Nucleic Acid Base Pairs Research Articles

Metal‐Ion‐Mediated Base Pairs in Nucleic Acids

AbstractNucleic acids and their analogues raise more and more interest in research areas outside biology and biochemistry. The functionalization of these evolutionary optimized self‐assembling macromolecules with metal ions widens their applicability even further. Previous efforts to incorporate metal ions site‐specifically into nucleic acids focused on the covalent attachment of appropriate ligands to either the sugar phosphate backbone or the nucleobases. More recently, the use of metal‐ion‐mediated base pairs, i.e. the replacement of natural nucleobases by ligands, was suggested as an alternative means. This microreview discusses selected examples of metal‐ion‐mediated base pairs, including those that comprise unmodified natural nucleobases, and describes possible applications for the resulting metal‐modified nucleic acids. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

Study of the Thymine Molecule: Equilibrium Structure from Joint Analysis of Gas-Phase Electron Diffraction and Microwave Data and Assignment of Vibrational Spectra Using Results of Ab initio Calculations

Thymine is one of the nucleobases which forms the nucleic acid (NA) base pair with adenine in DNA. The study of molecular structure and dynamics of nucleobases can help to understand and explain some processes in biological systems and therefore it is of interest. Because the scattered intensities on the C, N, and O atoms as well as some bond lengths in thymine are close to each other the structural problem cannot been solved by the gas phase electron diffraction (GED) method alone. Therefore the rotational constants from microvawe (MW) studies and differences in the groups of N-C, C=O, N-H, and C-H bond lengths from MP2 (full)/cc-pVQZ calculations were used as supplementary data. The analysis of GED data was based on the C(s) molecular symmetry according to results of the structure optimizations at the MP2 (full) level using 6-311G (d,p), cc-pVTZ, and cc-pVQZ basis sets confirmed by vibrational frequency calculations with 6-311G (d,p) and cc-pVTZ basis sets. Mean-square amplitudes as well as harmonic and anharmonic vibrational corrections to the internuclear distances (r(e)-r(a)) and to the rotational constants (B(e)(k)-B(0)(k), where k = A, B, C) were calculated from the quadratic (MP2 (full)/cc-pVTZ) and cubic (MP2 (full)/6-311G (d,p)) force constants (the latter were used only for anharmonic corrections). The harmonic force field was scaled using published IR and Raman spectra of the parent and N1,N3-dideuterated species, which were for the first time completely assigned in the present work. The main equilibrium structural parameters of the thymine molecule determined from GED data supplemented by MW rotational constants and results of MP2 calculations are the following (bond lengths in Angstroms and bond angles in degrees with 3sigma in parentheses): r(e) (C5=C6) = 1.344 (16), r(e) (C5-C9) = 1.487 (8), r(e) (N1-C6) = 1.372 (3), r(e) (N1-C2) = 1.377 (3), r(e) (C2-N3) = 1.378 (3), r(e) (N3-C4) = 1.395 (3), r(e) (C2=O7) = 1.210 (1), r(e) (C4=O8) = 1.215 (1), angle e (N1-C6=C5) = 123.1 (5), angle e (C2-N1-C6) = 123.7 (5), angle e (N1-C2-N3) = 112.8 (5), angle e (C2-N3-C4) = 128.0 (5), angle e (N3-C4-C5) = 114.8 (5), angle e (C6=C5-C9) = 124.4 (9). The experimental structural parameters are in good agreement with those from MP2 (full) calculations with use of cc-pVTZ and cc-pVQZ basis sets.

Metahybrid Density Functional Theory and Correlated ab Initio Studies on Microhydrated Adenine−Thymine Base Pairs

Monohydrated and dihydrated adenine-thymine base pairs are characterized using metahybrid density functional theory and correlated ab initio approaches. The motivation of this work is twofold. First, the high-level geometries and interaction energies computed for different complexes serve as a reference for the testing of recently developed density functional theory (DFT) with respect to its ability to correctly describe the balance between the electrostatic and the dispersion contributions that bind these complexes. Second, these studies of nucleic acid base pairs are important for finding binding sites of water molecules around bases and for a better understanding of the influence of the solvent on the stability of the structure of DNA duplexes.

