Interaction Of Cytosine Research Articles

Thermochemical Study of the Interaction of Cytosine and Uracil with Peptides in a Buffered Saline: Complex Formation with beta-Endorphin 30-31 (Human), L-Glutathion (Reduced) and α-L-Alanyl-L-Tyrosine.

The complex formation of uracil and cytosine with glycyl-L-glutamic acid (β-endorphin 30-31), γ-L-glutamyl-L-cysteinyl-glycine (glutathione reduced), α-L-alanyl-L-tyrosine, and α-L-alanyl-α-L-alanine in a buffered saline has been studied using dissolution calorimetry. The values of the reaction constant, the change in Gibbs energy, enthalpy, and entropy were obtained. It is shown that the ratio of the enthalpy and entropy factors depends on the charge of the peptide ion, and the number of H-bond acceptors in the peptide structure. The contributions of interaction between charged groups and polar fragments, hydrogen bonding, and stacking interaction are discussed, taking into account the effect of solvent reorganization around the reactant molecules.

Fabrication of ssDNA functionalized MoS[formula omitted] nanoflakes based label-free electrochemical biosensor for explicit silver ion detection at sub-pico molar level

A novel, robust, reliable, low-cost, and convenient electrochemical silver ion sensing technique is proposed based on poly(cytosine) functionalized carboxylated 2D MoS2 nanoflakes. Relying upon cytosine–cytosine mismatch, all electroanalytic measurements carried out on this sensor proved its superiority in detecting Ag(I) ions through cytosine-Ag(I)-cytosine interaction down to pico molar (pM) concentration with an approximated limit of detection of 0.8 pM in the potable water medium. In the environmental sample tests and competitive experiments with other metal ions, this proposed biosensor showed enough potential for trace amount determination of silver ions in the potable water medium for environmental monitoring applications.

Quadruple Anticounterfeiting Encryption: Anion-Modulated Forward and Reverse Excitation-Dependent Multicolor Afterglow in Two-Component Ionic Crystals.

Molecule-based afterglow materials with ultralong-lived excited states have attracted great attention owing to their unique applications in light-emitting devices, information storage, and anticounterfeiting. Herein, a series of new types of two-component ionic crystalline materials were fabricated by the self-assembly of cytosine and different anions under ambient conditions. The multiple intermolecular interactions of cytosine with phosphate and halogens anions can lead to abundant energy levels and different crystal stacking modes to control molecular aggregation and excited-state intermolecular proton transfer (ESIPT) process. Interestingly, H-aggregation-induced green to yellow room-temperature phosphorescence (RTP) and ESIPT-dominated cyan RTP to deep blue thermally activated delayed fluorescence (TADF) emission can be generated by tuning excitation wavelength, time evolution, and temperature. Furthermore, the combination of two-component ionic crystals can be used as multicolored candidates for quadruple information encryption. Therefore, this work not only develops an anion-modulated strategy to achieve color-tunable afterglow from both static and dynamic fashions but also provides a guideline for designing forward/reverse excitation-dependent luminescent materials.

The functionalization of gold nanoparticles as a novel platform for the highly efficient electrochemical detection of silver ions.

Herein, a novel electrochemical biosensor was constructed for the highly efficient detection of silver ions. A porous platform constructed with functionalized gold nanoparticles (AuPP) was electropolymerized on the gold electrode surface. The obtained polymer, analogous to a metal-organic framework, was used as the sensing platform together with cytosine-Ag+-cytosine interaction for dual signal amplification. The scanning electron microscopy (SEM) image of the AuPP platform exhibited a porous structure and considerable binding sites for C-riched single stranded DNA, leading to predictable silver ion preconcentration. Based on this strategy, the biosensor showed that the peak current in differential pulse voltammetry rose linearly as the concentration of silver ion increased from 0.005 to 3 μM with a detection limit of 1.3 nM. In addition, in the presence of other metal ions, such as Pb2+, Mn2+, Ni2+, Co2+, Cu2+, Zn2+, Na+, Ca2+, and Cd2+, at the same concentration, the current signal remained almost unchanged, manifesting high selectivity for Ag+. This proposed sensor might exhibit a novel fabrication method for metal ion detection with the aid of multiple AuPP materials by designing ligands with different functional groups.

