Guanine-cytosine Base Pair Research Articles

Revisiting the Hole Size in Double Helical DNA with Localized Orbital Scaling Corrections.

The extent of electronic wave function delocalization for the charge carrier (electron or hole) in double helical DNA plays an important role in determining the DNA charge transfer mechanism and kinetics. The size of the charge carrier's wave function delocalization is regulated by the solvation induced localization and the quantum delocalization among the π stacked base pairs at any instant of time. Using a newly developed localized orbital scaling correction (LOSC) density functional theory method, we accurately characterized the quantum delocalization of the hole wave function in double helical B-DNA. This approach can be used to diagnose the extent of delocalization in fluctuating DNA structures. Our studies indicate that the hole state tends to delocalize among 4 guanine-cytosine (GC) base pairs and among 3 adenine-thymine (AT) base pairs when these adjacent bases fluctuate into degeneracy. The relatively small delocalization in AT base pairs is caused by the weaker π-π interaction. This extent of delocalization has significant implications for assessing the role of coherent, incoherent, or flickering coherent carrier transport in DNA.

A Kinetic Approach to Double Proton Transfer in Watson-Crick DNA Base Pairs.

Double proton transfer (DPT) in guanine-cytosine (GC) base pairs and adenine-thymine (AT) base pairs produces tautomeric forms, denoted G*C* and A*T*. To examine DPT, (i) intrinsic reaction coordinates for DPT, (ii) probabilities of change from GC to G*C* and from AT to A*T*, and (iii) infrared absorption intensities of GC and G*C* were investigated on the basis of density functional theory and Eyring's chemical kinetics. The probabilities of change from GC to G*C* were 3 × 10-8, and those from AT to A*T* were 2 × 10-10. These values are consistent with the rate of mutation previously reported by Drake et al. (Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 7160-7164). G*C* exhibited two vibrational modes around 3000 cm-1, whereas GC exhibited no vibrational modes around the same frequency. The infrared intensity calculated for G*C* showed that the strong absorption obtained around 3000 cm-1 was caused by one of the two modes.

Tautomeric effect of guanine on stability, spectroscopic and absorbance properties in cytosine–guanine base pairs: a DFT and TD-DFT perspective

A comparative study of the tautomeric effect of guanine (G) on stability, spectral properties, and optical response in canonical and noncanonical cytosine–guanine (C–G) base pairs has been investigated by employing density functional theory (DFT) and time-dependent DFT. Three keto-G tautomers (G1, G2, G3) have taken to interact with the C monomer of W–C type which in turn gives three C–G base pairs (C–G1, C–G2, and C–G3) with three conventional H-bonds. The geometry optimization with various ground-state properties and spectroscopic details has been estimated in the gas phase using Cam-B3LYP functional with two different basis sets 6-311++G (d, p) and Aug-cc-pVDZ at the DFT level. The W–C base pair C–G1 possesses the lowest electronic energy although G1 is not the lowest energy structure of guanine. C–G3 is found to have maximum binding and H-bond energies. Significant changes have been observed in IR and Raman spectra of C–G clusters due to the tautomeric effect of G monomer. All the absorption spectra of C–G clusters belong to the UV region, and the electronic excitations are associated with π → π* transition. The molecular orbitals associated with the electronic transitions reveal the intermolecular charge transfer characteristic of G1, G3 to C monomer. Besides this, the electrostatic potential surface plots have been used to explore the possible binding sites of isolated bases and base pairs. As the tautomeric effect influences the chemical reactions, this study can be useful for drug designing and to find the best fit between the receptors and important ligands.

Is non-statistical dissociation a general feature of guanine-cytosine base-pair ions? Collision-induced dissociation of a protonated 9-methylguanine-1-methylcytosine Watson-Crick base pair, and comparison with its deprotonated and radical cation analogues.

