate aim is to attain valuable physicochemical insights regarding the nature of the fundamental molecular interactions and how they shape RNA structures, dynamics, function, and evolution.

Modeling the dissociative hydrolysis of the natural DNA nucleosides

Two-dimensional PCM-B3LYP/6-31+G(d) potential energy surfaces for the hydrolysis of the four natural 2'-deoxyribonucleosides (2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and thymidine) are characterized using a model that includes both implicit (bulk) solvent effects and (three or four) explicit water molecules in the optimization routine. For the first time, the experimentally predicted dissociative (S(N)1) mechanism is found to be favored over the synchronous (S(N)2) pathway for all nucleosides studied. Due to the success of our model in stabilizing the charge-separated intermediates along the S(N)1 pathway, it is proposed that the new model presented here is the smallest system capable of generating the experimentally predicted oxacarbenium cation intermediate. We therefore stress that dissociative mechanisms should be studied with methodologies that account for the (bulk) environment in the optimization routine, where these effects are often only included as a correction to the energy in the current literature. In addition to accounting for charge stabilization through implicit solvation, nucleophile activation and leaving group stabilization should also be explicitly introduced into the model to further stabilize the system. Our work also emphasizes the importance of studying the Gibbs surface, which in some cases provides a better description of chemically important regions of the reaction surface or changes the calculated trend in the magnitude of dissociative barriers. In addition, it is proposed that the methodology presented in this study can be used to calculate uncatalyzed deglycosylation barriers for a range of DNA nucleosides, which when compared to the corresponding enzyme-catalyzed reactions, will allow the prediction of the rate enhancement (barrier reduction) due to the enzyme.

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems.

A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm

The S-adenosylmethionine-1 (SAM-I) riboswitch mediates expression of proteins involved in sulfur metabolism via formation of alternative conformations in response to binding by SAM. Models for kinetic trapping of the RNA in the bound conformation require annealing of nonadjacent mRNA segments during a transcriptional pause. The entropic cost required to bring nonadjacent segments together should slow the folding process. To address this paradox, we performed molecular dynamics simulations on the SAM-I riboswitch aptamer domain with and without SAM, starting with the X-ray coordinates of the SAM-bound RNA. Individual trajectories are 200 ns, among the longest reported for an RNA of this size. We applied principle component analysis (PCA) to explore the global dynamics differences between these two trajectories. We observed a conformational switch between a stacked and nonstacked state of a nonadjacent dinucleotide in the presence of SAM. In the absence of SAM the coordination between a bound magnesium ion and the phosphate of A9, one of the nucleotides involved in the dinucleotide stack, is destabilized. An electrostatic potential map reveals a 'hot spot' at the Mg binding site in the presence of SAM. These results suggest that SAM binding helps to position J1/2 in a manner that is favorable for P1 helix formation.

Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling

Conformational dynamics play a key role in the properties and functions of proteins and nucleic acids. Heteronuclear NMR spin relaxation is a uniquely powerful site-specific probe of dynamics in proteins and has found increasing applications to nucleotide base side chains and anomeric sites in RNA. Applications to the nucleic acid ribose backbone, however, have been hampered by strong magnetic coupling among ring carbons in uniformly 13C-labeled samples. In this work, we apply a recently developed, metabolically directed isotope labeling scheme that places 13C with high efficiency and specificity at the nucleotide ribose C2' and C4' sites. We take advantage of this scheme to explore backbone dynamics in the well-studied GCAA RNA tetraloop. Using a combination of CPMG (Carr-Purcell-Meiboom-Gill) and R(1rho) relaxation dispersion spectroscopy to explore exchange processes on the microsecond to millisecond time scale, we find an extensive pattern of dynamic transitions connecting a set of relatively well-defined conformations. In many cases, the observed transitions appear to be linked to C3'-endo/C2'-endo sugar pucker transitions of the corresponding nucleotides, and may also be correlated across multiple nucleotides within the tetraloop. These results demonstrate the power of NMR spin relaxation based on alternate-site isotope labeling to open a new window into the dynamic properties of ribose backbone groups in RNA.

Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA

Canonical forms of duplex DNA are known to sample well-defined regions of the alpha, beta, gamma, epsilon, and zeta dihedral angles that define the conformation of the phosphodiester linkage in the backbone of oligonucleotides. While extensive studies of base composition and base sequence dependent effects on the sampling of the A, B1, and BII canonical forms of duplex DNA have been presented, our understanding of the intrinsic contribution of the five dihedral degrees of freedom associated with the phosphodiester linkage to the conformational properties of duplex DNA is still limited. To better understand this contribution, ab initio quantum mechanical (QM) calculations were performed on a model compound representative of the phosphodiester backbone to systematically sample the energetics about the alpha, beta, gamma, epsilon, and zeta dihedral angles relevant to the conformational properties of duplex DNA. Low-energy regions of dihedral potential energy surfaces are shown to correlate with the regions of dihedral space sampled in experimental crystal structures of the canonical forms of DNA, validating the utility of the model compound and emphasizing the contribution of the intrinsic mechanical properties of the phosphodiester backbone to the conformational properties of duplex DNA. Those contributions include the relative stability of the A, BI, and BII conformations of duplex DNA, where the gas-phase energetics favor the BI form over the A and BII forms. In addition, subtle features of the potential energy surfaces mimic changes in the probability distributions of alpha, beta, gamma, epsilon, and zeta dihedral angles in A, BI, and BII forms of DNA as well as with conformations sampled in single-stranded DNA. These results show that the intrinsic mechanical properties of the phosphodiester backbone make a significant contribution to conformational properties of duplex DNA observed in the condensed phase and allow for the prediction that single-stranded DNA primarily samples folded conformations thereby possibly lowering the entropic barrier to the formation of duplex DNA.

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids

The anionic sugar-phosphate backbone of nucleic acids substantially contributes to their structural flexibility. To model nucleic acid structure and dynamics correctly, the potentially sampled substates of the sugar-phosphate backbone must be properly described. However, because of the complexity of the electronic distribution in the nucleic acid backbone, its representation by classical force fields is very challenging. In this work, the three-dimensional potential energy surfaces with two independent variables corresponding to rotations around the alpha and gamma backbone torsions are studied by means of high-level ab initio methods (B3LYP/6-31+G*, MP2/6-31+G*, and MP2 complete basis set limit levels). The ability of the AMBER ff99 [Wang, J. M.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074] and parmbsc0 [Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E.; Laughten, C. A.; Orozco, M. Biophys. J. 2007, 92, 3817-3829] force fields to describe the various alpha/gamma conformations of the DNA backbone accurately is assessed by comparing the results with those of ab initio quantum chemical calculations. Two model systems differing in structural complexity were used to describe the alpha/gamma energetics. The simpler one, SPM, consisting of a sugar and methyl group linked through a phosphodiester bond was used to determine higher-order correlation effects covered by the CCSD(T) method. The second, more complex model system, SPSOM, includes two deoxyribose residues (without the bases) connected via a phosphodiester bond. It has been shown by means of a natural bond orbital analysis that the SPSOM model provides a more realistic representation of the hyperconjugation network along the C5'-O5'-P-O3'-C3' linkage. However, we have also shown that quantum mechanical investigations of this model system are nontrivial because of the complexity of the SPSOM conformational space. A comparison of the ab initio data with the ff99 potential energy surface clearly reveals an incorrect ff99 force-field description in the regions where the gamma torsion is in the trans conformation. An explanation is proposed for why the alpha/gamma flips are eliminated so successfully when the parmbsc0 force-field modification is used.