Modelling the nanoscale patterning of nucleic acid base pairs deposited on graphite

Interactions between graphite and nucleic-acid base pairs are investigated. An existing polarizable potential that uses distributed multipoles up to and including quadrupoles is extended to describe the graphite surface and the nucleic-acid bases cytosine and guanine. Adsorption energies and structures calculated with this potential are compared with data obtained using electronic structure theory. Structures of co-adsorbed cytosine and guanine layers are optimised and two competing arrangements, the ‘dimer-row’ and ‘quartet-row’ patterns, are compared with experimental scanning tunnelling microscopy images. We include two factors not considered in previous studies: the presence of the graphite surface and the inter-row packing. However, our findings agree with previous calculations in that the ‘quartet-row’ is energetically preferred, despite STM experiments suggesting the ‘dimer-row’ structure is observed.

Studies on Tautomeric Forms of Guanine-Cytosine Base Pairs of Nucleic Acids and Their Interactions with Water Molecules

The relative stabilities of Guanine-Cytosine (G-C) DNA bare base pairs, its tautomeric forms and microhydrated base pairs are theoretically investigated with a focus on the keto-enol tautomerism as well as on the cis-trans isomerism using ab initio and density functional theory methods. The stabilities of the G-C bare base pairs, its tautomeric forms and microhydrated base pairs were affected by various factors including keto-enol tautomerization, cis-trans enol isomerization, and steric hindrance between the base pair and water molecules. The Atoms in Molecules theory (AIM) is employed to investigate H-bonding patterns both in bare and microhydrated base pairs. From the above topological results, an excellent linear correlation is shown between electron density [ρ(r)], and its Laplacian [▿2ρ(r)] at the bond critical points. NBO analysis has been carried out to study the charge transfer between proton acceptor to the antibonding orbital of the X-H bond both in bare and microhydrated base pairs.

QUANTUM MECHANICAL DESCRIPTION OF THE INTERACTIONS BETWEEN DNA AND 9,10-ANTHRAQUINONE

Molecular geometries of the 9,10-anthraquinone (AQ) and DNA bases (Adenine, Guanine, Cytosine, and Thymine) were optimized using B3LYP/6-31G** method. Properties of isolated intercalator (9,10-anthraquinone) and their stacking interactions with adenine ⋯ thymine (AT) and guanine ⋯ cytosine (GC) nucleic acid base pairs were investigated by means of DFTB method. DFTB method, an approximate version of the DFT method, was extended to cover London dispersion energy. AQ exhibits a large charge delocalization and it has no site with dominant charge. This intercalator has a large polarizability and is a good electron acceptor, while base pairs are good electron donors. B3LYP/6-31G** stabilization energies of intercalator ⋯ base pair complexes are large (-18.83 kcal/mol for AT ⋯ AQ and -15.69 kcal/mol for GC ⋯ AQ). It is concluded that, the dispersion energy predominantly contributes to the stability of intercalator ⋯ DNA base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation. The results showed that AQ changes the structure of DNA on bond length, bond angle, torsion angle, and charges.

A Theoretical Study on Interactions Between Mitoxantrone as an Anticancer Drug and DNA: Application in Drug Design

This research is an effort to further understand the physicochemical interaction between the novel drug, mitoxantrone (MTX) and its biologic receptor, DNA. The ultimate goal is to design drugs that interact more with DNA. Understanding the physicochemical properties of the drug as well as the mechanism by which it interacts with DNA, it should ultimately allow the rational design of novel anti-cancer or anti-viral drugs. Molecular modelling on the complex formed between MTX and DNA presented that this complex was indeed fully capable of participating in the formation of a stable intercalation site. Furthermore, the molecular geometries of MTX and the DNA bases (adenine, guanine, cytosine and thymine) were optimized with the aid of the B3LYP/6-31G* method. The properties of the isolated intercalator and its stacking interactions with the adenine...thymine (AT) and guanine...cytosine (GC) nucleic acid base pairs were studied with the DFTB method (density functional tight-binding), an approximate version of the DFT method, that was extended to cover the London dispersion energy. The B3LYP/6-31G* stabilization energies of the intercalator...base pair complexes were found 10.06 kcal/mol and 21.64 kcal/mol for AT...MTX and GC...MTX, respectively. It was concluded that the dispersion energy and the electrostatic interaction contributed to the stability of the intercalator.DNA base pair complexes. The results concluded from the comparison of the DFTB method and the Hartree-fock method point out that these methods show close results and support each other.