A guided-ion beam tandem mass spectrometric study was performed on collision-induced dissociation (CID) of a protonated 9-methylguanine-1-methylcytosine Watson-Crick base pair (designated as WC-[9MG·1MC + H]+), from which dissociation pathways and dissociation energies were determined. Electronic structure calculations at the DFT, RI-MP2 and DLPNO-CCSD(T) levels of theory were used to identify product structures and delineate reaction mechanisms. Intra-base-pair proton transfer (PT) of WC-[9MG·1MC + H]+ results in conventional base-pair conformations that consist of hydrogen-bonded [9MG + H]+ and 1MC and proton-transferred conformations that are formed by PT from the N1 of [9MG + H]+ to the N3' of 1MC. Two types of conformers were distinguished by CID in which the conventional conformers produced [9MG + H]+ product ions whereas the proton-transferred conformers produced [1MC + H]+. The conventional conformers have a higher population (99.8%) and lower dissociation energy than the proton-transferred counterparts. However, in contrast to what was expected from the statistical dissociation of the equilibrium base-pair conformational ensemble, the CID product ions of WC-[9MG·1MC + H]+ were dominated by [1MC + H]+ rather than [9MG + H]+. This finding, alongside the non-statistical CID reported for deprotonated guanine-cytosine (Lu et al.; PCCP, 2016, 18, 32222) and guanine-cytosine radical cation (Sun et al.; PCCP, 2020, 22, 14875), reinforces that non-statistical dissociation is a distinctive feature of singly-charged Watson-Crick guanine-cytosine base pairs. It implies that intra-base-pair PT facilitates the formation of proton-transferred conformers in these systems and the ensuing conformers have loose transition states for dissociation. The monohydrate of WC-[9MG·1MC + H]+ preserves non-statistical CID kinetics and introduces collision-induced methanol elimination via the reaction of the water ligand with a methyl group.

Energy decomposition analysis based on broken symmetry unrestricted density functional theory.

In this paper, the generalized Kohn-Sham energy decomposition analysis (GKS-EDA) scheme is extended to molecular interactions in open shell singlet states, which is a challenge for many popular EDA methods due to the multireference character. Based on broken symmetry (BS) unrestricted density functional theory with a spin projection approximation, the extension scheme, named GKS-EDA(BS) in this paper, divides the total interaction energy into electrostatic, exchange-repulsion, polarization, correlation, and dispersion terms. Test examples include the pancake bond in the phenalenyl dimer, the ligand interactions in the Fe(ii)-porphyrin complexes, and the radical interactions in dehydrogenated guanine-cytosine base pairs and show that GKS-EDA(BS) is a practical EDA tool for open shell singlet systems.

DFT simulation of Watson–Crick-like guanine–thymine mismatch in quaternary systems involving DNA bases

ABSTRACTThe aim of this work is to theoretically investigate the guanine–thymine mismatch in the presence of adenine–thymine and guanine–cytosine base pairs. At M06-2X/6-311++G(d,p) level, the absolute values of formation energy of quaternary systems increase by going from systems having enol form of guanine (G*) to those containing enol tautomer of thymine (T*). Moreover, the stacking between T* and purine bases, in comparison with pyrimidine bases, increases the stability of quaternary systems having T*. On the other hand, the stacking between G* and pyrimidine bases more stabilises systems involving G*. From a thermodynamic point of view, the quaternary systems containing G−T* can transform their geometries into systems having G*−T. To gain a better understanding of the influence of hydrogen bonds on the stability of systems, the atoms in molecules and natural bond orbital analyses are used to evaluate the strength of hydrogen bonds in the investigated systems.

Proton Transfer in Guanine-Cytosine Base Pairs in B-DNA.

