Nucleic Acid Base Pairs Research Articles

The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking

The performance of the recently introduced X3LYP density functional which was claimed to significantly improve the accuracy for H-bonded and van der Waals complexes was tested for extended H-bonded and stacked complexes (nucleic acid base pairs and amino acid pairs). In the case of planar H-bonded complexes (guanine...cytosine, adenine...thymine) the DFT results nicely agree with accurate correlated ab initio results. For the stacked pairs (uracil dimer, cytosine dimer, adenine...thymine and guanine...cytosine) the DFT fails completely and it was even not able to localize any minimum at the stacked subspace of the potential energy surface. The geometry optimization of all these stacked clusters leads systematically to the planar H-bonded pairs. The amino acid pairs were investigated in the crystal geometry. DFT again strongly underestimates the accurate correlated ab initio stabilization energies and usually it was not able to describe the stabilization of a pair. The X3LYP functional thus behaves similarly to other current functionals. Stacking of nucleic acid bases as well as interaction of amino acids was described satisfactorily by using the tight-binding DFT method, which explicitly covers the London dispersion energy.

Cofactor‐Apoprotein Hydrogen Bonding in Oxidized and Fully Reduced Flavodoxin Monitored by Trans‐Hydrogen‐Bond Scalar Couplings

Hydrogen bonding plays a key role in the tight binding of the FMN cofactor and the regulation of its redox properties in flavodoxins. Hydrogen bonding interactions can be directly observed in solution by multidimensional heteronuclear NMR spectroscopy through the scalar couplings between donor and acceptor nuclei. Here we report on the detection of intermolecular trans-hydrogen-bond couplings ((h)J) between the flavin ring system and the backbone of Desulfovibrio vulgaris flavodoxin in the oxidized and the two-electron reduced states. For this purpose, experiments are adapted from pulse sequences previously applied to determining (h)J coupling constants in nucleic acid-base pairs and proteins. The resulting (h2)J(N,N), (h4)J(N,N), (h3)J(C,N), and (h1)J(H,N) couplings involve the (15)N(1), (13)C(2), and (15)N(3) nuclei of the pyrimidine moiety of FMN, whereas no such interactions are detectable for (13)C(4) and (15)N(5). Several long-range (15)N-(15)N, (13)C-(15)N, and (1)H-(15)N J-coupling constants within the flavin are obtained as "by-products". The magnitudes of both (h)J and regular J couplings are found to be dependent on the redox state. In general, good correlations between (h)J coupling constants and donor-group (1)H chemical shifts and also crystallographic donor-acceptor distances are observed.

Accurate interaction energies of hydrogen-bonded nucleic acid base pairs.

Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. The study presents reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from -5 to -47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc-pVTZ basis set of atomic orbitals. The RI-MP2 method provides results essentially identical with the standard MP2 method. The interaction energies are calculated using the Complete Basis Set (CBS) extrapolation at the RI-MP2 level. For some base pairs, Coupled-Cluster corrections with inclusion of noniterative triple contributions (CCSD(T)) are given. The calculations are compared with selected medium quality methods. The PW91 DFT functional with the 6-31G basis set matches well the RI-MP2/CBS absolute interaction energies and reproduces the relative values of base pairing energies with a maximum relative error of 2.6 kcal/mol when applied with Becke3LYP-optimized geometries. The Becke3LYP DFT functional underestimates the interaction energies by few kcal/mol with relative error of 2.2 kcal/mol. Very good performance of nonpolarizable Cornell et al. force field is confirmed and this indirectly supports the view that H-bonded base pairs are primarily stabilized by electrostatic interactions.

Development and testing of a general amber force field.

We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching.

Grid-Based Hydrogen Bond Potentials with Improved Directionality

Grid-based methods are widely used for evaluation of conformations in automated docking and other techniques of structure-based drug design. Traditional non-directional and directional methods for evaluating hydrogen bonds in these methods, however, yield improper interactions in cases with adjacent hydrogen bonds, such as those that mediate base pairing in nucleic acids. An improved method of calculating hydrogen bond potentials is reported here, which predicts the proper geometry for ligands that form multiple hydrogen bonds with receptors. Keywords: hydrogen bond directionality, automated docking, grid-based energy evaluation

Identification of NH...N hydrogen bonds by magic angle spinning solid state NMR in a double-stranded RNA associated with myotonic dystrophy.

