The Effect of Metal Binding to the N7 Site of Purine Nucleotides on Their Structure, Energy, and Involvement in Base Pairing

A refreshing approach to understanding the action on DNA of vanadium (IV) and (V) complexes derived from the anticancer VCp2Cl2

A computational study based on derivatives of the anticancer VCp2Cl2 compound and their interaction with representative models of deoxyribonucleic acid (DNA) is presented. The derivatives were obtained by substituting the cyclopentadienes of VCp2Cl2 with H2O, NH3, OH-, Cl-, O2- and C2O42- ligands. The oxidation states IV and V of vanadium were considered, so a total of 20 derivative complexes are included. The complexes interactions with DNA were studied using two different models, the first model considers the interactions of the complexes with the pair Guanine-Cytosine (G-C) and the second involves the interaction of the complexes with adjacent pairs, that is, d(GG). This study compares methodologies based on density functional theory with coupled cluster like calculations (DLPNO-CCSD(T)), the gold standard of electronic structure methods. Furthermore, the change in the electron density of the hydrogen bonds that keep bonded the G-C pair and d(GG) pairs, due to the presence of vanadium (IV) and (V) complexes is rationalize. To this aim, quantities obtained from the topology of the electron densities are inspected, particularly the value of the electron density at the hydrogen bond critical points. The approach allowed to identify vanadium complexes that lead to significant changes in the hydrogen bonds indicated above, a key aspect in the understanding, development, and proposal of mechanisms of action between metal complexes and DNA.

Prediction and Control in DNA Nanotechnology

DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.

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.

A prebiotic basis for ATP as the universal energy currency

ATP is universally conserved as the principal energy currency in cells, driving metabolism through phosphorylation and condensation reactions. Such deep conservation suggests that ATP arose at an early stage of biochemical evolution. Yet purine synthesis requires 6 phosphorylation steps linked to ATP hydrolysis. This autocatalytic requirement for ATP to synthesize ATP implies the need for an earlier prebiotic ATP equivalent, which could drive protometabolism before purine synthesis. Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleoside triphosphates, remains a mystery. Here, we show that the deep conservation of ATP might reflect its prebiotic chemistry in relation to another universally conserved intermediate, acetyl phosphate (AcP), which bridges between thioester and phosphate metabolism by linking acetyl CoA to the substrate-level phosphorylation of ADP. We confirm earlier results showing that AcP can phosphorylate ADP to ATP at nearly 20% yield in water in the presence of Fe3+ ions. We then show that Fe3+ and AcP are surprisingly favoured. A wide range of prebiotically relevant ions and minerals failed to catalyse ADP phosphorylation. From a panel of prebiotic phosphorylating agents, only AcP, and to a lesser extent carbamoyl phosphate, showed any significant phosphorylating potential. Critically, AcP did not phosphorylate any other nucleoside diphosphate. We use these data, reaction kinetics, and molecular dynamic simulations to infer a possible mechanism. Our findings might suggest that the reason ATP is universally conserved across life is that its formation is chemically favoured in aqueous solution under mild prebiotic conditions.

Gas-Phase Internal Ribose Residue Loss from Mg-ATP and Mg-ADP Complexes: Experimental and Theoretical Evidence for Phosphate-Mg-Adenine Interaction

Gas-phase decompositions of magnesium complexes with adenosine-5'-triphosphate (ATP) and adenosine-5'-diphosphate (ADP) were studied by using electrospray ionization-collision-induced dissociation-tandem mass spectrometry, in the negative ion mode. The loss of internal ribose residue was observed and was found to occur directly from the [ADP-3H+Mg]^- ion. The occurrence of this process indicates the presence of a strong phosphate-Mg-adenine interaction. The performed quantum mechanics calculations confirmed the occurrence of this interaction in the [ADP-3H+Mg]^- ion, namely the presence of Mg-N7 bond and hydrogen bond between the phosphate oxygen atom and amino group. Although the finding concerns the gas phase, it indicates that phosphate-Mg-adenine interaction may be also of importance for biological processes. The loss of an internal ribose residue was also observed for calcium and zinc complexes with ATP/ADP as well as for magnesium complexes with guanosine-5'-triphosphate (GTP) or guanosine-5'-diphosphate (GDP). Therefore, it is reasonable to conclude that the presence of the phosphate-metal-nucleobase interaction is a feature of gas phase [NDP-3H+metal]^- ion (NDP, nucleoside-5'-diphosphate) and may also be important for biological processes.