Direct detection of N−H⋯N hydrogen bonds in biomolecules by NMR spectroscopy

A nuclear magnetic resonance (NMR) experiment is described for the direct detection of N-H[...]N hydrogen bonds (H-bonds) in 15N isotope-labeled biomolecules. This quantitative HNN-COSY (correlation spectroscopy) experiment detects and quantifies electron-mediated scalar couplings across the H-bond (H-bond scalar couplings), which connect magnetically active (15)N nuclei of the H-bond donor and acceptor. Detectable H-bonds comprise the imino H-bonds in canonical Watson-Crick base pairs, many H-bonds in unusual nucleic acid base pairs and H-bonds between protein backbone or side-chain N-H donor and N acceptor moieties. Unlike other NMR observables, which provide only indirect evidence of the presence of H-bonds, the H-bond scalar couplings identify all partners of the H-bond, the donor, the donor proton and the acceptor in a single experiment. The size of the scalar couplings can be related to H-bond geometries and as a time average to H-bond dynamics. The time required to detect the H-bonds is typically less than 1 d at millimolar concentrations for samples of molecular weight < or = approximately 25 kDa. A C15N/13C-labeled potato spindle tuber viroid T1 RNA domain is used as an example to illustrate this procedure.

Hybrid QM/MM calculations on the structure and electronic properties of hydrated RNA base pair

Structures of hydrated A–U base pair were investigated by using DFT and hybrid ONIOM methods in order to examine the efficacy of the ONIOM (QM:MM) approach in describing the structure of the hydrated RNA base pair. Comparison of these results reveals that the ONIOM (DFT:AMBER) approach, in which the nucleic acid base pair is treated quantum chemically by DFT and ambient water molecules treated by AMBER molecular mechanics, maintains the structures of the hydrated A–U base pair optimized by full DFT quantum chemical methods.

Detection and Evaluation of Hydrogen Bond Strength in Nucleic Acid Base Pairs

The strengths of N-H---N and N-H---O hydrogen bonds in 15 nucleic acid base pairs have been investigated using different descriptors. Geometrical and energetic criteria, atoms in molecules topological parameters, natural bond orbital analysis, and spectroscopic measurements have been used to detect the H-bonds and evaluate their strengths in the intermolecular interactions between five nucleic acid bases. Different correlations have been obtained between many of these descriptors to provide a global view of H-bond interaction. We found good linear correlations for the dependence of some descriptors such as atomic interpenetration and hyperconjugation energy on density at bond critical point, while others like destabilization of H-atom energy, variation in N-H frequency, and NMR parameters correlate in a much worse fashion. The calculations suggest that almost all H-bonds in different base pairs belong to medium strength H-bonds. We found in thymine the H-bond interaction is more likely through the amide-type oxygen while the situation is reverse for uracil in which the urea-type oxygen is more accessible to form an H-bond. Cytosine and guanine can also form H-bonds via their amine-type or amide-type nitrogens. In cytosine, the amine-type nitrogen is involved in an N-H---O bond interaction, while, in guanine, the amide-type nitrogen has a greater contribution to H-bond interaction.

Parametrization of an Empirical Correction Term to Density Functional Theory for an Accurate Description of π-Stacking Interactions in Nucleic Acids

We present an accurate parametrization of density functional theory augmented with an empirical correction term to describe properly pi-stacking interactions in nucleic acids. The approach is based on the popular Perdew-Burke-Ernzerhof (PBE), Becke-Perdew (BP), and hybrid Becke-Lee-Yang-Parr (B3LYP) density functionals augmented by a classical London C(6)R(-6) dispersion term. The novelty of our implementation lies in the accurate tuning of the empirical parameters, included in the [formula: see text] damping function, to reproduce high-level post Hartree-Fock calculations. In particular, we present sets of parameters and the needed code to correct the PBE, BP, and B3LYP results from the Turbomole and ADF packages in connection with basis sets of double and triple zeta quality. The developed approach is validated by comparison with the JSCH-2005 benchmark and with best quality stacking energies reported in the literature for the stacking of H-bonded nucleic acids base pairs.