RNA plays a central role in biological processes and exhibits a variety of secondary and tertiary structural features that are often stabilized via hydrogen bonds. The distance between the donor and acceptor nitrogen nuclei involved in NH...N hydrogen bonds in nucleic acid base pairs is typically in the range of 2.6-2.9 A. Here, we show for the first time that such spatial proximity between 15N nitrogen nuclei can be conveniently monitored via magic angle spinning solid state NMR on a uniformly 15N-labelled RNA. The presence of NH.N hydrogen bonds is reflected as cross-peaks between the donor and acceptor nitrogen nuclei in 2D 15N dipolar chemical shift correlation spectra. The RNA selected for this experimental study was a CUG repeat expansion implicated in the neuromuscular disease myotonic dystrophy. The results presented provide direct evidence that the CUG repeat expansion adopts a double-stranded conformation.

Monte Carlo study of three-dimensional organization of water molecules around DNA fragments

Interactions with water molecules are important for the stabilization of three-dimensional structures of nucleic acids and for their functioning. The first hydration shells of macromolecules can be considered as structural parts of nucleic acid. We performed a Monte Carlo study of systems containing a nucleic acid base or base pair with water molecules using improved potential functions. These potential functions enable experimental data on both single base–single water interaction energies and enthalpies of base hydration to be reproduced. Hydration shell structures of base pairs are dependent on the pair geometry. Structural elements of hydration shells can contribute to the pair stability and hence to the probability of mispair formation during nucleic acid biosynthesis. The distribution of water molecules around bases and base pairs is essentially nonhomogeneous.

Caffeine interactions with nucleic acids. Molecular mechanics calculations of model systems for explanation of mechanisms of biological actions

To understand the molecular mechanisms of the influence of caffeine (CAF) on DNA functioning, molecular mechanics calculations of the interaction energy of CAF with nucleic acid bases and base pairs have been performed. The calculations reveal three types of mutual CAF–base (and CAF–base pair) arrangements corresponding to minima of the interaction energy. Besides well-known stacking mutual positions of the molecules, two other types of arrangements are revealed and studied. One of these arrangements corresponds to the nearly in-plane position of CAF and base (or base pair) and the formation of a single hydrogen bond. Another type of minimum corresponds to nearly perpendicular arrangements of the molecular planes and the formation of intermolecular hydrogen bonds. These two arrangements are possible both for individual nucleic acid monomers and for DNA duplexes. The calculations suggest the molecular mechanisms of the influence of CAF on DNA interactions with other biologically active molecules.

New parameterization of the Cornell et al. empirical force field covering amino group nonplanarity in nucleic acid bases.

The Cornell et al. empirical potential (Cornell et al., J Am Chem Soc 1995, 117, 5197) was modified by the introduction of nonplanarity of the amino group in guanine, adenine, and cytosine. Reparameterization was performed for 12 bond parameters of the amino group (three valence angles (C-N-H(1), C-N-H(2), and H(1)-N-H(2)) and the improper dihedral angle at nitrogen, four dihedral angles (X-C-N-H(1), Y-C-N-H(2), X-X-C-N, Y-Y-C-N), three valence angles (X-C-N, Y-C-N, X-C-Y), and the improper dihedral angle at the adjacent carbon), and was based on correlated ab initio potential energy surfaces. Calculations were performed using the resolution of identity MP2 (RIMP2) method with SVP (3s2p1d/2s1p), TZVP (5s3p1d/3s1p), TZVPP (5s3p2d1f/3s2p1d), and augTZVPP (6s4p3d2f/4s3p2d) basis sets. Results obtained on the latter two levels are practically identical with the literature reference data [MP2/6-311++G(2df,p)] and the RIMP2/augTZVPP data can be considered a new reference set. The potential energy surface used for reparameterization was evaluated at the RIMP2/SVP level because respective geometry as well as energy data were close to the reference ones, and the computational time was very favorable. The modified potential was tested for 19 H-bonded and eight stacked nucleic acid base pairs. Interaction energies as well as geometries were described by the modified potential considerably better than by the original one and significant improvement resulted in the description of the nonplanar H-bonded and stacked complexes.

Hydrogen bonds lengths in nucleic acids estimated from longitudinal nitrogen-15 relaxation

A new NMR method has been designed for the measurement of the longitudinal relaxation rates of both donor and acceptor nitrogen-15 nuclei in Watson–Crick base pairs in 15N-enriched nucleic acids. The experiment was applied to a 22-nucleotide RNA hairpin. The lengths of four hydrogen bonds could be estimated from the longitudinal relaxation rates.

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.