Guanine Tautomerism in Ionic Complexes with Ag+ Investigated by IRMPD Spectroscopy and Mass Spectrometry

In this paper, we present the IRMPD spectra of three ionic complexes between guanine (G) and silver (Ag⁺): [GAg-H₂O]⁺, [GAgG]⁺ produced in the electrospray ionization source of the mass spectrometer, and [GAg]⁺ produced by collision induced dissociation of the [GAgG]⁺ complex. On the basis of the comparison of theoretically calculated IR spectra, we show that there are two isomers of each complex containing two different keto-amino (KA) tautomers of G (GKA(1,9) and GKA(1,7)). The observed isomers are the most stable structures in aqueous solution, and their experimentally estimated relative populations are in better agreement with the calculated relative populations in solution than in the gas phase, both at 298 K. We concluded that these observations suggest that GKA(1,9) and GKA(1,7) coexist in solution according to previous theoretical reports (Colominas, C.; et al. J. Am. Chem. Soc. 1996, 118, 6811). We were unable to find any evidence of the presence of the GEA(9), GKA(3,7), GKA(3,9), or GKA(7,9), whose relative stabilities in solution are strongly dependent on the theoretical method used to account for the solvent effect (Hanus, M.; et al. J. Am. Chem. Soc. 2003, 125, 7678).

Contributions and competition of Mg2+ and K+ in folding and stabilization of the Twister ribozyme

Native folded and compact intermediate states of RNA typically involve tertiary structures in the presence of divalent ions such as Mg²⁺ in a background of monovalent ions. In a recent study, we have shown how the presence of Mg²⁺ impacts the transition from partially unfolded to folded states through a "push-pull" mechanism where the ion both favors and disfavors the sampling of specific phosphate-phosphate interactions. To further understand the ion atmosphere of RNA in folded and partially folded states results from atomistic umbrella sampling and oscillating chemical potential grand canonical Monte Carlo/molecular dynamics (GCMC/MD) simulations are used to obtain atomic-level details of the distributions of Mg²⁺ and K⁺ ions around Twister RNA. Results show the presence of 100 mM Mg²⁺ to lead to increased charge neutralization over that predicted by counterion condensation theory. Upon going from partially unfolded to folded states, overall charge neutralization increases at all studied ion concentrations that, while associated with an increase in the number of direct ion-phosphate interactions, is fully accounted for by the monovalent K⁺ ions. Furthermore, K⁺ preferentially interacts with purine N7 atoms of helical regions in partially unfolded states, thereby potentially stabilizing the helical regions. Thus, both secondary helical structures and formation of tertiary structures leads to increased counterion condensation, thereby stabilizing those structural features of Twister. Notably, it is shown that K⁺ can act as a surrogate for Mg²⁺ by participating in specific interactions with nonsequential phosphate pairs that occur in the folded state, explaining the ability of Twister to self-cleave at submillimolar Mg²⁺ concentrations.

Synthesis of a soluble adenine-functionalized polythiophene through direct arylation polymerization and its fluorescence responsive behavior

An adenine-functionalized polythiophene is synthesized via direct arylation polymerization using Boc-protection to overcome catalyst deactivation. The resulting copolymer is highly soluble and shows reversible fluorescence quenching.

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.

Consequences of Mg2+ binding on the geometry and stability of RNA base pairs

Quantum chemical calculations reveal the role of magnesium in stabilizing the geometries of intrinsically unstable RNA base pairs.

Mg2+ ions: do they bind to nucleobase nitrogens?

Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for divalent metals. Further, Mg2+ coordination to N7 has been implied in several ribozyme catalytic mechanisms. We report that Mg2+ assigned near imine nitrogens derive mostly from poor interpretations of electron density patterns and are most often misidentified Na+, K+, NH4+ ions, water molecules or spurious density peaks. Consequently, apart from few documented exceptions, Mg2+ ions do not bind to N7 atoms. Without much of a surprise, Mn2+, Zn2+ and Cd2+, which have a higher affinity for nitrogens, may contact N7 atoms when present in crystallization buffers. In this respect, we describe for the first time a potential Zn2+ ribosomal binding site involving two purine N7 atoms. Further, we provide a set of guidelines to help in the assignment of Mg2+ in crystallographic, cryo-EM, NMR and model building practices and discuss implications of our findings related to ion substitution experiments.