Analyzing the flexibility of RNA structures by constraint counting

RNA requires conformational dynamics to undergo its diverse functional roles. Here, a new topological network representation of RNA structures is presented that allows analyzing RNA flexibility/rigidity based on constraint counting. The method extends the FIRST approach, which identifies flexible and rigid regions in atomic detail in a single, static, three-dimensional molecular framework. Initially, the network rigidity of a canonical A-form RNA is analyzed by counting on constraints of network elements of increasing size. These considerations demonstrate that it is the inclusion of hydrophobic contacts into the RNA topological network that is crucial for an accurate flexibility prediction. The counting also explains why a protein-based parameterization results in overly rigid RNA structures. The new network representation is then validated on a tRNA(ASP) structure and all NMR-derived ensembles of RNA structures currently available in the Protein Data Bank (with chain length >/=40). The flexibility predictions demonstrate good agreement with experimental mobility data, and the results are superior compared to predictions based on two previously used network representations. Encouragingly, this holds for flexibility predictions as well as mobility predictions obtained by constrained geometric simulations on these networks. Potential applications of the approach to analyzing the flexibility of DNA and RNA/protein complexes are discussed.

Effect of a water molecule on the sugar puckering of uridine, 2'-deoxyuridine, and 2'-O-methyl uridine inserted in duplexes

We used high-level quantum mechanical calculations to determine the pucker (north type or south type) of various compounds: uridine, 2'-deoxyuridine, and 2'-O-methyl uridine. Although the dihedrals of the backbone are set close to their experimental values in double-stranded nucleic acids, calculations using density functional theory show that, in vacuo or in a continuum mimicking the dielectric properties of water, the south puckering conformations of uridine is favored. This contrasts with experimental data: most ribonucleosides inserted into a duplex have the north puckering. We show here that the north puckering is favored when an explicit water molecule is introduced into the calculation. The orientations of the 2' group and of the water molecule have implications for the prevalence of the north puckering. We studied several orientations of the water molecule binding uracil O2 and the 2' group and estimated the energy barriers in the path between the north-to-south conformations. The north puckering is more favored in 2'-OH than in 2'-OCH3 compounds in the presence of the explicit water molecule.

Engineering the quadruplex fold: nucleoside conformation determines both folding topology and molecularity in guanine quadruplexes

Nucleic acid quadruplexes, based on the guanine quartet, can arise from one or several strands, depending on the sequence. Those consisting of a single strand are usually folded in one of two principal topologies: antiparallel, in which all or half of the guanine stretches are antiparallel to each other, or parallel, in which all guanine stretches are parallel to each other. In the latter, all guanine nucleosides possess the anti conformation about the glycosidic bond, while in the former, half possess the anti conformation, and half possess the syn conformation. While antiparallel is the more common fold, examples of biologically important, parallel quadruplexes are becoming increasingly common. Thus, it is of interest to understand the forces that determine the quadruplex fold. Here, we examine the influence of individual nucleoside conformation on the overall folding topology by selective substitution of rG for dG. We can reverse the antiparallel fold of the thrombin binding aptamer (TBA) by this approach. Additionally, this substitution converts a unimolecular quadruplex into a bimolecular one. Similar reverse substitutions in the all-RNA analogue of TBA result in a parallel to antiparallel change in topology and alter the strand configuration from bimolecular to unimolecular. On the basis of the specific substitutions made, we conclude that the strong preference of guanine ribonucleosides for the anti conformation is the driving force for the change in topology. These results demonstrate how conformational properties of guanine nucleosides govern not only the quadruplex folding topology but also impact quadruplex molecularity and provide a means to control these properties.

Toward a full characterization of nucleic acid components in aqueous solution: simulations of nucleosides

