Uracil Base Pairs Research Articles

Intramolecular vibrational energy redistribution in nucleobases: Excitation of NH stretching vibrations in adenine-uracil + H2O.

Redistribution of vibrational energy in the adenine-uracil base pair is studied when the base pair undergoes an intermolecular interaction with an overtone-bending vibration excited H2O(2νbend) molecule. Energy transfer is calculated using the structural information obtained from density functional theory in the solution of the equations of motion. Intermolecular vibrational energy transfer (VET) from H2O(2νbend) to the uracil-NH stretching mode is efficient and rapidly followed by intramolecular vibrational energy redistribution (IVR) resulting from coupling between vibrational modes. An important pathway is IVR carrying energy to the NH-stretching mode of the adenine moiety in a subpicosecond scale, the energy build-up being sigmoidal, when H2O interacts with the uracil-NH bond. The majority of intermolecular hydrogen bonds between the base pair and H2O are weakened but unbroken during the ultrafast energy redistribution period. Lifetimes of intermolecular HB are on the order of 0.5ps. The efficiency of IVR in the base pair is due to near-resonance between coupled CC and CN vibrations. The resonance also exists between the frequencies of H2O bend and NH stretch, thus facilitating VET. When H2O interacts with the NH bond at the adenine end of the base pair, energy flow in the reverse direction to the uracil-NH stretch is negligible, the unidirectionality discussed in terms of the effects of uracil CH stretches. The energy distributed in the CH bonds is found to be significant. The IVR process is found to be nearly temperature independent between 200 and 400K.

Dinuclear Metal-Mediated Guanine–Uracil Base Pairs: Theoretical Studies of GUM22+ (M = Cu, Ag, and Au) Ions

Dinuclear metal-mediated hetero base pairs with the d10–d10 closed-shell interactions have significant stability. It is interesting to identify whether coinage metal-mediated Wobble base pairs are also stable. Geometric and electronic structures of the lowest-lying isomers of GUM22+ (G = guanine, U = uracil, M = Cu, Ag, and Au) cluster ions were investigated with density functional theory. In the lowest-lying isomers of these dinuclear metal-mediated base pairs, the 2-oxo-4-hydroxy-trans-N1H isomer of uracil is derived from the canonical tautomer of uracil by the hydrogen atom transfer. M22+ cations remain as an unbroken unit and interact with the G···U ligand through two sets of closely linear N···M···O units, while the reciprocal hydrogen bonds between the Wobble base pair (G–U) are entirely substituted by the M–N or M–O interactions in these complexes. The atoms in molecules and EDA–NOCV calculations really reveal that the σ interactions in GUM22+ cations are the paramount term of ΔEOrb. The obtained instantaneous interaction energies ΔEint and bond dissociation energies of the metal–ligand interactions give the trend of the bond strength as Cu > Au > Ag.

Role of Inosine⁻Uracil Base Pairs in the Canonical RNA Duplexes.

Adenosine to inosine (A–I) editing is the most common modification of double-stranded RNA (dsRNA). This change is mediated by adenosine deaminases acting on RNA (ADARs) enzymes with a preference of U>A>C>G for 5′ neighbor and G>C=A>U or G>C>U=A for 3′ neighbor. A–I editing occurs most frequently in the non-coding regions containing repetitive elements such as ALUs. It leads to disruption of RNA duplex structure, which prevents induction of innate immune response. We employed standard and biased molecular dynamics (MD) simulations to analyze the behavior of RNA duplexes with single and tandem inosine–uracil (I–U) base pairs in different sequence context. Our analysis showed that the I–U pairs induce changes in base pair and base pair step parameters and have different dynamics when compared with standard canonical base pairs. In particular, the first I–U pair from tandem I–U/I–U systems exhibited increased dynamics depending on its neighboring 5′ base. We discovered that UII sequence, which is frequently edited, has lower flexibility compared with other sequences (AII, GII, CII), hence it only modestly disrupts dsRNA. This might indicate that the UAA motifs in ALUs do not have to be sufficiently effective in preventing immune signaling.