Multisite ion model in concentrated solutions of divalent cations (MgCl2 and CaCl2): osmotic pressure calculations

Accurate force field parameters for ions are essential for meaningful simulation studies of proteins and nucleic acids. Currently accepted models of ions, especially for divalent ions, do not necessarily reproduce the right physiological behavior of Ca(2+) and Mg(2+) ions. Saxena and Sept (J. Chem. Theor. Comput. 2013, 9, 3538-3542) described a model, called the multisite-ion model, where instead of treating the ions as an isolated sphere, the charge was split into multiple sites with partial charge. This model provided accurate inner shell coordination of the ion with biomolecules and predicted better free energies for proteins and nucleic acids. Here, we expand and refine the multisite model to describe the behavior of divalent ions in concentrated MgCl2 and CaCl2 electrolyte solutions, eliminating the unusual ion-ion pairing and clustering of ions which occurred in the original model. We calibrate and improve the parameters of the multisite model by matching the osmotic pressure of concentrated solutions of MgCl2 to the experimental values and then use these parameters to test the behavior of CaCl2 solutions. We find that the concentrated solutions of both divalent ions exhibit the experimentally observed behavior with correct osmotic pressure, the presence of solvent separated ion pairs instead of direct ion pairs, and no aggregation of ions. The improved multisite model for (Mg(2+) and Ca(2+)) can be used in classical simulations of biomolecules at physiologically relevant salt concentrations.

Assessing the importance of proton transfer reactions in DNA

Although engineered by millions of years of evolution, the cellular machinery is not flawless, and errors regularly appear during DNA replication. The subsequent alteration of the stored genetic message results in a mutation and might be the starting point of important health disorders. The question therefore is what causes DNA mutations? All living organisms are constantly exposed to a number of external agents such as free radicals and to radiation, which may lead to induced mutations. There are also mutations happening without invoking the action of any exogenous element, the so-called spontaneous mutations. The former can be partially controlled by avoiding exposure to high-risk environments, while the latter are more intriguing because their origin is unclear and difficult to determine. As noted by Watson and Crick when they first discovered the DNA structure, the correct replication of DNA rests on the assumption that the base pairs remain in their most stable, canonical form. However, protons along the interbase hydrogen-bond network are not static entities. They can in fact interchange their positions in DNA bases through proton transfer (PT) reactions before strands unwind, giving rise to noncanonical structures defined as rare tautomers. The importance of these rare tautomers was also cleverly anticipated by Watson and Crick and some years later claimed by Löwdin to be a source of spontaneous mutations. In Watson and Crick's words: "It would be of interest to know the precise difference in free energy between the various tautomeric forms under physiological conditions." Unfortunately, rare tautomeric forms are very difficult to detect, so no direct and accurate free energy measure has been discerned. In contrast, theoretical chemistry is making good progress toward the quantification of PT reactions in DNA and their biological consequences. This Account touches upon the theoretical studies devoted to appraising the importance of rare tautomers as promoters of spontaneous mutations. We focus in particular on the crucial role played by the biological environment on DNA stability. It has now been demonstrated that valuable macroscopic predictions require not only highly accurate theories but also refined chemical models. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations performed on short but complete DNA sequence fragments emerge in this context as the most adequate tools. In addition, these methods can be used to quantify the effect of different external agents on the PT tautomeric equilibria and, eventually, to conveniently handle them. This is the case for the possible alteration of the naturally observed mutation rate by exposure to intense electric fields. Theoretical predictions envision in this respect promising applications of ultrashort electric pulses in medicine to selectively modify the mutated/canonical ratio in DNA.

Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson-Boltzmann approach

The ion atmosphere created by monovalent (Na(+) ) or divalent (Mg(2+) ) cations surrounding a B-form DNA duplex were examined using atomistic molecular dynamics (MD) simulations and the nonlinear Poisson-Boltzmann (PB) equation. The ion distributions predicted by the two methods were compared using plots of radial and two-dimensional cation concentrations and by calculating the total number of cations and net solution charge surrounding the DNA. Na(+) ion distributions near the DNA were more diffuse in PB calculations than in corresponding MD simulations, with PB calculations predicting lower concentrations near DNA groove sites and phosphate groups and a higher concentration in the region between these locations. Other than this difference, the Na(+) distributions generated by the two methods largely agreed, as both predicted similar locations of high Na(+) concentration and nearly identical values of the number of cations and the net solution charge at all distances from the DNA. In contrast, there was greater disagreement between the two methods for Mg(2+) cation concentration profiles, as both the locations and magnitudes of peaks in Mg(2+) concentration were different. Despite experimental and simulation observations that Mg(2+) typically maintains its first solvation shell when interacting with nucleic acids, modeling Mg(2+) as an unsolvated ion during PB calculations improved the agreement of the Mg(2+) ion atmosphere predicted by the two methods and allowed for values of the number of bound ions and net solution charge surrounding the DNA from PB calculations that approached the values observed in MD simulations.