The eight nucleoside constituents of nucleic acids were simulated for 50 ns in explicit water with molecular dynamics. This provides equilibrium populations of the torsional degrees of freedom, their kinetics of interconversion, their couplings, and how they are influenced by water. This is important, given that a full and quantitative characterization of the nucleosides in aqueous solution by experimental means has been elusive, despite immense efforts in that direction. It is with the anti/syn equilibrium that the simulations are most complementary to experiment, by accessing directly the influence of the sugar type, sugar pucker, and base on the anti/syn populations. The glycosidic torsion distributions in the anti conformation are strongly affected by water and depart from the corresponding X-ray modal values and the associated energy minima in vacuo. Water also preferentially stabilizes some sugar conformations, showing that potential energies in vacuo are not sufficient to understand the nucleosides. Deoxythymidine (but not other pyrimidines) significantly populates the syn orientation. Guanine favors the syn orientation more than adenine. The ribose favors the syn orientation significantly more than the deoxyribose. The NORTH pucker coexists with the syn conformers. A hydrogen bond is frequently formed between the 5'-OH group and the syn bases, despite competition by water. The rate of the anti/syn transitions with purines is on the nanosecond time scale, confirming a long held assumption underpinning the interpretation of ultrasonic relaxation studies. Therefore, our knowledge of the structure and dynamics of nucleosides in solvent is only limited by the accuracy of the potential used to simulate them, and it is shown that such simulations provide a distinct and unique test of nucleic acid force fields. This confirmed that the widely distributed CHARMM27 force field is, overall, well-balanced with a particularly good representation of the ribose. Specific improvements, however, are suggested for the deoxyribose and torsion gamma.

Comprehensive Conformational Analysis of the Nucleoside Analogue 2‘-β-Deoxy-6-azacytidine by DFT and MP2 Calculations

A comprehensive conformational analysis of isolated 2'-beta-deoxy-6-azacytidine (d6AC), an analogue of therapeutically active 6-azacytidine (6AC), has been performed by means of ab initio calculations at the MP2/6-311++G(2df,pd)//DFT B3LYP/6-31G(d,p) level of theory. Among the 81 conformers located within a 7.83 kcal/mol Gibbs energy range at T = 298.15 K, 38 contain syn-oriented bases with respect to 2'-deoxyribose; the other conformers include anti-oriented bases. Energetic analysis of these conformers shows that conformational equilibrium of isolated d6AC at T = 298.15 K is shifted to syn conformation with a syn/anti ratio estimated as 61.4%:38.6%. As far as the sugar conformation is concerned, 40 conformers contain north (N) (with 0.3 degrees < or = P < or = 40.1 degrees), and the rest possess south (S) (with 157.1 degrees < or = P < or = 207.0 degrees) puckers, where P is the pseudorotational angle of the furanose ring. The S/N occupancy ratio is estimated as 80.2%:19.8% (T = 298.15 K). The two most stable conformers are energetically quasidegenerate and correspond to both C2'-endo/syn conformers differing only by orientation of the O3'H hydroxyl group. They are both stabilized by means of similar intramolecular H-bonds, i.e., O5'H...O2, C2'H2...O2, and C2'H2...O5'. As examined by AIM criteria, from 1 to 3 H-bonds per conformer were identified among 13 possible interactions: O5'H...O2, O5'H...N6, O3'H...O5', O5'H...O3', C1'H...O2, C2'H2...O2, C2'H2...O5', C3'H...O2, C3'H...N6, C5'H1...O2, C5'H2...O2, C5'H1...N6, and C5'H2...N6. The biological effect of d6AC is conceived as an inhibition of replicative DNA polymerase caused by an unusual orientation of the sugar residue against the base in the only A form DNA-like conformer.

Are Isolated Nucleic Acid Bases Really Planar? A Car−Parrinello Molecular Dynamics Study

Car-Parrinello molecular dynamics simulations of the flexibility of isolated DNA bases have been carried out. The comparison of lowest ring out-of-plane vibrations calculated by using MP2/cc-pvdz and BLYP/PW methods reveals that the DFT method with the plane wave basis set reasonably reproduces out-of-plane deformability of the pyrimidine ring in nucleic acid bases and could be used for reliable modeling of conformational flexibility of nucleobases. The conformational phase space of pyrimidine rings in thymine, cytosine, guanine, and adenine has been investigated by using the ab initio Car-Parrinello molecular dynamics method. It is demonstrated that all nucleic acid bases are highly flexible molecules and possess a nonplanar effective conformation of the pyrimidine ring despite the fact that the planar geometry corresponds to a minimum on the potential energy surface. The population of the planar geometry of the pyrimidine ring does not exceed 30%. Among the nonplanar conformations of the pyrimidine rings, the boat-like and half-chair conformations are the most populated.