A double proton transfer reaction in a guanine-cytosine (GC) base pair has been proposed as a possible mechanism for rare tautomer (G*C*) formation and thus a source of spontaneous mutations. We analyze this system with free energy calculations based on extensive Quantum Mechanics/Molecular Mechanics simulations to properly consider the influence of the DNA biomolecular environment. We find that, although the G*C* rare tautomer is metastable in the gas phase, it is completely unstable in the conditions found in cells. Thus, our calculations show that a double proton reaction cannot be the source of spontaneous point mutations. We have also analyzed the intrabase H transfer reactions in guanine. Our results show that the DNA environment gives rise to a large free energy difference between the rare and canonical tautomers. These results show the key role of the DNA biological environment for the stability of the genetic code.

Electron Attachment to DNA Base Pairs: An Interplay of Dipole- and Valence-Bound States.

We have investigated the electron-attached states in Watson-Crick guanine-cytosine and adenine-thymine base pairs using the highly accurate equation-of-motion coupled-cluster (EOM-CC) method and extended basis sets. Both base pairs have two bound anionic states. The dipole-bound state is stable even at the neutral geometry, but the valence-bound state is only adiabatically bound. The initial electron attachment results in the formation of a dipole-bound state that acts as a doorway to the valence-bound anionic state. The adiabatic potential energy surface of ground and first excited states of an anion shows an avoided crossing, indicating mixing of the electronic and nuclear degrees of freedom. We have calculated the coupling strength between the valence- and dipole-bound states by fitting a simple diabatic model potential to a cut through the two adiabatic surfaces of the anions obtained from the EOM-CC calculations. The transfer of the electron from the initial dipole-bound to the final valence-bound state has been found to happen at an ultrafast time scale.

Remote sensing of Salmonella-specific DNA fragment by using nanoporous alumina modified with the single-strand DNA probe

Foodborne Salmonella disease is a major public health concern. Therefore, it is crucial to design a reliable biosensor to the diagnosis of this disease. Herein, we fabricated an interferometric reflectance spectroscopy (IRS) based DNA sensor for the determination of Salmonella-specific DNA fragment concentration. For this purpose, the nanoporous anodic alumina (NAA) was first fabricated. The pore walls of NAA were then functionalized with 3-aminopropyl tri-methoxy silane (NAA-NH2). After that, the amino-terminated single strand DNAsal (ssDNAsal) probe was immobilized on NAA-NH2 by the use of glutaraldehyde (Glu) as cross-linker. To detect the amount of Salmonella-specific DNA fragment, the different concentrations of Salmonella-specific DNA fragment were pumped to the analytical flow cell. Subsequently, methylene blue (MB) was pumped to the analytical flow cell to intercalate between guanine-cytosine base pairs. The intercalated MB into double-strand DNA absorbed the transferred white light to the DNA sensor and therefore, the intensity of the reflected light from the DNA sensor to the charge-coupled device detector decreased. The decrease in the intensity of the reflected light consequent on the decrease in the peak area of the IRS in the wavelength range of 450–1050 nm (peak area450-1050 nm). The decrease in the peak area450-1050 nm had a good linear relationship with the concentration of Salmonella-specific DNA fragment in the range of 0.25–50.0 nM. The limit of detection was found to be 0.01 nM. The fabricated DNA sensor had a good selectivity to Salmonella-specific DNA fragment in the presence of Staphylococcus aureus-specific DNA fragment and Escherichia coli-specific DNA fragment.

Unraveling the Modulation of the Activity in Drugs Based on Methylated Phenanthroline When Intercalating between DNA Base Pairs.

Phenanthroline derivatives intercalate between base pairs of DNA and produce cytotoxic effects against tumoral cells. Nevertheless, modulation of their efficiency by substitution remains unclear in bibliography. In this work, the effects of methylation of phenanthroline, in number and position, when it intercalates between guanine-cytosine base pairs (GC/CG), were studied with PM6-DH2 and DFT-D methods including dispersion corrections. An analysis of the geometries, electronic structure, and energetics in the interaction was carried out for the studied systems. Our results were compared to experimental works to gain insight on the relation structure-interaction for the intercalated system with cytotoxicity. The trends are explained including not only intrinsic contributions to energy, ΔEPauli, ΔEdisp, ΔEorb, and ΔEelstat, but also the solvation energy, ΔESolv. A subtle balance between the number of stabilizing weak interactions (CH/π, CH/n, etc.) and steric hindrance seems to be related to the efficiency of such drugs.

