Ground- and excited-state properties of DNA base molecules from plane-wave calculations using ultrasoft pseudopotentials

We present equilibrium geometries, vibrational modes, dipole moments, ionization energies, electron affinities, and optical absorption spectra of the DNA base molecules adenine, thymine, guanine, and cytosine calculated from first principles. The comparison of our results with experimental data and results obtained by using quantum chemistry methods show that in specific cases gradient-corrected density-functional theory (DFT-GGA) calculations using ultrasoft pseudopotentials and a plane-wave basis may be a numerically efficient and accurate alternative to methods employing localized orbitals for the expansion of the electron wave functions.     

Reactions of silylated Schiff bases with organotitanium(IV) and organotin(IV) chlorides

The interactions of silylated dibasic quadridentate Schiff bases derived fromo-hydroxyacetophenone and ethylenediamine and orthophenylenediamine with (π-C₅H₅)TiCl₃, (π-C₅H₅)(MeO)TiCl₂, (MeO)₂TiCl₂, Me₂SnCl₂ and MeSnCl₃ yield a new series of organotitanium(IV) and tin(IV) compounds. The reactivity of (π- C₅H₅)Ti(L₁)Cl and MeSn(L₁)Cl, towards MeSH, Me₂NSiMe₃, SiMe₃N₃ and Me₃SiC = CPh are also described. The structures for the compounds isolated are proposed on the basis of elemental analyses, molecular weights, IR and¹H nmr spectroscopic studies.     

Rapid evaluation of the binding energies between peptide amide and DNA base

The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 20 hydrogen‐bonded amide–base dimers are evaluated from the analytic potential energy function established in our laboratory recently. The analytic potential energy function is used to calculate the N? H···N, N? H···O?C, C? H···N, and C? H···O?C dipole–dipole attractive interaction energies and C?O···O?C, N? H···H? N, and N? H···H? C dipole–dipole repulsive interaction energies in the 20 dimers composed of DNA bases adenine, guanine, cytosine, or thymine and peptide amide. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6‐311+G** calculations by including the basis set superposition error (BSSE) correction. For all the 20 dimers, the analytic potential energy function yields the binding energies of the MP2/6‐311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 19 dimers, only one difference is larger than 0.50 kcal/mol and the difference is only 0.61 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6‐311+G** with BSSE correction within the error limits of 0.030 Å for all the 20 dimers. The analytic potential energy function is further applied to four more complicated DNA base‐peptide amide systems involving amino acid side chain and β‐sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen‐bonded peptide amide–DNA base dimers quickly and accurately. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Complexes of cadmium ion with guanine bases detected by electrospray ionization mass spectrometry

The complexations of cadmium ion with guanine bases were detected by electrospray ionization mass spectrometry (ESI-MS). In order to explore the toxicity of cadmium, such as oxidative stress to DNA and carcinogenesis, it is very important to determine the interactions between the cadmium ion and nucleotide. The analysis of mixed cadmium ion-guanosine aqueous solution (molar ratio 1 : 9) using ESI-MS (cone voltage 20 V) showed the presence of various cadmium complex ions, such as [n (guanosine) + Cd](2+) (n = 3-8), [2guanine + Cd](2+), [guanosine + guanine + Cd](2+) and [guanosine + 2guanine + Cd](2+). The observed [2guanine + Cd](2+), [guanosine + guanine + Cd](2+) and [guanosine + guanine + Cd](2+) ions are formed through the dissociation of the N-glycoside bond at the interface of ESI-MS. For deoxyguanosine and ethylguanine, similar cadmium complexes were observed. However, the complexes between the cadmium ion and 8-hydroxydeoxyguanosine were not detected. Furthermore, when a higher molar ratio (Cd : guanosine) or cone voltage were used, more of the monovalent ion peaks, such as [Cd(guanine - H)(2) + H](+) and [Cd(guanosine - H)(2) + H](+), were observed and a decrease in the abundance of the divalent ions, such as [n(guanosine)+Cd](2+), occurred.     