We present a comprehensive software package, 3DNA, for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. Starting from a coordinate file in Protein Data Bank (PDB) format, 3DNA can handle antiparallel and parallel double helices, single-stranded structures, triplexes, quadruplexes and other complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines identify and categorize all base interactions and classify the double helical character of appropriate base pair steps. The program makes use of a recently recommended reference frame for the description of nucleic acid base pair geometry and a rigorous matrix-based scheme to calculate local conformational parameters and rebuild the structure from these parameters. The rebuilding routines produce rectangular block representations of nucleic acids as well as full atomic models with the sugar-phosphate backbone and publication quality 'standardized' base stacking diagrams. Utilities are provided to locate the base pairs and helical regions in a structure and to reorient structures for effective visualization. Regular helical models based on X-ray diffraction measurements of various repeating sequences can also be generated within the program.

Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations.

Molecular dynamics free-energy calculations of base pair opening within double helical DNA and RNA are used to explain why A-tracts (oligo-adenine repeats) greatly increase the lifetimes of AT base pairs, whereas the structural and the chemical changes involved in passing from B-DNA to A-RNA have comparatively small effects.

Adaptive nudged elastic band approach for transition state calculation

We present a method for the location of transition states in complicated physical systems. Our algorithm is a variation of the well-established nudged elastic band method and leads to significant improvements in efficiency and accuracy. We assess the applicability of our method by testing it on several systems of practical interest representing a variety of physical situations. At the molecular level, we apply the method to tautomerization processes in nucleic acid bases and the double proton transfer in nucleic acid base pairs. For bulk systems, we considered the concerted exchange mechanism in Si, which is a complicated pathway for defect-free diffusion in the diamond lattice. For surface systems, we considered ad-dimer diffusion mechanisms on Si(100). We incorporated the climbing image extension of the nudged elastic band method and compared it against the original approach on two-dimensional model potential energy surfaces. Based on favorable comparisons with related methods and the general implementation of our method, we believe that this is well suited for efficient estimates of activation barriers with sophisticated electronic structure codes.

Comment on “Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory treatment” [J. Chem. Phys. 114, 5149 (2001)

A density-functional-theory (DFT) based treatment for calculating the interaction energies of nucleic acid base pairs proposed recently by Elstner et al. [J. Chem. Phys. 114, 5149 (2001)] is criticized. It is shown that dispersion energy that they evaluated amounts to approximately only 30% of the value obtained in rigorous ab initio calculations. The use of the second-order Mo/ller–Plesset perturbation theory results obtained with the 6-31G*(0.25) basis set as a benchmark for validating the DFT results is also criticized. It is suggested that the method of Elstner et al. requires much more stringent testing before it can be deemed to be “very accurate.”

Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study.

Properties of isolated intercalators (ethidium (E), daunomycin (D), ellipticine (EL), and 4,6'-diaminide-2-phenylindole (DAPI)) and their stacking interactions with adenine...thymine (AT) and guanine...cytosine (GC) nucleic acid base pairs were investigated by means of a nonempirical correlated ab initio method. All intercalators exhibit large charge delocalization, and none of them (including the DAPI dication) exhibits a site with dominant charge. All intercalators have large polarizability and are good electron acceptors, while base pairs are good electron donors. MP2/6-31G*(0.25) stabilization energies of intercalator...base pair complexes are large (E...AT, 22.4 kcal/mol; D...GC, 17.8 kcal/mol; EL...GC, 18.2 kcal/mol; DAPI...GC, 21.1 kcal/mol) and are well reproduced by modified AMBER potential (van der Waals radii of intercalator atoms are enlarged and their energy depths are increased). Standard AMBER potential underestimates binding, especially for DAPI-containing complexes. Because the DAPI dication is the best electron acceptor (among all intercalators studied), this difference is explained by the importance of the charge-transfer term, which is not included in the AMBER potential. For the neutral EL molecule, the standard AMBER force field provides correct results. The Hartree-Fock and DFT/B3LYP methods, not covering the dispersion energy, fail completely to reveal any energy minimum at the potential energy curve of the E...AT complex, and these methods thus cannot be recommended for a study of intercalation process. On the other hand, an approximate version of the DFT method, which was extended to cover London dispersion energy, yields for all complexes very good stabilization energies that are well comparable with referenced ab initio data. Besides the vertical dependence of the interaction, an energy twist dependence of the interaction energy was also investigated by a reference correlated ab initio method and empirical potentials. It is concluded that, despite the cationic (E +1, D +1, DAPI +2) or polar (EL) character of the intercalators investigated, it is the dispersion energy which predominantly contributes to the stability of intercalator...base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation.