Hydrogen-bonded proton transfer in the hydrated adenine–thymine anion

The proton transfer processes of microhydrated adenine–thymine anions are studied using density functional theory with the B3LYP method and DZP++ basis set. The microhydration effects on the geometrical structures, adsorption site, and the proton transfer reaction of the adenine–thymine anion are investigated. The site N10 atom of the adenine moiety has a larger proton affinity than the site O24 atom of thymine, which facilitates the proton H26 transfers from the N25 site of thymine to the N10 site of adenine. Therefore, the first single-proton transfer pathway (SPT1) is found for the all of the monohydrated adenine–thymine anions (AN4T)−·H2O, (AN13T)−·H2O, (ATO24)−·H2O, and (ATO28)−·H2O and tetrahydrated adenine–thymine anions (AT)−·4H2O. The proton H9 at the N7 site of adenine is also found to transfer to the O24 site of thymine for (AN4T)−·H2O and (AN13T)−·H2O in the gas phase. The double-proton transferred pathway is found when one water molecule interacts with the O28 atom of thymine. The reactant structures before the proton transfer are more stable than the product structures, and the structural changes mainly occur in thymine. The reaction energies of the microhydrated adenine–thymine anion in the gas phase and in the aqueous environment predict that the proton transfer process of the microhydrated adenine–thymine anion are more favorable in the gas phase than in aqueous solution.

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

In this review primarily written for non-experts we explain basic methodological aspects and interpretation of modern quantum chemical (QM) computations applied to nucleic acids. We introduce current reference QM computations on small model systems consisting of dozens of atoms. Then we comment on recent advance of fast and accurate dispersion-corrected density functional theory methods, which will allow computations of small but complete nucleic acids building blocks in the near future. The qualitative difference between QM and molecular mechanics (MM, force field) computations is discussed. We also explain relation of QM and molecular simulation computations to experiments.

Mechanism of the cis-[Pt(1R,2R-DACH)(H2O)2]2+ intrastrand binding to the double-stranded (pGpG)·(CpC) dinucleotide in aqueous solution: a computational DFT study

A mechanism of the intrastrand 1,2-cross-link formation between the double-stranded pGpG·CpC dinucleotide (ds(pGpG)) and fully aquated oxaliplatin cis-[Pt(DACH)(H2O)2](2+) (DACH = cyclohexane-1R,2R-diamine) is presented. All structures of the reaction pathways including the transition states (TSs) were fully optimized in water solvent using DFT methodology with dispersion corrections. Both 5' → 3' and 3' → 5' binding directions were considered. In the first step there is a slight kinetic preference for 5'-guanine (5'G) monoadduct formation with an activation Gibbs free energy of 18.7 kcal/mol since the N7 center of the 5'G base is fully exposed to the solvent. On the other hand, the N7 atom of 3'-guanine (3'G) is sterically shielded by 5'G. The lowest energy path for formation of the 3'G monoadduct with an activation barrier of 19.3 kcal/mol is connected with a disruption of the 'DNA-like' structure of ds(pGpG). Monoadduct formation is the rate-determining process. The second step, chelate formation, is kinetically preferred in the 3' → 5' direction. The whole process of the platination is exergonic by up to -18.8 kcal/mol. Structural changes of ds(pGpG), charge transfer effects, and the influence of platination on the G·C base pair interaction strengths are also discussed in detail.

Ionic microenvironmental effects on triplex DNA stabilization: cationic counterion effects on poly(dT)·poly(dA)·poly(dT)

The structure and conformation of nucleic acids are influenced by metal ions, polyamines, and the microenvironment. In poly(purine) · poly(pyrimidine) sequences, triplex DNA formation is facilitated by metal ions, polyamines and other ligands. We studied the effects of mono- and di-valent metal ions, and ammonium salts on the stability of triple- and double-stranded structures formed from poly(dA) and poly(dT) by measuring their respective melting temperatures. In the presence of metal ions, the absorbance versus temperature profile showed two transitions: Tm1 for triplex to duplex and single stranded DNA, and Tm2 for duplex DNA melting to single stranded DNA. Monovalent cations (Li(+), Na(+), K(+), Rb(+), Cs(+) and [Formula: see text] ) promoted triplex DNA at concentrations ≥150 mM. Tm1 varied from 49.8 °C in the presence of 150 mM Li(+) to 30.6 °C in the presence of 150 mM K(+). [Formula: see text] was very effective in stabilizing triplex DNA and its efficacy decreased with increasing substitution of the hydrogen atoms with methyl, ethyl, propyl and butyl groups. As in the case of monovalent cations, a concentration-dependent increase in Tm1 was observed with divalent ions and triplex DNA stabilization decreased in the order: Mg(2+) > Ca(2+) > Sr(2+) > Ba(2+). All positively charged cations increased the melting temperature of duplex DNA. Values of Δn (number of ions released) on triplex DNA melting were 0.46 ± 0.06 and 0.18 ± 0.02, respectively, for mono- and di-valent cations, as calculated from 1/Tm1 versus ln[M(+,2+)] plots. The corresponding values for duplex DNA were 0.25 ± 0.02 and 0.12 ± 0.02, respectively, for mono- and di-valent cations. Circular dichroism spectroscopic studies showed distinct conformational changes in triplex DNA stabilized by alkali metal and ammonium ions. Our results might be useful in developing triplex forming oligonucleotide based gene silencing techniques.