DNA photocleavage and anticancer activity of terpyridine copper(II) complexes having phenanthroline bases

Copper(II) complexes [Cu(ph-tpy)(B)](ClO₄) (1–3), where ph-tpy is (4′-phenyl)-2,2′:6′,2″-terpyridine and B is N,N-donor phenanthroline base, viz. 1,10-phenanthroline (phen, 1), dipyridoquinoxaline (dpq, 2), and dipyridophenazine (dppz, 3), were prepared and characterized from analytical and spectral data. Complex 1, characterized by X-ray crystallography, shows a distorted square-pyramidal (4 + 1) CuN₅ coordination geometry having the tridentate ph-tpy ligand at the basal plane and bidentate phen bound to the axial-equatorial sites. The complexes display a d–d band near 650 nm in aqueous DMF. The complexes are avid binders to calf thymus DNA giving the binding order: 3 (dppz) > 2 (dpq) > 1 (phen). The dpq and dppz complexes show photo-induced DNA cleavage activity in red light via photo-redox pathway forming hydroxyl radicals. The cytotoxicity of the dppz complex 3 was studied by MTT assay in HeLa cancer cells. The IC₅₀ values are 3.7 and 12.4 μM in visible light of 400–700 nm and dark, respectively.     

Number of graphene layers exhibiting an influence on oxidation of DNA bases: Analytical parameters

This article investigates the analytical performance of double-, few- and multi-layer graphene upon oxidation of adenine and guanine. We observed that the sensitivity of differential pulse voltammetric response of guanine and adenine is significantly higher at few-layer graphene surface than single-layer graphene. We use glassy carbon electrode as substrate coated with graphenes. Our findings shall have profound influence on construction of graphene based genosensors.     

Studies on DNA binding behavior of biologically active Cu(II) complexes of Schiff bases containing acyl pyrazolones and 2-ethanolamine

Pyrazolone derivatives (Z)-4-((2-hydroxyethylimino)(p-tolyl)methyl)-3-methyl-1-phenyl-1H-pyrazol-5(4H)-one [PMP-EA] (1), (Z)-1-(3-chlorophenyl)-4-((2-hydroxyethylimino)(p-tolyl)methyl)-3-methyl-1H-pyrazol-5(4H)-one [MCPMP-EA] (2), and (Z)-4-((2-hydroxyethylimino)(p-tolyl)methyl)-3-methyl-1-p-tolyl-1H-pyrazol-5(4H)-one [PTPMP-EA] (3) have been synthesized and characterized. The molecular geometry of 2 has been determined by single-crystal X-ray study. These ligands exist in amine-one tautomeric form in the solid state. Three copper(II) complexes, [Cu(PMP-EA)(H₂O)₂] (4), [Cu(MCPMP-EA)(H₂O)₂] (5), and [Cu(PTPMP-EA)(H₂O)₂] (6), respectively, have been synthesized using these ligands and characterized by microanalytical data, molar conductivity, IR, UV–Visible, FAB-Mass, magnetic measurement, TG-DTA studies, and ESR spectral studies; Cu(II) is five-coordinated with [ML(H₂O)₂] composition. The interaction of the complexes with CT-DNA (calfthymus) was investigated using different methods. The results suggest that the copper complexes bind to DNA via intercalation and can quench the fluorescence intensity of EB bound to DNA.     