Base-Pair Contents and Sequences of DNA Double Helices Differentiated by Surface-Enhanced Raman Spectroscopy.

Direct, label-free sequence analysis of DNA hybridization has been achieved by surface-enhanced Raman spectroscopy. In this work, aluminum-ion-aggregated and iodide-modified silver nanoparticles were used as substrates to obtain Raman spectra of the DNA strands with the same base composition but different sequences, which form random coils or various hairpin conformations. Upon DNA hybridization, reproducibly enhanced bands were easily observed, corresponding well to the formation of Watson-Crick hydrogen bonds, base ring breathing vibrations, and hairpin loops. These characteristic bands can be used to unambiguously distinguish the hairpins from the random DNA conformation. Moreover, by using the deoxyribose band (959 cm-1) as an internal standard to normalize the characteristic bands at 1703 cm-1 corresponding to the dG νC=O H bond, the guanine-cytosine base-pair contents and sequence in DNA hairpins can be accurately measured. Applying this method, a single base mutation in a functional double helix was confidently identified.

Excited States of One-Electron Oxidized Guanine-Cytosine Base Pair Radicals: A Time Dependent Density Functional Theory Study.

One-electron oxidized guanine (G•+) in DNA generates several short-lived intermediate radicals via proton transfer reactions resulting in the formation of neutral guanine radicals. The identification of these radicals in DNA is of fundamental interest to understand the early stages of DNA damage. Herein, we used time-dependent density functional theory (TD-ωB97XD-PCM/6-31G(3df,p)) to calculate the vertical excitation energies of one-electron oxidized G and G-cytosine (C) base pair in various protonation states: G•+, G(N1-H)•, and G(N2-H)•, as well as G•+-C, G(N1-H)•-(H+)C, G(N1-H)•-(N4-H+)C), G(N1-H)•-C, and G(N2-H)•-C in aqueous phase. The calculated UV-vis spectra of these radicals are in good agreement with the experiment for the G radical species when the calculated values are red-shifted by 40-70 nm. The present calculations show that the lowest energy transitions of proton transfer species (G(N1-H)•-(H+)C, G(N1-H)•-(N4-H+)C, and G(N1-H)•-C) are substantially red-shifted in comparison to the spectrum of G•+-C. The calculated spectrum of G(N2-H)•-C shows intense absorption (high oscillator strength), which matches the strong absorption in the experimental spectra of G(N2-H)• at 600 nm. The present calculations predict the lowest charge transfer transition of C → G•+ is π → π* in nature and lies in the UV region (3.4-4.3 eV) with small oscillator strength.

Heterogeneity and chaos in the Peyrard-Bishop-Dauxois DNA model.

We discuss the effect of heterogeneity on the chaotic properties of the Peyrard-Bishop-Dauxois nonlinear model of DNA. Results are presented for the maximum Lyapunov exponent and the deviation vector distribution. Different compositions of adenine-thymine (AT) and guanine-cytosine (GC) base pairs are examined for various energies up to the melting point of the corresponding sequence. We also consider the effect of the alternation index, which measures the heterogeneity of the DNA chain through the number of alternations between different types (AT or GC) of base pairs, on the chaotic behavior of the system. Biological gene promoter sequences have been also investigated, showing no distinct behavior of the maximum Lyapunov exponent.

The prediction of intermolecular proton-transfer of guanine-cytosine base pair under the influence of fragments from decomposed MOFs.