Spectral study on the unique enhanced fluorescence of guanosine triphosphate by zinc ions

Binding effect of guanosine triphosphate (GTP) with metal ions is involved in many biologically important processes, and so its investigation has been one interesting research focus for many chemical and biochemical research groups. In this contribution, we presented the unique fluorescence recovery and enhancement of GTP induced by Zn(II) based on the spectrofluorometric method. When excited at 280 nm, GTP is hardly fluorescent at the alkaline condition. However, the presence of Zn(II) caused an obvious fluorescence emission of GTP at 346 nm, and the binding molar ratio between GTP and Zn(II) had been proved to be 1. The investigations of binding property of various nucleotides with metal ions demonstrated that this fluorescence recovery and enhancement of GTP with Zn(II) was highly specific, which could successfully discriminate GTP from other structurally similar nucleotides including GDP and GMP. Furthermore, similar fluorescence response of the bacterial alarmone ppGpp to Zn(II) had also been identified.

Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations

Monovalent (Na(+)) and divalent (Mg(2+)) ion distributions around the Dickerson-Drew dodecamer were studied by atomistic molecular dynamics (MD) simulations with AMBER molecular modeling software. Different initial placements of ions were tried and the resulting effects on the ion distributions around DNA were investigated. For monovalent ions, results were found to be nearly independent of initial cation coordinates. However, Mg(2+) ions demonstrated a strong initial coordinate dependent behavior. While some divalent ions initially placed near the DNA formed essentially permanent direct coordination complexes with electronegative DNA atoms, Mg(2+) ions initially placed further away from the duplex formed a full, nonexchanging, octahedral first solvation shell. These fully solvated cations were still capable of binding with DNA with events lasting up to 20 ns, and in comparison were bound much longer than Na(+) ions. Force field parameters were also investigated with modest and little differences arising from ion (ions94 and ions08) and nucleic acid description (ff99, ff99bsc0, and ff10), respectively. Based on known Mg(2+) ion solvation structure, we conclude that in most cases Mg(2+) ions retain their first solvation shell, making only solvent-mediated contacts with DNA duplex. The proper way to simulate Mg(2+) ions around DNA duplex, therefore, should begin with ions placed in the bulk water.

A ratiometric fluorescence recognition of guanosine triphosphate on the basis of Zn(II) complex of 1,4-bis(imidazol-1-ylmethyl) benzene

As one vital member among the family of phosphates, guanosine triphosphate (GTP) not only plays a very important role in many critical biological processes but also closely associates with definite pathological states. Based on the ratiometric fluorescence response of the zinc complex of 1,4-bis(imidazol-1-ylmethyl) benzene (bix) in this contribution, a highly selective recognition of GTP has been successfully developed. The fluorescence of bix-Zn(II) at 289 nm decreased in the presence of GTP with the appearance of one new emission band at 341 nm, resulting in ratiometric fluorescence changes with the concentration of GTP. With that, ratiometric fluorescence recognition for GTP could be effectively established, and so GTP could be successfully discriminated from other structurally similar anions, including ATP and PPi. Furthermore, bix-Zn(II) also has a ratiometric fluorescence response to DNA sequences containing guanine.

Conformational flexibility of C8-phenoxylguanine adducts in deoxydinucleoside monophosphates

M06-2X/6-31G(d,p) is used to calculate the structure of all natural deoxydinucleoside monophosphates with G in the 5' or 3' position, the anti or syn conformation, and each natural (A, C, G, T) base in the corresponding flanking position. When the ortho or para C8-phenoxyl-2'-deoxyguanosine (C8-phenoxyl-dG) adduct replaces G in each model, there is little change in the relative base-base orientation or backbone conformation. However, the orientation of the C8-phenoxyl group can be characterized according to the position (5' versus 3'), conformation (anti versus syn), and isomer (ortho versus para) of damage. Although the degree of coplanarity between the phenoxyl ring and G base in the ortho adduct is highly affected by the sequence since the hydroxyl group can interact with neighboring bases, the para adduct generally does not exhibit discrete interactions with flanking bases. For both adducts, steric clashes between the phenoxyl group and the backbone or flanking base destabilize the anti conformation preferred by the natural nucleotide and thereby result in a clear preference for the syn conformation regardless of the sequence or position. This contrasts the conclusions drawn from smaller (nucleoside, nucleotide) models previously used in the literature, which stresses the importance of using models that address the steric constraints present due to the surrounding environment. Since replication errors for other C8-dG bulky adducts have been linked to a preference for the syn conformation, our findings provide insight into the possible mutagenicity of phenolic adducts.

Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs

Reverse kink-turn is a recurrent elbow-like RNA building block occurring in the ribosome and in the group I intron. Its sequence signature almost matches that of the conventional kink-turn. However, the reverse and conventional kink-turns have opposite directions of bending. The reverse kink-turn lacks basically any tertiary interaction between its stems. We report unrestrained, explicit solvent molecular dynamics simulations of ribosomal and intron reverse kink-turns (54 simulations with 7.4 μs of data in total) with different variants (ff94, ff99, ff99bsc0, ff99χOL, and ff99bsc0χOL) of the Cornell et al. force field. We test several ion conditions and two water models. The simulations characterize the directional intrinsic flexibility of reverse kink-turns pertinent to their folded functional geometries. The reverse kink-turns are the most flexible RNA motifs studied so far by explicit solvent simulations which are capable at the present simulation time scale to spontaneously and reversibly sample a wide range of geometries from tightly kinked ones through flexible intermediates up to extended, unkinked structures. A possible biochemical role of the flexibility is discussed. Among the tested force fields, the latest χOL variant is essential to obtaining stable trajectories while all force field versions lacking the χ correction are prone to a swift degradation toward senseless ladder-like structures of stems, characterized by high-anti glycosidic torsions. The type of explicit water model affects the simulations considerably more than concentration and the type of ions.

Presence of divalent cation is not mandatory for the formation of intramolecular purine-motif triplex containing human c-jun protooncogene target

Modulation of endogenous gene function, through sequence-specific recognition of double helical DNA via oligonucleotide-directed triplex formation, is a promising approach. Compared to the formation of pyrimidine motif triplexes, which require relatively low pH, purine motif appears to be the most gifted for their stability under physiological conditions. Our previous work has demonstrated formation of magnesium-ion dependent highly stable intermolecular triplexes using a purine third strand of varied lengths, at the purine•pyrimidine (Pu•Py) targets of SIV/HIV-2 (vpx) genes (Svinarchuk, F., Monnot, M., Merle, A., Malvy, C., and Fermandjian, S. (1995) Nucleic Acids Res. 23, 3831-3836). Herein, we show that a designed intramolecular version of the 11-bp core sequence of the said targets, which also constitutes an integral, short, and symmetrical segment (G(2)AG(5)AG(2))•(C(2)TC(5)TC(2)) of human c-jun protooncogene forms a stable triplex, even in the absence of magnesium. The sequence d-C(2)TC(5)TC(2)T(5)G(2)AG(5)AG(2)T(5)G(2)AG(5)AG(2) (I-Pu) folds back twice onto itself to form an intramolecular triple helix via a double hairpin formation. The design ensures that the orientation of the intact third strand is antiparallel with respect to the oligopurine strand of the duplex. The triple helix formation has been revealed by non-denaturating gel assays, UV-thermal denaturation, and circular dichroism (CD) spectroscopy. The monophasic melting curve, recorded in the presence of sodium, represented the dissociation of intramolecular triplex to single strand in one step; however, the addition of magnesium bestowed thermal stability to the triplex. Formation of intramolecular triple helix at neutral pH in sodium, with or without magnesium cations, was also confirmed by gel electrophoresis. The triplex, mediated by sodium alone, destabilizes in the presence of 5'-C(2)TC(5)TC(2)-3', an oligonucleotide complementary to the 3'-oligopurine segments of I-Pu, whereas in the presence of magnesium the triplex remained impervious. CD spectra showed the signatures of triplex structure with A-like DNA conformation. We suggest that the possible formation of pH and magnesium-independent purine-motif triplexes at genomic Pu•Py sequences may be pertinent to gene regulation.

Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics

The glmS catalytic riboswitch is part of the 5'-untranslated region of mRNAs encoding glucosamine-6-phosphate (GlcN6P) synthetase (glmS) in numerous gram-positive bacteria. Binding of the cofactor GlcN6P induces site-specific self-cleavage of the RNA. However, the detailed reaction mechanism as well as the protonation state of the glmS reactive form still remains elusive. To probe the dominant protonation states of key active site residues, we carried out explicit solvent molecular dynamic simulations involving various protonation states of three crucial active site moieties observed in the available crystal structures: (i) guanine G40 (following the Thermoanaerobacter tengcongensis numbering), (ii) the GlcN6P amino/ammonium group, and (iii) the GlcN6P phosphate moiety. We found that a deprotonated G40(-) seems incompatible with the observed glmS active site architecture. Our data suggest that the canonical form of G40 plays a structural role by stabilizing an in-line attack conformation of the cleavage site A-1(2'-OH) nucleophile, rather than a more direct chemical role. In addition, we observe weakened cofactor binding upon protonation of the GlcN6P phosphate moiety, which explains the experimentally observed increase in K(m) with decreasing pH. Finally, we discuss a possible role of cofactor binding and its interaction with the G65 and G1 purines in structural stabilization of the A-1(2'-OH) in-line attack conformation. On the basis of the identified dominant protonation state of the reaction precursor, we propose a hypothesis of the self-cleavage mechanism in which A-1(2'-OH) is activated as a nucleophile by the G1(pro-R(p)) nonbridging oxygen of the scissile phosphate, whereas the ammonium group of GlcN6P acts as the general acid protonating the G1(O5') leaving group.

The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine-thymine and guanine-cytosine base pairs

The substituent effects on the geometrical parameters and the individual hydrogen bond (HB) energies of base pairs such as X-adenine-thymine (X-A-T), X-thymine-adenine (X-T-A), X-guanine-cytosine (X-G-C), and X-cytosine-guanine (X-C-G) have been studied by the quantum mechanical calculations at the B3LYP and MP2 levels with the 6-311++G(d,p) basis set. The electron withdrawing (EW) substituents (F and NO(2)) increase the total binding energy (DeltaE) of X-G-C derivatives and the electron donating (ED) substituent (CH(3)) decreases it when they are introduced in the 8 and 9 positions of G. The effects of substituents are reversed when they are located in the 1, 5, and 6 positions of C, with exception of CH(3) in the 1 position and F in the 5 position, which in both cases the DeltaE value decreases negligibly small. With minor exceptions (X=8-CH(3), 8-F, and 9-NO(2)), both ED and EW substituents increase slightly the DeltaE values of X-A-T derivatives. The individual HB energies (E (HB)s) have been estimated using electron densities that calculated at the hydrogen bond critical points (HBCPs) by the atoms in molecules (AIM) method. Most of changes of individual HBs are in consistent with the ED/EW nature of substituents and the role of atoms entered H-bonding. The remarkable change is observed for NO(2) substituted derivative in each case.

Metal ion-N7 coordination in a ribozyme branch domain by NMR

The N7 of purine nucleotides presents one of the most dominant metal ion binding sites in nucleic acids. However, the interactions between kinetically labile metal ions like Mg(2+) and these nitrogen atoms are inherently difficult to observe in large RNAs. Rather than using the insensitive direct (15)N detection, here we have used (2)J-[(1)H,(15)N]-HSQC (Heteronuclear Single Quantum Coherence) NMR experiments as a fast and efficient method to specifically observe and characterize such interactions within larger RNA constructs. Using the 27 nucleotides long branch domain of the yeast-mitochondrial group II intron ribozyme Sc.ai5gamma as an example, we show that direct N7 coordination of a Mg(2+) ion takes place in a tetraloop nucleotide. A second Mg(2+) ion, located in the major groove at the catalytic branch site, coordinates mainly in an outer-sphere fashion to the highly conserved flanking GU wobble pairs but not to N7 of the sandwiched branch adenosine.

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in

Structure and dynamics are both critical to RNA’s vital functions in biology. Numerous techniques can elucidate the structural dynamics of RNA, but computational approaches based on experimental data arguably hold the promise of providing the most detail. In this Account, we highlight areas wherein molecular dynamics (MD) and quantum mechanical (QM) techniques are applied to RNA, particularly in relation to complementary experimental studies.

We have expanded on atomic-resolution crystal structures of RNAs in functionally relevant states by applying explicit solvent MD simulations to explore their dynamics and conformational changes on the submicrosecond time scale. MD relies on simplified atomistic, pairwise additive interaction potentials (force fields). Because of limited sampling, due to the finite accessible simulation time scale and the approximated force field, high-quality starting structures are required.

Despite their imperfection, we find that currently available force fields empower MD to provide meaningful and predictive information on RNA dynamics around a crystallographically defined energy minimum. The performance of force fields can be estimated by precise QM calculations on small model systems. Such calculations agree reasonably well with the Cornell et al. AMBER force field, particularly for stacking and hydrogen-bonding interactions. A final verification of any force field is accomplished by simulations of complex nucleic acid structures.