NIR-SERS studies of DNA and DNA bases attached on polyvinyl alcohol (PVA) protected silver grass-like nanostructures

In this work, polyvinyl alcohol (PVA) protected silver grass-like nanostructure (PVA–Ag–GNS) with near infrared surface-enhanced Raman scattering (NIR-SERS) activity was prepared and employed to detect DNA and DNA bases. The PVA–Ag–GNS demonstrated high NIR-SERS activity and good optical reproducibility in the detection of adsorbates such as the case of crystal violet, DNA and DNA bases. By using of the tested molecule of thymine, the PVA–Ag–GNS shows a high enhancement factor (EF) of ∼10⁸. For NIR-SERS detection of DNA molecules, Raman signals from the DNA bases of guanine (630 cm⁻¹) and adenine (720 cm⁻¹) are greatly enhanced. For DNA molecules NIR-SERS detection, Raman signals from the DNA bases of guanine (630 cm⁻¹), adenine (720 cm⁻¹) and cytosine (1010 cm⁻¹) are greatly enhanced. The experimental results show that the NIR-SERS spectrum of DNA is dominated by guanine mode, which is followed by adenine and cytosine modes, respectively. Meanwhile, the NIR-SERS signal intensities of the DNA bases increase in the order of thymine (T) < cytosine (C) < adenine (A) < guanine (G). One can conclude that the adsorption strength of the DNA bases in DNA molecule with the silver surface is in the order T < C < A < G, which is different from that of the four DNA bases in individual molecule adsorbed on silver surface (T < A < G < C). On the other hand, the geometry optimization and calculated wavenumber of the complexes of adenine–Ag, guanine–Ag, cytosine–Ag and thymine–Ag for the ground states are performed with DFT, B3LYP functional and the LanL2DZ basis set. The calculated wavenumbers match well with the experimental results. According to our experiment and calculations, DNA base molecules adsorbed on silver surface via the intra-annular nitrogen atom which is adsorbed on the silver nanoparticle and formed metal–molecule complexes by the available lone pair.     

Reactivities of hydroxyl and perhydroxyl radicals toward cytosine and thymine: A comparative study

As the hydroxyl (OH) and perhydroxyl (OOH) radicals are known to play important roles in biological systems, their reactions with cytosine and thymine were studied. Addition reactions of these radicals at different sites of cytosine and thymine, and hydrogen abstraction reactions by each of the two radicals from the different sites of the two molecules were studied at the B3LYP/6‐31G(d,p), B3LYP/AUG‐cc‐pVDZ and BHandHLYP/AUG‐cc‐pVDZ levels of density functional theory. Effect of solvation in aqueous media on the reactions was studied at all these levels of theory using single point energy calculations using the polarizable continuum model. The present study shows that whereas the OH radical would abstract H atoms from the various sites of cytosine and thymine efficiently, the OOH radical would have poor reactivity in this regard. The OH radical is also predicted to be much more reactive than the OOH radical with regard to addition reactions at the C5 and C6 sites of both thymine and cytosine, though the OOH radical is also predicted to have significant reactivity in this respect. © 2012 Wiley Periodicals, Inc.     

6-烷基鸟嘌呤与DNA碱基间氢键作用的理论研究

用密度泛函B3LYP方法在6-311＋G**基组水平上对鸟嘌呤及顺(cis-)、反式(anti-)-6-烷基鸟嘌呤(O⁶-AlkylG)与DNA碱基(胸腺嘧啶T、胞嘧啶C、腺嘌呤A、鸟嘌呤G)的氢键二聚体结构进行了优化. 在MP2/cc-pVXZ(X＝D,T)// B3LYP/6-311＋G**水平上, 采用完全基组外推方法校正了氢键二聚体的相互作用能, 并用完全均衡校正法(CP)校正了基组重叠误差(BSSE). 在B3LYP/6-311＋G**水平上计算了各氢键碱基对的全电子波函数, 并用分子中的原子理论(AIM)分析了碱基间的弱相互作用. 计算结果显示, 鸟嘌呤6-O烷基化改变了碱基间的氢键作用模式, 使碱基对发生了明显的螺旋桨式扭转和不同程度的位移, 碱基间的电子密度分布和氢键作用能明显减小. O⁶-AlkylG对DNA碱基间的氢键作用是去稳定化的, 去稳定化影响的顺序为GC＞GG＞GA≈GT. 计算结果与文献给出的实验结论基本一致.     