Transcription Termination Factor Rho Can Displace Streptavidin from Biotinylated RNA

In Escherichia coli, binding of the hexameric Rho protein to naked C-rich Rut (Rho utilization) regions of nascent RNA transcripts initiates Rho-dependent termination of transcription. Although the ring-shaped Rho factor exhibits in vitro RNA-dependent ATPase and directional RNA-DNA helicase activities, the actual molecular mechanisms used by Rho to disrupt the intricate network of interactions that cement the ternary transcription complex remain elusive. Here, we show that Rho is a molecular motor that can apply significant disruptive forces on heterologous nucleoprotein assemblies such as streptavidin bound to biotinylated RNA molecules. ATP-dependent disruption of the biotin-streptavidin interaction demonstrates that Rho is not mechanistically limited to the melting of nucleic acid base pairs within molecular complexes and confirms that specific interactions with the roadblock target are not required for Rho to operate properly. We also show that Rho-induced streptavidin displacement depends significantly on the identity of the biotinylated transcript as well as on the position, nature, and length of the biotin link to the RNA chain. Altogether, our data are consistent with a "snow plough" type of mechanism of action whereby an early rearrangement of the Rho-substrate complex (activation) is rate-limiting, physical force (pulling) is exerted on the RNA chain by residues of the central Rho channel, and removal of structural obstacles from the RNA track stems from their nonspecific steric exclusion from the hexamer central hole. In this context, a simple model for the regulation of Rho-dependent termination based on the modulation of disruptive dynamic loading by secondary factors is proposed.

Density functional theory-symmetry adapted perturbation treatment energy decomposition of nucleic acid base pairs taken from DNA crystal geometry

First- and second-order perturbation energies for H-bonded and stacked structures of nucleic acid base pairs in DNA crystal geometries were determined using the density functional theory symmetry adapted perturbation treatment method. Considerably larger stabilization of the former pairs is due to electrostatic and induction energies. Total E(1) energies for both pairs are, however, similar and the same is true for dispersion energy.

Assessment of the MP2 Method, along with Several Basis Sets, for the Computation of Interaction Energies of Biologically Relevant Hydrogen Bonded and Dispersion Bound Complexes

In the past several years the MP2 method has been used extensively in studies of noncovalent interactions within biological systems such as proteins, DNA/RNA, and protein-ligand complexes. In this work we assess the performance that can be expected of this method, when paired with several different medium and extended basis sets, for the accurate computation of binding energies of hydrogen bonded and dispersion bound biologically derived complexes. It is found that, overall, the MP2/cc-pVTZ method produces the best, most well balanced, description of noncovalent interactions. Another interesting observation made in this study is that generally the MP2 technique, when paired with any basis set, does not yield reliable results for cyclic hydrogen bonds such as those found in nucleic acid base pairs.

Proteomic studies of an Antarctic cold-adapted bacterium, Shewanella livingstonensis Ac10, for global identification of cold-inducible proteins

Proteomic analysis of a cold-adapted bacterium, Shewanella livingstonensis Ac10, isolated from Antarctic seawater was carried out to elucidate its cold-adaptation mechanism. The cells were grown at 4 degrees C and 18 degrees C, and soluble and membrane proteins were analyzed by two-dimensional gel electrophoresis. At 4 degrees C, the relative abundance of 47 soluble proteins and five membrane proteins increased more than twofold, and these proteins were analyzed by peptide mass fingerprinting. Twenty-six soluble proteins and two membrane proteins were identified. These included proteins involved in RNA synthesis and folding (RpoA, GreA, and CspA), protein synthesis and folding (TufB, Efp, LysU, and Tig), membrane transport (OmpA and OmpC), and motility (FlgE and FlgL). Cold-inducible RpoA, GreA, and CspA may be required for efficient and accurate transcription and proper folding of RNA at low temperatures, where base pairing of nucleic acids is stable and undesired secondary structures of RNA tend to form. Tig is supposed to have peptidyl-prolyl cis-trans isomerase activity and facilitate proper folding of proteins at low temperatures. The cold induction of OmpA and OmpC is likely to counteract the low diffusion rate of solutes at low temperatures and enables the efficient uptake of nutrients. These results provided many clues to understand microbial cold-adaptation mechanisms.

Nucleic Acid Unwinding by Hepatitis C Virus and Bacteriophage T7 Helicases Is Sensitive to Base Pair Stability

Helicases are motor enzymes that convert the chemical energy of NTP hydrolysis into mechanical force for motion and nucleic acid strand separation. Within the cell, helicases process a range of nucleic acid sequences. It is not known whether this composite rate of moving and opening the strands of nucleic acids depends on the base sequence. Our presteady state kinetic studies of helicases from two classes, the ring-shaped T7 helicase and two forms of non-ring-shaped hepatitis C virus (HCV) helicase, show that both the unwinding rate and processivity depend on the sequence and decrease as the nucleic acid stability increases. The DNA unwinding activity of T7 helicase and the RNA unwinding activity of HCV helicases decrease steeply with increasing base pair stability. On the other hand, the DNA unwinding activity of HCV helicases is less sensitive to base pair stability. These results predict that helicases will fall into a spectrum of modest to high sensitivity to base pair stability depending on their biological role in the cell. Modeling of the dependence provided the degree of the active involvement of helicase in base pair destabilization during the unwinding process and distinguished between passive and active mechanisms of unwinding.