Theoretical study of mechanisms for double proton transfer in adenine–uracil base pair via steered molecular dynamic simulations

Gibbs free energy profiles for the A–U ⇆ A*–U* tautomeric equilibrium between the canonical and non-canonical base pair in aqueous solution have been obtained by applying Steered Molecular Dynamic (SMD) technique. Concerted and stepwise mechanisms have been considered to explain the double proton transfer process. Among the different mechanisms studied, the stepwise mechanism was the fastest due to the lower energy barrier (∆G‡ = 31.72 kcal·mol−1) respect to the concerted process, both having a reaction energy about 25 kcal·mol−1. The inclusion of two water molecules to assist the transfer process slightly modified the reaction energy (∆G = 28.09 kcal·mol−1), while increasing the barrier considerably (∆G‡ = 65.76 kcal·mol−1). From the results obtained, we can say that the A–U pair of bases presents a Gibbs free energy profile similar to the A–T pair and that it could participate in a process of spontaneous genetic mutation depending on the mechanism followed. Finally, the stationary points along the energy profile for all the mechanisms were analyzed at molecular dynamics levels, finding that the transition states have geometries very similar to those of the products.

Effect on frontier molecular orbitals of substituents in 5-position of uracil base pairs in vacuum and water

The most stable structure of 5-substituted uracil base pairs and metal-mediated-5-substituted uracil complexes are determined. Density functional theory (DFT) method is used in the calculations which are carried out both in vacuum and water. LANL2DZ and 6–311[Formula: see text]G(d,p) basis sets are used for metals and the rest atoms, respectively. Effects on frontier molecular orbitals and energy gaps of substituents in 5-position of uracil base pairs in vacuum and water are found. Conductivity of base pairs or complexes are investigated for single nanowires studied by band theory. It is expected that this study will be an example for future studies that require new nanotechnological applications.

DFT study on metal-mediated uracil base pair complexes

The most stable of metal-mediated uracil base pair complexes were determined. Method was used density functional theory, B3LYP. The calculations of systems containing C, H, N, O were described by 6-311++G(d,p) and cc-PVTZ basis sets and LANL2DZ and SDD basis sets was used for transition metals. Then Egap values of complexes were calculated and the electrical conductivity of the complexes for single nanowires was studied by band theory. Metal-mediated uracil base pair complexes which will be used as conductive wires in nanotechnology were predicted. In nanoworld, this study is expected to show a way for practical applications.

Conflict RNA modification, host-parasite co-evolution, and the origins of DNA and DNA-binding proteins1.

Nearly 150 different enzymatically modified forms of the four canonical residues in RNA have been identified. For instance, enzymes of the ADAR (adenosine deaminase acting on RNA) family convert adenosine residues into inosine in cellular dsRNAs. Recent findings show that DNA endonuclease V enzymes have undergone an evolutionary transition from cleaving 3' to deoxyinosine in DNA and ssDNA to cleaving 3' to inosine in dsRNA and ssRNA in humans. Recent work on dsRNA-binding domains of ADARs and other proteins also shows that a degree of sequence specificity is achieved by direct readout in the minor groove. However, the level of sequence specificity observed is much less than that of DNA major groove-binding helix-turn-helix proteins. We suggest that the evolution of DNA-binding proteins following the RNA to DNA genome transition represents the major advantage that DNA genomes have over RNA genomes. We propose that a hypothetical RNA modification, a RRAR (ribose reductase acting on genomic dsRNA) produced the first stretches of DNA in RNA genomes. We discuss why this is the most satisfactory explanation for the origin of DNA. The evolution of this RNA modification and later steps to DNA genomes are likely to have been driven by cellular genome co-evolution with viruses and intragenomic parasites. RNA modifications continue to be involved in host-virus conflicts; in vertebrates, edited cellular dsRNAs with inosine-uracil base pairs appear to be recognized as self RNA and to suppress activation of innate immune sensors that detect viral dsRNA.