DNA Hydrolysis and Voltammetric Determination of Guanine and Adenine Using Different Electrodes

Abstract

This work reports the development of a biosensor method for the label‐free detection of specific DNA sequences. In the initial phase, square wave voltammetry (SWV) was used in a comparative investigation into the electrochemical oxidation of purines (guanine and adenine) and DNA fragments at various electrode surfaces: carbon paste (CPE), glassy carbon electrode (GCE), and gold (AuE). Relative to the carbon electrodes, an approximate 4.0‐fold, 6.0‐fold, and 3.25‐fold increase in the anodic response was observed when guanine, adenine, and hydrolyzed DNA, respectively, were measured on the AuE. It was shown that the guanine and adenine bases could be successfully determined by use of SWV for a deoxyribonucleic acid sample following acid hydrolysis. This label‐free detection of hydrolyzed DNA on gold electrodes has significant advantages over methods using existing carbon electrode materials because of its higher sensitivity and the potential applicability of microfabrication techniques for the production of the requisite gold electrodes.

In another phase of development, the times and conditions for DNA hydrolysis and purine release were investigated. It was shown that under optimal conditions, trace levels of the purine bases could be readily detected following 20 min of hydrolysis at room temperature. The proposed method can be used to estimate the guanine and adenine contents in DNA with in a linear range of 5–30 ng ml^?1.

Finally, when appropriate probe sequences were first adsorbed on the surface of the screen‐printed gold electrode (SPGE), this electrochemical biosensor could be used to specifically detect sequences from ss corona virus aviair following hybridization and hydrolysis reactions on the sensor surface. No enhancement of the voltammetric response was observed when the sensor was challenged with a non‐complementary DNA sequence.     

CE analysis and molecular characterisation of depurinated DNA samples

A DNA sample was partially degraded by scalar heat-acid treatments to study the extent of apurinic-apyrimidinic (A-P) lesions produced along the molecule. A CE-UV method allowed us to measure the rate of depurination at pH 5.0 and 70°C which was calculated to be 5.41×10(-6) s(-1) for adenine and 6.27×10(-6) s(-1) for guanine. CE identified depurination on treated samples when it occurred with a loss of >4% of the basic moieties. The molecular features of the A-P enriched samples were investigated by using molecular assays (agarose gel electrophoresis, UV spectrophotometry and quantitative PCR) and the consistency of the results of the STR typing were compared with the degree of depurination of the PCR template. The treated DNA samples showed molecular features such as fragmentation, altered OD(260) /OD(280) ratios and decreased ability of the quantitative PCR to synthesise the human target, related to the severity of depurination. A satisfactory correlation between the degree of damage and the amount of residual PCR-sensitive target sequences was also demonstrated (r(2) =0.9717). The conventional and mini-STR typing of the samples showed that the genetic outcome was influenced by a depurination damage that exceeded 4% when locus drop-outs and artefactual PCR results were evident. As the success of STR typing depends on the integrity of the DNA recovered from the samples, the CE-UV, physical and molecular assays described here are proposed as a set of useful methods in the analysis of certain forensic and clinical samples, for a critical evaluation of the outcome of the genetic testing.     

Copper(II) complexes with neutral Schiff bases: Syntheses, crystal structures and DNA interactions

The synthesis and X-ray structural characterisation of a new Cu(II) complex, [Cu(L¹)Cl](ClO₄)·CH₃OH (1) [L¹ = N,N′-bis((pyridine-2-yl)phenylidene)-1,3-diaminopropan-2-ol], has been described in this work. The structural study reveals that the Cu(II) centre in 1 has a square pyramidal geometry with a trigonality index τ = 0.43, being coordinated by the organic ligand and a chloro group. The interaction of complex 1 and another complex previously reported by our group, [Cu(L²)](ClO₄)₂ (2) [L² = N-(1-pyridin-2-yl-phenylidene)-N′-[2-({2-[(1-pyridin-2-ylphenylidene)amino]ethyl}amino)ethyl]ethane-1,2diamine], with calf thymus DNA (CT-DNA) has been investigated using absorption and emission spectral studies. The binding constant (K_b) and the linear Stern-Volmer quenching constant (K_sv) have been determined.     