Leading RNA Tertiary Interactions: Structures, Energies, and Water Insertion of A-Minor and P-Interactions. A Quantum Chemical View

Complex molecular shapes of ribosomal RNA molecules are stabilized by recurrent types of tertiary interactions involving highly specific and conserved non-Watson-Crick base pairs, triplets, and quartets. We analyzed the intrinsic structure and stability of the P-motif and the four basic types of A-minor interactions (types I, II, III, and 0), which represent the most prominent RNA tertiary interaction patterns refined in the course of evolution. In the studied interactions, the electron correlation component of the stabilization usually exceeds the Hartree-Fock (HF) term, leading to a strikingly different balance of forces as compared to standard base pairing stabilized primarily by the HF term. In other words, the A-minor and P-interactions are considerably more influenced by the dispersion energy as compared to canonical base pairs, which makes them particularly suitable to zip the folded RNA structures that are substantially hydrated even in their interior. Continuum solvent COSMO calculations confirm that the stability of the canonical GC base pair is affected (reduced) by the continuum solvent screening considerably more than the stability of the A-minor interaction. Among the studied systems, the strong A-minor II and weak A-minor III interactions require water molecules to stabilize the experimental geometry. Gas-phase optimization of the canonical A-minor II A/CG triplet without water results in a geometry that is clearly inconsistent with the RNA structure. The gas-phase structure of the P-interaction and the most stable A-minor I interaction nicely agrees with the geometries occurring in the ribosome. A-minor I can also adopt an alternative water-mediated substate rather often observed in X-ray and molecular dynamics studies. The A-minor I water bridge, however, does not appear to stabilize the tertiary contact, and its role is to provide structural flexibility to this binding pattern within the context of the RNA structure. Interestingly, the insertion of a polar water molecule in the A-minor I A/CG tertiary contact occurring in the A/C tertiary pair is stabilized primarily by the HF (electrostatic) interaction energy, while the dispersion-controlled A/G contact remains firmly bound. Thus, the intrinsic balance of forces as revealed by quantum mechanics (QM) calculations nicely correlates with many behavioral aspects of the studied interactions inside RNA. The comparison of interaction energies computed using quantum chemistry and an AMBER force field reveals that common molecular mechanics calculations perform rather well, except that the strength of the P-interaction is modestly overestimated. We also briefly discuss the non-negligible methodological differences when evaluating simple base-base nucleic acids base pairs and the complex RNA tertiary base pairing patterns using QM procedures.

Estimation on the Individual Hydrogen-Bond Strength in Molecules with Multiple Hydrogen Bonds

A simple atom-replacement approach is proposed for estimating the individual contributions of each intermolecular hydrogen bond (HB) in multiple hydrogen-bonded systems. The approach is validated by calculations on the homodimer of formylformamide and then applied to nucleic acid base pairs (adenine-thymine and guanine-cytosine) and some quadruply hydrogen-bonded dimers. With the help of this method, it is easy to distinguish the relative strength of each HB, and identify the main factors contributing to the total binding energies of multiple HBs.

Stability of Nucleic Acid Base Pairs in Organic Solvents: Molecular Dynamics, Molecular Dynamics/Quenching, and Correlated Ab Initio Study

The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations.

Computation of large systems with an economic basis set: Structures and reactivity indices of nucleic acid base pairs from density functional theory

We show here that an economic basis set can describe nucleic acid base pairs involving the hydrogen bond interactions in density functional calculations. The economic basis set in which the polarization function is added only to oxygen and nitrogen atoms of strong electronegativity can predict reliable geometric structures and dipole moment of nucleic acid base pairs, comparable to those obtained from the basis set of 6-31G* in B3LYP calculations. Combining single point calculations with the standard basis set on the geometric structures optimized by the economic basis set, the present approach has predicted accurate natural bond orbital charge, binding energy, electronegativity, hardness, softness, and electrophilicity index. The principle for basis selection presented in this study can be regarded as a general guideline in the computation of large biological systems with considerably high accuracy and low computational expense.