Enzymatic Excision of Uracil Residues in Nucleosomes Depends on the Local DNA Structure and Dynamics

The excision of uracil bases from DNA is accomplished by the enzyme uracil DNA glycosylase (UNG). Recognition of uracil bases in free DNA is facilitated by uracil base pair dynamics, but it is not known whether this same mechanistic feature is relevant for detection and excision of uracil residues embedded in nucleosomes. Here we investigate this question using nucleosome core particles (NCPs) generated from Xenopus laevis histones and the high-affinity "Widom 601" positioning sequence. The reactivity of uracil residues in NCPs under steady-state multiple-turnover conditions was generally decreased compared to that of free 601 DNA, mostly because of anticipated steric effects of histones. However, some sites in NCPs had equal or even greater reactivity than free DNA, and the observed reactivities were not readily explained by simple steric considerations or by global DNA unwrapping models for nucleosome invasion. In particular, some reactive uracils were found in occluded positions, while some unreactive uracils were found in exposed positions. One feature of many exposed reactive sites is a wide DNA minor groove, which allows penetration of a key active site loop of the enzyme. In single-turnover kinetic measurements, multiphasic reaction kinetics were observed for several uracil sites, where each kinetic transient was independent of the UNG concentration. These kinetic measurements, and supporting structural analyses, support a mechanism in which some uracils are transiently exposed to UNG by local, rate-limiting nucleosome conformational dynamics, followed by rapid trapping of the exposed state by the enzyme. We present structural models and plausible reaction mechanisms for the reaction of UNG at three distinct uracil sites in the NCP.

Identification of Escherichia coli Mismatch-specific Uracil DNA Glycosylase as a Robust Xanthine DNA Glycosylase

The gene for the mismatch-specific uracil DNA glycosylase (MUG) was identified in the Escherichia coli genome as a sequence homolog of the human thymine DNA glycosylase with activity against mismatched uracil base pairs. Examination of cell extracts led us to detect a previously unknown xanthine DNA glycosylase (XDG) activity in E. coli. DNA glycosylase assays with purified enzymes indicated the novel XDG activity is attributable to MUG. Here, we report a biochemical characterization of xanthine DNA glycosylase activity in MUG. The wild type MUG possesses more robust activity against xanthine than uracil and is active against all xanthine-containing DNA (C/X, T/X, G/X, A/X and single-stranded X). Analysis of potentials of mean force indicates that the double-stranded xanthine base pairs have a relatively narrow energetic difference in base flipping, whereas the tendency for uracil base flipping follows the order of C/U > G/U > T/U > A/U. Site-directed mutagenesis performed on conserved motifs revealed that Asn-140 and Ser-23 are important determinants for XDG activity in E. coli MUG. Molecular modeling and molecular dynamics simulations reveal distinct hydrogen-bonding patterns in the active site of E. coli MUG that account for the specificity differences between E. coli MUG and human thymine DNA glycosylase as well as that between the wild type MUG and the Asn-140 and Ser-23 mutants. This study underscores the role of the favorable binding interactions in modulating the specificity of DNA glycosylases.

Double proton transfer mechanism in the adenine–uracil base pair and spontaneous mutation in RNA duplex

We study the mechanism of double proton transfer (DPT) in the adenine–uracil (AU) base pair, both in gas phase and under the influence of surrounding water molecules. According to our ab initio calculations, no stable proton transfer product exists in gas phase, while in solution, the DPT process may occur only through the catalysis of water molecules. Nevertheless, a thermodynamic analysis confirms that AU does not contribute to spontaneous mutation in RNA duplex, and thus guanine–cytosine (GC) would be the only base pair contributing to spontaneous mutation.

Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description.