Metal-organic frameworks (MOFs) can be decomposed into various fragments, including negative/positive charges, Zn+ or Cu2+ when used as drug delivery materials. To evaluate the safety of MOFs, different mechanisms of intermolecular proton-transfer in guanine-cytosine (GC) base pair under the influence of such fragments were investigated by density functional theory methods. In a vacuum, calculation results show that an excess electron assists proton transfer in the anionic GC radical, and a hole assists proton transfer in the cationic GC radical with small energy barriers. The mechanism for Zn+-GC transfer is that the located hole assists proton transfer from G to C. All proton-transfers of Cu2+-GC become spontaneous with stable proton-transferred structures, and the driving force is the Cu2+ due to its electrostatic and oxidative effects. However, in a micro-water environment, the average energy barrier of all proton-transfer processes increases by 2.8kcalmol-1 because of the redistribution of charges. Water molecules play a very important role in buffering, and the influence of fragments on intermolecular proton-transfer processes of GC is reduced.

Association of Nucleobases in Hydrated Ionic Liquid from Biased Molecular Dynamics Simulations.

We employed metadynamics-based classical molecular dynamics simulations to methylated adenine-thymine (mA-mT) and guanine-cytosine (mG-mC) base pairs to see favorable conformations in various concentrations of hydrated 1-ethyl, 3-methyl imidazolium acetate. We investigated various stacked and hydrogen-bonded conformations of association of base pairs through appropriately chosen collective variables. Stacked conformations more favored in water for both base pairs, whereas Watson-Crick (WC) hydrogen-bonding conformations are favored in pure and hydrated ionic liquids (ILs) except for 0.75 mol fraction IL. We observe that EMIm cations surround the base pairs in WC conformations creating a kind of hydrophobic cavity and protect the hydrogen bonds between base pairs. However, the five-membered heteroaromatic rings of cations stack with the nucleobases in the cation-base-cation (π-π-π) model, which resembles the base-base-base stacking in a DNA duplex. Interestingly, from additional simulations of 0.5 mol fraction hydrated choline dihydrogen phosphate IL, we observe that the stacked conformations become more favored than the WC conformation due to the absence of π-bonds in cations. The calculated values of relative solubility of base pairs in pure and hydrated ionic liquids compared to those in pure water correlate well with the free energy values of WC and stacked conformations.

Effects of Intense Electric Fields on the Double Proton Transfer in the Watson-Crick Guanine-Cytosine Base Pair.

The double proton transfer reaction in the guanine-cytosine (GC) base pair is studied, using density functional theory, to understand the chances of mutations under the effect of uniform electric fields in the order of 108 to 109 V m-1. On the basis of potential energy surfaces, reaction Gibbs energies, equilibrium constants, imaginary frequencies, forward and reverse barrier heights, tunneling-corrected rate constants, half-lives of the forward and reverse reactions, percent tautomerization, and Boltzmann distributions, it was found that fields ≥+3.60 × 109 V m-1 facilitate the mutation in the GC base pair and reduce the rectification of point mutations. Fields applied along the double proton transfer in the - x (defined in the C to G direction) direction favor the canonical over the rare tautomers. Tunneling-corrected rate constants of the forward reaction increase exponentially with stronger fields in the - x direction and follow a Gaussian curve for the reverse reaction.

Singlet O2 Oxidation of a Deprotonated Guanine-Cytosine Base Pair and Its Entangling with Intra-Base-Pair Proton Transfer.