Modeling of nucleobase/oligonucleotide interaction with graphene and graphene oxide: the role of charging and/or oxidizing the graphene surface

We analyze the influence of the charge and the degree of oxidation of the surface of graphene (Gr) on its interaction with cytosine and oligonucleotide r(C)10. This is a computational study involving DFT calculations and molecular dynamics simulations. It is shown that cytosine interacts stronger with graphene oxide (GO) than with Gr, while the energy of the interaction of cytosine with GO only weakly depends on the degree of the Gr oxidation. A correlation between the shifts of vibrational frequencies of cytosine due to complexation with GO and the degree of the Gr oxidation is found. The adsorption of anionic oligonucleotide r(C)10 onto neutral and positively charged surfaces has a certain conformational similarity to conformations formed with similar van der Waals interactions. Also, for charged surfaces, the Coulombic attraction gives a noticeable contribution to the total interaction energy. For a negatively charged graphene surface the electrostatic repulsion between Gr surface and negatively charged phosphate backbone of oligonucleotide weakens the total binding energy. Competition between the Coulombic repulsion and the van der Waals attraction results in formation of a unique oligonucleotide conformation where all 10 cytosines are stacked onto Gr.

Unexpected cytosine-AuCl4- interaction under electrospray ionization mass spectrometry conditions-Formation of cytosine-Au(I) complexes.

The interaction of cytosine with AuCl4-, under electrospray ionization mass spectrometric conditions, is discussed. On the basis of respective full scan mass spectra and product ion spectra, obtained in positive and negative ion mode, it has been deduced that cytosine is very prone to form Au(I)-containing complexes. The complexes may be formed in the gas phase by decomposition of Au(III)-containing complexes and also in the electrospray ionization source as a result of the occurrence of redox process. It has also been found that the interaction of cytosine with Au+ is stronger than that with Cu+ or Ag+, although taking into account the electrostatic attraction, it is not expected.

An experimental and theoretical vibrational study of the interaction of cytosine and uracil with artificial seawaters: A prebiotic chemistry experiment

Solids of uracil and cytosine lyophilized from different solutions were characterized using FT-IR and Raman spectroscopies and the frequencies in the spectra were compared to theoretical calculations. The effect of pH and of cations in artificial seawaters on the frequencies of FT-IR and Raman spectra were studied. The solid cytosine and uracil obtained from alkaline solutions indicated the formation of a mesomeric anion as a result of the deprotonation of N1 and N3, respectively. The spectroscopic analysis of cytosine obtained from an acid solution showed bands characteristic of cytosine hydrochloride. For uracil, no changes were observed because of its low pKa1. Cytosine interacts with the cations (Na+, Mg2+, Ca2+ and Sr2+) in the different seawaters. For these samples a shift of a band attributed to ν(C2N1) stretching was observed. The theoretical calculations indicate an interaction of the metallic cations through C2O, forming an “A” structure complex. For uracil, an interaction with the cations present in the artificial seawaters was also observed. The spectroscopic analysis showed new bands attributed to the C4O group which indicates that the interaction occurs at a carbonyl resulting in a “B” structure complex. The reactivity of cytosine and uracil were studied using 2 parameters the nucleophilicity and energy of the molecular orbital HOMO. The Mulliken charges at N1 for the two tautomers of both cytosine and uracil were compared. It was concluded that the enol-imino form has lower energy and, consequently, higher nucleophilicity. Thus, these complexes could have played an important role on nucleoside formation. The HOMO has a contribution to N1 in the enol-imino and keto-amino tautomers for both nucleic acid bases.

Effect of a molecule of imidazolium bromide ionic liquid on the structure and properties of cytosine by density functional theory

The geometric and electronic structures, energetics and spectroscopy of different complexes formed between cytosine and a molecule of [Cnmim]Br (n = 2,4,6,8,10) are investigated in detail using the M06-2X and ωB97XD methods with 6-311++G(2d, p) basis set. A great number of stable C-[C2mim]Br and C-[C4mim]Br complexes were obtained, these structures are classified as three types: approximately coplanar, parallel and perpendicular. The BSSE-corrected binding energies of the most stable structures (Cn1) at the M06-2X method are −108.3 to −97.3 kJ·mol−1, which higher than the results of ɷB97XD. The aqueous solvation environment has an extremely weaken impact on the cytosine interaction with imidazolium bromide ionic liquid.

Lateral flow test for visual detection of silver (I) based on cytosine-Ag(I)-cytosine interaction in C-rich oligonucleotides.

The authors describe an oligonucleotide-based lateral flow test for visual detection of Ag(I). The assay is based on cytosine-Ag(I)-cytosine [C-Ag(I)-C] coordination chemistry to capture gold nanoparticle (AuNP) tags in the test zone. A thiolated C-rich oligonucleotide probe was immobilized on the AuNPs via gold-thiol chemistry, and a biotinylated C-rich oligonucleotide probe was immobilized on the test zone. The AuNPs labelled with C-rich oligonucleotides are captured by Ag(I) ions in the test zone through the C-Ag(I)-C coordination. The resulting accumulation of AuNPs produces a readily visible red band in the test zone. Under optimized conditions, the test is capable of visually detecting 1.0 ppb of Ag(I) which is 50 times lower than the maximum allowable concentration as defined by the US Environmental Protection Agency for drinking water. Hence, the test is inexpensive and highly sensitive. It was applied to the detection of Ag(I) in spiked samples of tap water and river water. In our perception, the test is a particularly valuable tool in limited resource settings.