We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantum-mechanics (QM) methods. Nonparallel stacking geometries often occur in nucleic acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the short-range repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference QM calculations have been carried out using the MP2 method extrapolated to the complete basis-set limit and corrected for higher-order electron-correlation contributions using CCSD(T) calculations with a medium-sized basis set. These reference calculations have been used as benchmark data to test the performance of the DFT-D, SCS(MI)-MP2, and DFT-SAPT QM methods and of the AMBER molecular-mechanics (MM) force field. The QM methods show close to quantitative agreement with the reference data, albeit the DFT-D method tends to modestly exaggerate the repulsion of steric clashes. The force field in general also provides a good description of base stacking for the systems studied here. However, for geometries with close interatomic contacts and clashes, the repulsion effects are rather severely exaggerated. The discrepancy reported here should not affect the overall stability of MD simulations and qualitative applications of the force field. However, it may affect the description of subtle quantitative effects such as the local conformational variations in B-DNA. Preliminary calculations for two H-bonded uracil base pairs, including one with a C-H···O H-bond, indicate excellent performance of the tested QM methods for all intermonomer distances. The force field, on the other hand, is less satisfactory, especially in the repulsive regions.

Do Anionic Gold Clusters Modify Conventional Hydrogen Bonds? The Interaction of Anionic Aun (n = 2−4) with the Adenine−Uracil Base Pair

Density functional approximation (B3LYP) calculations have been used in order to analyze the interaction of gold anionic clusters (Au(n) with n = 2-4) with uracil ([uracil-Au(n)](-1)), adenine ([adenine-Au(n)](-1)), and the adenine-uracil base pair ([uracil-adenine-Au(n)](-1)). It was found that there is only one stable isomer for [uracil-Au(2)](-1) and [uracil-Au(3)](-1), whereas there are two or more stable structures for [uracil-Au(4)](-1), [adenine-Au(n)](-1), and [uracil-adenine-Au(n)](-1). For all these systems, nonconventional hydrogen bonds are formed. Strengthening the bond between anionic gold clusters and the nitrogen base pair weakens the conventional hydrogen bond of the adenine-uracil base pair. This destabilization is not very strong (2-4 kcal/mol) and is at the limits of calculations, but anionic gold clusters bound in between the uracil-adenine base pair indicate that gold anionic clusters may dissociate it. These results will be useful for further experimental studies and may be important for future applications.

Structures and Energetics of the Deprotonated Adenine−Uracil Base Pair, Including Proton-Transferred Systems

The B3LYP/DZP++ level of theory has been employed to investigate the structures and energetics of the deprotonated adenine-uracil base pairs, (AU-H)-. Formation of the lowest-energy structure, [A(N9)-U]- (which corresponds to deprotonation at the N9 atom of adenine), through electron attachment to the corresponding neutral is accompanied by proton transfer from the uracil N3 atom to the adenine N1 atom. The driving force for this proton transfer is a significant stabilization from the base pairing in the proton transferred form. Such proton transfer upon electron attachment is also observed for the [A(N6b)-U]- and [A(C2)-U]- anions. Electron attachment to the A-U(N3) radical causes strong lone pair repulsion between the adenine N1 and the uracil N3 atoms, driving the two bases apart. Similarly, lone pair repulsion in the anion A(N6a)-U causes the loss of coplanarity of the two base units. The computed adiabatic electron attachment energies for nine AU-H radicals range from 1.86 to 3.75 eV, implying that the corresponding (AU-H)- anions are strongly bound. Because of the large AEAs of the (AU-H) radicals, the C-H and N-H bond dissociation in the AU- base pair anions requires less energy than the neutral AU base pair. The computed C-H and N-H bond dissociation energies for the AU- anion (i.e., the AU base pair plus one electron) are in the range 1.0-3.2 eV, while those for neutral AU are 4.08 eV or higher.