We report an experimental and computational study on the 1 O2 oxidation of gas-phase deprotonated guanine-cytosine base pair [G ⋅ C-H]- that is composed of 9HG ⋅ [C-H]- and 7HG ⋅ [C-H]- (pairing 9H- or 7H-guanine with N1-deprotonated cytosine), and 9HG ⋅ [C-H]- _PT and 7HG ⋅ [C-H]- _PT (formed by intra-base-pair proton transfer from the N1 of guanine to the N3 of [C-H]- ). The conformer-averaged reaction product ions and cross section were measured over a center-of-mass collision energy range from 0.1 to 0.5 eV using a guided-ion-beam tandem mass spectrometer. To explore conformation-specific reactivity, collision dynamics of 1 O2 with each of the four [G ⋅ C-H]- conformers was simulated at B3LYP/6-31G(d). Trajectories showed that the 1 O2 oxidation of the base pair entangles with intra-base-pair proton transfer, and prefers to occur in a collision when the base pair adopts a proton-transferred structure; trajectories also indicate that the 9HG-containing base pair favors stepwise formation of 4,8-endoperoxide of guanine, whereas the 7HG-containing base pair prefers concerted formation of guanine 5,8-endoperoxide. Using trajectory results as a guide, potential energy surfaces (PESs) along all possible reaction pathways were established using the approximately spin-projected ωB97XD/6-311++G(d,p)//B3LYP/6-311++G(d,p) method. PESs have not only rationalized trajectory findings but provided more accurate energetics and indicated that the proton-transferred base-pair conformers have lower activation barriers for oxidation than their non-proton-transferred counterparts.

The Control of the Tautomeric Equilibrium of Isocytosine by Intermolecular Interactions

Isocytosine has two stable tautomers, which can form a dimer with each other, stabilised by three intermolecular hydrogen bonds similar to those in the guanine–cytosine base pair. Molecules with suitable donor/acceptor hydrogen‐bonding patterns can form intermolecular complexes with one or the other isocytosine tautomer. These intermolecular interactions stabilise the selected isocytosine tautomer, leading to an increase of its relative concentration. The integration of the 1H NMR spectra acquired at various temperatures and concentrations was used for the determination of free‐energy changes of the formation of the isocytosine dimer/complex. The experimental free‐energy changes contain contributions from the formation of the isocytosine dimer/complex itself and from the rearrangement of the solvation shell. The latter contribution was estimated through a comparison of the experimental free‐energy changes with those calculated for the dimer/complex formation at the DFT level. The study demonstrates that the molecular environment can change relative tautomer stabilities, which supports the hypothesis of the involvement of rare nucleobase tautomers in the catalytic function of RNA enzymes.

Distribution of Base Pair Alternations in a Periodic DNA Chain: Application of Pólya Counting to a Physical System

In modeling DNA chains, the number of alternations between Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs can be considered as a measure of the heterogeneity of the chain, which in turn could affect its dynamics. A probability distribution function of the number of these alternations is derived for circular or periodic DNA. Since there are several symmetries to account for in the periodic chain, necklace counting methods are used. In particular, Polya's Enumeration Theorem is extended for the case of a group action that preserves partitioned necklaces. This, along with the treatment of generating functions as formal power series, allows for the direct calculation of the number of possible necklaces with a given number of AT base pairs, GC base pairs and alternations. The theoretically obtained probability distribution functions of the number of alternations are accurately reproduced by Monte Carlo simulations and fitted by Gaussians. The effect of the number of base pairs on the characteristics of these distributions is also discussed, as well as the effect of the ratios of the numbers of AT and GC base pairs.

Solvent effect on the intermolecular proton transfer of the Watson and Crick guanine-cytosine and adenine-thymine base pairs: a polarizable continuum model study.

Herein we present our results on the study of the double proton transfer (DPT) mechanism in the adenine-thymine (AT) and guanine-cytosine (GC) base pairs, both in gas phase and in solution. The latter was modeled using the polarizable continuum method (PCM) in different solvents. According to our DFT calculations, the DPT may occur for both complexes in a stepwise mechanism in condensate phase. In gas phase only the GC base pair exhibits a concerted DPT mechanism. Using the Wigner's tunneling corrections to the transition state theory we demonstrate that such corrections are important for the prediction of the rate constants of both systems in gas and in condensate phase. We also show that (i) as the polarity of the medium decreases the equilibrium constant of the DPT reaction increases in both complexes, and (ii) that the equilibrium constant in the GC complex is four orders of magnitude larger than in AT. This observation suggests that the spontaneous mutations in DNA base pairs are more probable in GC than in AT.