Electrochemical biosensor for silver ions based on amplification of DNA–Au bio–bar codes and silver enhancement

A highly sensitive and selective electrochemical DNA biosensor for detection of Ag+ was developed based on amplification of DNA–Au bio–bar codes and silver enhancement. Cytosine-rich single stranded DNA oligonucleotide (sub–DNA) was immobilized on the surface of the gold electrode via Au–S chemical interaction. In the presence of Ag+, with the interaction of cytosine–Ag+–cytosine (C–Ag+–C), cytosine-rich DNA oligonucleotide probes-labeled AuNPs have a hybridization with sub–DNA and then form a duplex-like structure, following the AuNPs-catalyzed silver enhancement. The whole detection procedure of Ag+ based on the developed biosensor was evaluated by electrochemical techniques. Owing to the hybridization of sandwich assay format and distinct electrochemical signal amplification of silver enhancement, the proposed biosensors exhibited a good analytical performance for sensitive transduction of Ag+ recognition with a wide detection linear range from 5pM to 50μM, and a low detection limit of 2pM. The developed biosensor was highly selective and its practical applicability in real water samples was also tested with satisfactory results.

A mass spectrometric study and computer modeling of noncovalent interactions of cytosine with polyethylene glycol oligomers

Data on intermolecular noncovalent interactions of nitrogen base components of nucleic acid with organic polyethers are of interest both for fundamental molecular biophysics and for applications in the production of pharmaceutical organic nanoparticles. In the present work, systems composed of pyrimidine nitrogen base cytosine (Cyt) or its methyl derivatives and polyethylene glycol PEG-400 oligomers Mn have been examined by electrospray ionization (ESI) and fast atom bombardment mass spectrometry. Detection of a set of associates of the Mn · Cyt · H+ type (n = 3–17) in ESI mass spectra evidences the formation of protonated complexes of the base with oligomers of different chain lengths in all of the studied systems. Computer modeling by molecular dynamics gave answers to the questions concerning the stability and structure of these complexes under different conditions. It has been shown that Mn · Cyt · H+ clusters in the gas phase (vacuum) adopt a compact structure with a quasi-cyclic or quasi-helical self-organization of the polymer chain around the protonated base. It has been found that the compact structure of the M8 · Cyt · H+ complex characteristic for its state in the gas phase is preserved in a liquid medium of methanol (used as a solvent in ESI). The results of simulation of the evolution of a methanol droplet in vacuum, which mimics the droplet disintegration under ESI conditions, have shown that the M8 · Cyt · H+ complex initially present in the droplet does not disintegrate in the course of droplet evaporation. After the completion of desolvation, the complex returns to the conformation characteristic for the gas phase. Thus, the evidence has been found confirming that the M8 · Cyt · H+ clusters recorded in ESI mass spectra adequately reflect the presence of corresponding noncovalent complexes in the analyzed liquid solution.

Selective detection of silver ions using mushroom-like polyaniline and gold nanoparticle nanocomposite-based electrochemical DNA sensor

A highly sensitive electrochemical DNA biosensor made of polyaniline (PANI) and gold nanoparticles (AuNPs) nanocomposite (AuNPs@PANI) has been used for the detection of trace concentration of Ag+. In the presence of Ag+, with the interaction of cytosine–Ag+–cytosine (C–Ag+–C), cytosine-rich DNA sequence immobilized onto the surface of AuNPs@PANI has a self-hybridization and then forms a duplex-like structure. The whole detection procedure of Ag+ based on the developed biosensor was evaluated by electrochemical impedance spectroscopy. On semi-logarithmic plots of the log Ag+ concentration versus peak current, the results show that the prepared biosensor can detect silver ions at a wide linear range of 0.01–100 nM (R = 0.9828) with a detection limit of 10 pM (signal/noise = 3). Moreover, the fabricated sensor exhibits good selectivity and repeatability. The detection of Ag+ was determined by Ag+ self-induced conformational change of DNA scaffold that involved only one oligonucleotide, showing its convenience and availability.