Effects of Microsolvation on the Adenine−Uracil Base Pair and Its Radical Anion: Adenine−Uracil Mono- and Dihydrates

Microhydration effects upon the adenine-uracil (AU) base pair and its radical anion have been investigated by explicitly considering various structures of their mono- and dihydrates at the B3LYP/DZP++ level of theory. For the neutral AU base pair, 5 structures were found for the monohydrate and 14 structures for the dihydrate. In the lowest-energy structures of the neutral mono- and dihydrates, one and two water molecules bind to the AU base pair through a cyclic hydrogen bond via the N(9)-H and N(3) atoms of the adenine moiety, while the lowest-lying anionic mono- and dihydrates have a water molecule which is involved in noncyclic hydrogen bonding via the O4 atom of the uracil unit. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of the AU base pair are predicted to increase upon hydration. While the VDE and AEA of the unhydrated AU pair are 0.96 and 0.40 eV, respectively, the corresponding predictions for the lowest-lying anionic dihydrates are 1.36 and 0.75 eV, respectively. Because uracil has a greater electron affinity than adenine, an excess electron attached to the AU base pair occupies the pi* orbital of the uracil moiety. When the uracil moiety participates in hydrogen bonding as a hydrogen bond acceptor (e.g., the N(6)-H(6a)...O(4) hydrogen bond between the adenine and uracil bases and the O(w)-H(w)...N and O(w)-H(w)...O hydrogen bonds between the AU pair and the water molecules), the transfer of the negative charge density from the uracil moiety to either the adenine or water molecules efficiently stabilizes the system. In addition, anionic structures which have C-H...O(w) contacts are energetically more favorable than those with N-H...O(w) hydrogen bonds, because the C-H...O(w) contacts do not allow the unfavorable electron density donation from the water to the uracil moiety. This delocalization effect makes the energetic ordering for the anionic hydrates very different from that for the corresponding neutrals.

A Theoretical Investigation of Excited-State Properties of the Adenine−Uracil Base Pair

Molecular geometries of adenine−uracil (AU) base pair were optimized in the ground and selected low-lying singlet ππ* and nπ* excited states. The ground-state geometry optimized at the Hartree−Fock level of theory without symmetry restrictions was found to be planar; the predicted planarity was validated by harmonic vibrational frequency calculations. Excited states were generated employing the configuration interaction technique involving singly excited configurations (CIS method) using a ground-state-optimized geometry, and this was followed by excited-state geometry optimizations under planar symmetry. The 6-31++G(d,p) basis set was used in all calculations. The computed electronic transitions of adenine and uracil after linear scaling were found to be in good agreement with the corresponding experimental data. Electronic excitations were found to be localized at either of the monomeric units. It is predicted that among the states studied here the AU base pair has one charge transfer type singlet excit...

A Novel Theoretical Model for Molecular Recognition of Multiple-Site Interacting Systems Using Density Response Functions

We present the first theoretical study of molecular recognition of systems interacting via multiple sites, using the density response functions. The model, so-called, localized reactive model derived on the basis of these functions, has been employed for studying the interactions between Watson−Crick type DNA base pairs and the effect of substitution of various groups in the adenine−uracil base pairs. The estimated interaction energies for these base pairs agree remarkably with the corresponding literature and experimental values. It confirms the applicability of the present model to such complex multiple-site interaction cases and can be used as potential predictive tool for the understanding of such general molecular interaction or recognition processes.

Combined Mass Spectrometric and ab Initio Study of the Point Contacts between 9-Methyladenine and the Amide Group