The performance of the Cornell et al. AMBER force field generally corresponds well with and augments experimental data, but one notable exception could be the capping loops of double-helical stems. In addition, the performance of pairwise additive force fields is obviously unsatisfactory for inclusion of divalent cations, because their interactions lead to major polarization and charge-transfer effects neglected by the force field. Neglect of polarization also limits, albeit to a lesser extent, the description accuracy of other contributions, such as interactions with monovalent ions, conformational flexibility of the anionic sugar−phosphate backbone, hydrogen bonding, and solute polarization by solvent. Still, despite limitations, MD simulations are a valid tool for analyzing the structural dynamics of existing experimental structures. Careful analysis of MD simulations can identify problematic aspects of an experimental RNA structure, unveil structural characteristics masked by experimental constraints, reveal functionally significant stochastic fluctuations, evaluate the structural role of base ionization, and predict structurally and potentially functionally important details of the solvent behavior, including the presence of tightly bound water molecules. Moreover, combining classical MD simulations with QM calculations in hybrid QM/MM approaches helps in the assessment of the plausibility of chemical mechanisms of catalytic RNAs (ribozymes).

In contrast, the reliable prediction of structure from sequence information is beyond the applicability of MD tools. The ultimate utility of computational studies in understanding RNA function thus requires that the results are neither blindly accepted nor flatly rejected, but rather considered in the context of all available experimental data, with great care given to assessing limitations through the available starting structures, force field approximations, and sampling limitations. The examples given in this Account showcase how the judicious use of basic MD simulations has already served as a powerful tool to help evaluate the role of structural dynamics in biological function of RNA.

Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM

Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations with the low computational cost of empirical molecular mechanical (MM) treatment allowing to capture dynamic properties to probe critical atomistic details of enzyme reactions. Catalysis by RNA enzymes (ribozymes) has only recently begun to be addressed with QM/MM approaches and is thus still a field under development. This review surveys methodology as well as recent advances in QM/MM applications to RNA mechanisms, including those of the HDV, hairpin, and hammerhead ribozymes, as well as the ribosome. We compare and correlate QM/MM results with those from QM and/or molecular dynamics (MD) simulations, and discuss scope and limitations with a critical eye on current shortcomings in available methodologies and computer resources. We thus hope to foster mutual appreciation and facilitate collaboration between experimentalists and theorists to jointly advance our understanding of RNA catalysis at an atomistic level.

The impact of monovalent ion force field model in nucleic acids simulations

Different classical models for monovalent ions (typically used to neutralize proteins or nucleic acids) are available in the literature and are widely used in molecular dynamics simulations without a great knowledge of their quality, consistency with the macromolecular force field and impact on the global simulation results. In this paper the ability of several of the most popular ion models to reproduce both quantum mechanics and experimental results is examined. Artefacts due to the use of incorrect ion models in molecular dynamics simulations of concentrated solutions of NaCl and KCl in water and of a short DNA duplex in 500 mM aqueous solutions of NaCl and KCl have been analyzed. Our results allow us to discuss the robustness and reliability of different ion models and to highlight the source of potential errors arising from non-optimal models. However, it is also found that the structural and dynamic characteristics of DNA (as an example of a heavily charged macromolecule) in near-physiological conditions are quite independent of the ion model used, providing support to most already-published simulations of macromolecules.

Evaluation of effects of bivalent cations on the formation of purine-rich triple-helix DNA by ESI-FT-MS

The GGA triplet repeats are widely dispersed throughout eukaryotic genomes. (GGA)n or (GGT)n oligonucleotides can interact with double-stranded DNA containing (GGA:CCT)n to form triple-stranded DNA. The effects of 8 divalent metal ions (3 alkaline-earth metals and 5 transition metals) on formation of these purine-rich triple-helix DNA were investigated by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-MS). In the absence of metal ions, no triplex but single-strand, duplex, and purine homodimer ions were observed in mass spectra. The triple-helix DNA complexes were observed only in the presence of certain divalent ions. The effects of different divalent cations on the formation of purine-rich triplexes were compared. Transition-metal ions, especially Co(2+) and Ni(2+), significantly boost the formation of triple-helix DNA, whereas alkaline-earth metal ions have no positive effects on triplex formation. In addition, Ba(2+) is notably beneficial to the formation of homodimer instead of triplex.

Separation of oligonucleotides with single-base mutation by capillary electrophoresis using specific interaction of metal ion with nucleotide

A unique tactic for the separation of single-base sequential isomers of oligomeric single-stranded DNA by a CE separation system employing the specific interaction of metal ion with nucleotide was demonstrated, enabling the separation of the mixture of a 12-mer oligonucleotide and its single-base mutants, as well as their positional isomers.