ChemInform Abstract: At Nonzero Temperatures, Stacked Structures of Methylated Nucleic Acid/Base Pairs and Mircrohydrated Nonmethylated Nucleic Acid Base Pairs are Favored over Planar Hydrogen‐Bonded Structures: A Molecular Dynamics Simulations Study.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

RNA silencing

RNA silencing

Protonation Studies of Modified Adenine and Adenine Nucleotides by Theoretical Calculations and 15N NMR

The acid/base character of nucleobases affects phenomena such as self-association, interaction with metal ions, molecular recognition by proteins, and nucleic acid base-pairing. Therefore, the investigation of proton-transfer equilibria of natural and synthetic nucleos(t)ides is of great importance to obtain a deeper understanding of these phenomena. For this purpose, a set of ATP prototypes was investigated using (15)N NMR spectroscopy, and the corresponding adenine bases were investigated by theoretical calculations. (15)N NMR measurements provided not only acidity constants but also information on the protonation site(s) on the adenine ring and regarding the ratio of the singly protonated species in equilibrium. Substituents of different nature and position on the adenine ring did not change the preferred protonation site, which remained N1. However, for 2-thioether-ATP derivatives a mixed population of N1 and N7 singly protonated species was observed. Reduction of basicity of 0.4-1 pK(a) units relative to ATP was also observed for all evaluated ATP derivatives, except for 2-Cl-ATP, for which K(a) was ca. 10,000-fold lower. To explain the substitution-dependent variations in the experimental pK(a) values of the ATP analogues, gas-phase proton affinities (PA), Delta Delta G(hyd), and pK(a) values of the corresponding adenine bases were calculated using quantum mechanical methods. The computed PA and Delta Delta G(hyd) values successfully explained the experimental pK(a) values. A computational procedure for the prediction of accurate pK(a) values was developed using density functional theory and polarizable continuum model calculations. In this procedure, we developed a set of parameters for the polarizable continuum model that was fitted to reproduce experimental pK(a) values of nitrogen heterocycles. This method is proposed for the prediction of pK(a) values and protonation site(s) of purine analogues that have not been synthesized or analyzed.

Labeling fluorescence in situ hybridization probes for RNA targets.

Ribonucleic acids (RNA) can be detected in cellular specimens by fluorescence in situ hybridization (FISH) using labeled RNA, deoxyribonucleic acid (DNA), or nucleic acids analogs. The RNA targets are often messenger RNA (mRNA) molecules that have been transcribed from the genomic DNA. Specific mRNA sequences can be selectively identified out of the many co-expressed mRNA molecules owing to the high specificity of nucleic acid base pairing. The analysis of selected mRNA sequences is an important measure of many cellular properties, including, for example, the identification of specific cell types, the identification of different stages of cell differentiation, and measuring abnormal mRNA expression, as often accompanies cancer development. RNA probes can be directly conjugated with fluorescent labels, or conjugated with labels that specifically associate with fluorescent compounds. Once hybridized, the presence and relative abundance of an RNA target can be qualitatively assessed visually based on the fluorescence intensity, or in a more quantitative fashion, by digital imaging and image analysis.

Intermolecular vibrations of the jet-cooled 2-pyridone⋅2-hydroxypyridine mixed dimer, a model for tautomeric nucleic acid base pairs

The 2-pyridone⋅2-hydroxypyridine mixed dimer, 2PY⋅2HP, is linked by antiparallel N–H⋯N and O–H⋯O hydrogen bonds, closely analogous to tautomeric hydrogen-bonded DNA base pairs such as isoguanine⋅uracil. Mass-selected S1←S0 vibronic spectra of supersonic jet-cooled 2PY⋅2HP and three N–D or O–D deuterated isotopomers were measured by two-color resonant two-photon ionization and UV/UV-holeburning techniques. S1→S0 fluorescence spectra show intense hydrogen bond stretching vibrations ν6″=158 cm−1, observed for all four isotopomers and the weak ν5″ “shear” vibration at 116 cm−1. The “slanting” intermolecular vibration ν4″=89 cm−1 was tentatively identified via the 2ν4″ overtone. The observation of 2-pyridone intramolecular overtone and combination transitions for two out-of-plane modes indicate slight nonplanarity of the 2-pyridone moiety in the S1 state. Ab initio calculations using Hartree–Fock, configuration interaction among single excitations (CIS), and B3LYP density functional methods were employed to calculate ground- and excited-state structures, rotational constants, harmonic intermolecular and intramolecular vibrational frequencies, binding energies De, and dissociation energies D0. The B3LYP/6-311++(d,p) ν4″ and ν6″ frequencies are in very good agreement with the experimental ground-state intermolecular frequencies. Electronic excitation of the 2-pyridone moiety in 2PY⋅2HP leads to a decrease of dissociation energy by 2.36 kcal/mol and a concurrent increase of H bond lengths by ≈0.08 Å, in qualitative agreement with the self-consistent field (SCF) and CIS ab initio calculations.