We applied the temperature-dependent field ionization mass spectrometry method to determine the interaction energy between 9-methyladenine and acrylamide. Acrylamide mimics the side chain amide group of the natural amino acids asparagine and glutamine. The experimental enthalpy of the dimer formation derived from van't Hoff's plot is −52.0 ± 5.0 kJ mol-1. This value is close to the interaction energy between acrylamide and 1-methylcytosine (−57.0 kJ mol-1) and much higher than the interaction energy between acrylamide and 1-methyluracil (−40.6 kJ mol-1). The DFT/B3LYP/6-31++G** and MP2/6-31++G** quantum-chemical methods were used to determine the structures and the interaction energies of the 9-methyladenine−acrylamide dimers. In the calculations, two energetically almost equivalent equilibrium structures were found. They are stabilized by intermolecular H-bonds formed between the acrylamide amide group and the Watson−Crick and Hoogsteen sites of 9-methyladenine, respectively. The calculated interaction energies of the dimers are −41.4 and −39.2 kJ mol-1, respectively, at the DFT level of theory and −40.9 and −38.8 kJ mol-1, respectively, at the MP2 level. We also performed calculations for 9-methyladenine−glutamine dimers at the DFT/B3LYP/6-31++G** level of theory. The interaction energy differences between the corresponding 9-methyladenine−acrylamide and 9-methyladenine−glutamine dimers of less than 1 kJ mol-1 were obtained in the calculations. This result demonstrates that acrylamide is a good model for the amino acid amide group. The experimantal and the calculated data indicate that the amino acid amide group can interact with the adenine residue in the single-stranded DNA, as well as in the major groove of double-stranded DNA. The influence of the interaction with the amide group on the stability of the adenine−uracil base pair is discussed.

Specific Solvation Effects on the Structures and Properties of Neutral and One-Electron Oxidized Formamidine−Formamide Complexes. A Theoretical ab Initio Study

Ab initio quantum chemical calculations were performed for the neutral and one-electron oxidized formamidine−formamide model systems in the gas phase and in a water solution. Full geometry optimizations without any constraints on the planarity of these complexes were carried out at the HF/6-31G* level. For the neutral dimers, the solvent effects were modeled by explicit inclusion of four, six, and nine water molecules, which creates the first, intermediate, and second hydration spheres around these dimers. For one-electron oxidized systems, we have accounted for the effects of the first hydration shell water molecules. Single point calculations were also performed at the correlated MP2/6-31G*//HF/6-31G* level. The interaction and solvation energies were corrected for the basis set superposition error. It was shown that the relative stability of the neutral model formamidine−formamide complexes is quite opposite to that of the analogous adenine−uracil base pairs (J. Phys. Chem. A 1998, 102, 6167): the double proton transferred FF2 dimer becomes more stable than the zwitterionic FF3 dimer. An increase in the number of water molecules from the first to the second hydration shell results in an overestimated stability for the FF3 zwitterionic structure. For a one-electron oxidation process, the FF3(+) cation−radical dimer is the most stable dimer while the double-proton-transfer process becomes the least favorable process in both the gas phase and in a water solution.

The exocyclic groups of DNA modulate the affinity and positioning of the histone octamer.

To investigate the nature of the chemical determinants in DNA required for nonspecific binding and bending by proteins we have created a novel DNA in which inosine-5-methylcytosine and 2, 6-diaminopurine-uracil base pairs are substituted for normal base pairs in a defined DNA sequence. This procedure completely switches the patterns of the base pair H bonding and attachment of exocyclic groups. We show that this DNA binds a histone octamer more tightly than normal DNA but, surprisingly, does not alter the orientation of the sequence on the surface of the protein. However, in general, the addition or removal of DNA exocyclic groups reduces or increases, respectively, the affinity for the histone octamer. The average incremental change in binding energy for a single exocyclic group is approximately 40 J/mol. The orientation of the DNA in core nucleosomes also is sensitive to the number and nature of the exocyclic groups present. Notably, substitution with the naturally occurring cytosine analogue, 5-methylcytosine, shifts the preferred rotational position by 3 bp, whereas incorporating 2,6-diaminopurine shifts it 2 bp in the opposite direction. These manipulations potentially would alter the accessibility of a protein recognition sequence on the surface of the histone octamer. We propose that exocyclic groups impose steric constraints on protein-induced DNA wrapping and are also important in determining the orientation of DNA on a protein surface. In addition, we consider the implications of the selection of A-T and G-C base pairs in natural DNA.

Synthesis of Artificial Receptors having Uracil Base Pairs Linked Through Spacers Containing Ether and Ester Moieties

Synthesis of Artificial Receptors having Uracil Base Pairs Linked Through Spacers Containing Ether and Ester Moieties