Interaction of iron carbonyls with Lewis bases

The interaction of iron carbonyls Fe _n (CO) _m (wheren = 1,m = 5;n = 2,m = 9;n = 3,m = 12) with anionic Lewis bases (H^–, F^–, Cl^–, Br^– , I^–, CN^–, SCN^–, N₃ ^–, MeSO₃ ^–, MeCO₂ ^–, CF₃CO₂ ^–, S₂ ^–, CO₃ ^2–, and SO₄ ^2–) passes through two-stage redox-disproportionation. The first stage is the formation of an iron carbonyl-base complex, [Fe _n (CO) _m–1C(O)L]^–, and the second is a single-electron reduction of this complex by another molecule of the initial iron carbonyl, giving rise to Fe(l) and Fe(–l) derivatives.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 248–249, January, 1996.     

Density functional theory study on the interaction of catechin and cytosine

The interacting patterns and mechanism of the catechin and cytosine have been investigated using the density functional theory B3LYP method with 6-31+G* basis set.Eleven stable structures of the catechin-cytosine complexes have been found respectively.The results indicate that the complexes are mainly stabilized by the hydrogen bonding interactions.Theories of atoms in molecules(AIM) and natural bond orbital(NBO) have been utilized to investigate the hydrogen bonds involved in all the systems.The interactio...     

Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform–water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER‐99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld‐I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld‐I method related to the unstable isolated anionic nitrogen pro‐atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc.     

Fabrication of Cu−CeO2 Coated Multiwall Carbon Nanotube Composite Electrode for Simultaneous Determination of Guanine and Adenine

A copper nano particles and cerium (IV) oxide modified carbon nanotube based composite on glassy carbon electrode (Cu−CeO₂/MWCNT/GCE) was fabricated for simultaneous determination of guanine and adenine. The surface morphology, chemistry and conductance of the prepared electrodes were characterized by scanning electron microscopy (SEM), energy dispersion X‐ray (EDX), X‐Ray photoelectron spectroscopy (XPS) and electrochemical impedance spectroscopy (EIS). The Cu−CeO₂/MWCNT/GCE improved electrochemical behaviour of guanine and adenine compared to other electrodes. The modified electrode was also used for individual and simultaneous determination of guanine and adenine. Under optimized conditions, the calibration curves were obtained linearly in the range of 0.20 to 6.00 μM for the guanine and 0.10 to 8.0 μM for the adenine by differential pulse voltammetry. The limits of detection of guanine and adenine were calculated as 0.128 and 0.062 μM, respectively. Interferences studies were also performed in the presence of inorganic and organic compounds. Moreover, the determination of guanine and adenine contents were carried out in a calf thymus DNA sample by the developed method with satisfactory results.     

Protonation of thymine,cytosine, adenine,and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory

Gradient-corrected density functional computations with triple-zeta-type basis sets were performed to determine the preferred protonation site and the absolute gas-phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero-point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 989–1000, 1998     

结构DNA纳米技术应用新进展

DNA具有非凡的分子识别性能和显著的结构特征,这使得它在材料的纳米级调控方面具有独特的优越性,在许多领域也展现出广阔的应用前景。本文从模块化DNA自组装和DNA折纸术两个方面综述了近些年DNA纳米技术,包括近年来DNA纳米技术中比较新型的组装方法;并从DNA纳米结构作为模板定位纳米粒子和蛋白以及用于生物医药等方面介绍了DNA纳米技术的应用;同时,对DNA纳米技术发展及应用进行了展望。