Biophysical and molecular docking insight into the interaction of cytosine β-D arabinofuranoside with human serum albumin

Interaction of pharmacologically important anticancer drug cytosine β-D arabinofuranoside with human serum albumin (HSA) at physiological pH 7.4 has been studied by utilizing various spectroscopic and molecular docking strategies. Fluorescence results revealed that cytosine β-D arabinofuranoside interacts with HSA through static quenching mechanism with binding affinity of 2.4×103M−1. The average binding distance between drug and Trp214 of HSA was found to be 2.23nm on the basis of the theory of Förster's energy transfer. Synchronous fluorescence data indicated that interaction of drug with HSA changed the microenvironment around the tryptophan residue. UV–visible spectroscopy and circular dichroism results deciphered the complex formation and conformational alterations in the HSA respectively. Dynamic light scattering was utilized to understand the topology of protein in absence and presence of drug. Thermodynamic parameters obtained from isothermal titration calorimetry (ΔH=−26.01kJmol−1 and TΔS=6.5kJmol−1) suggested the involvement of van der Waal interaction and hydrogen bonding. Molecular docking and displacement study with site specific markers suggested that cytosine β-D arabinofuranoside binds to subdomain IB of HSA which is also known as the hemin binding site. This study will be helpful to understand the binding mechanism of cytosine β-D arabinofuranoside with HSA and associated alterations.

Interaction of Cu(II) with Cytosine in Britton-Robinson Buffer Solution - A Cyclic Voltammetric Study

Electrochemical redox behavior of Cu(II) at different pH in Britton-Robinson (BR) buffer solution has been investigated using cyclic voltammetry at glassy carbon electrode (GCE). Cu(II) shows a cathodic peak and a hump-like peak, and an intense anodic peak at pH, 0.59, 1.59, 3.01 and 4.08. Although at lower pH (0.59 and 1.59) a cathodic peak, a hump and an anodic peak are observed, at higher pH (3.01 and 4.08) the hump-like cathodic peak disappeared. Cyclic voltammetry has also been used to observe the interaction of Cu(II) with cytosine in BR buffer solution at various pH. A reasonably strong interaction between Cu(II) and cytosine at different Cu(II)/cytosine molar ratio is observed at all the studied pH. However, maximum interaction occurs at 1:4 molar ratio at pH 4.08, this is perhaps the most suitable condition for Cu(II)-cytosine interaction. DOI: http://dx.doi.org/10.3329/dujs.v63i1.21765 Dhaka Univ. J. Sci. 63(1): 31-36, 2015 (January)

On the Ag(+)-cytosine interaction: the effect of microhydration probed by IR optical spectroscopy and density functional theory.

The gas-phase structures of cytosine-Ag(+) [CAg](+) and cytosine-Ag(+)-H2O [CAg-H2O](+) complexes have been studied by mass-selected infrared multiphoton dissociation (IRMPD) spectroscopy in the 900-1800 cm(-1) spectral region using the Free Electron Laser facility in Orsay (CLIO). The IRMPD experimental spectra have been compared with the calculated IR absorption spectra of the different low-lying isomers (computed at the DFT level using the B3LYP functional and the 6-311G++(d,p) basis set for C, H, N and O atoms and the Stuttgart effective core potential for Ag). For the [CAg](+) complex, only one isomer with cytosine in the keto-amino (KA) tautomeric form and Ag(+) interacting simultaneously with the C(2)[double bond, length as m-dash]O(7) group and N(3) of cytosine was observed. However, the mono-hydration of the complex in the gas phase leads to the stabilization of a two quasi-isoenergetic structure of the [CAg-H2O](+) complex, in which Ag(+) interacts with the O atom of the water molecule and with the N(3) or C(2)[double bond, length as m-dash]O(7) group of cytosine. The relative populations of the two isomers determined from the IRMPD kinetics plot are in good agreement with the calculated values. Comparison of these results with those of protonated cytosine [CH](+) and its mono-hydrated complex [CH-H2O](+) shows some interesting differences between H(+) and Ag(+). In particular, while a single water molecule catalyzes the isomerization reaction in the case of [CH-H2O](+), it is found that in the case of [CAg-H2O](+) the addition of water leads to the stabilization of two isomers separated by small energy barrier (0.05 eV).

Amplified and selective detection of Ag+ ions based on electrically contacted enzymes on duplex-like DNA scaffolds

In the present study, ultrasensitive detection of Ag+ is demonstrated by a biocatalytic signal amplification system which is realized by only one DNA sequence based electrical contacted enzyme structure and the Au nanoparticles/Carbon nanodots (AuNPs/C-dots) composite immobilization platform. In the presence of Ag+, with the interaction of cytosine–Ag+–cytosine (C–Ag+–C), cytosine-rich DNA sequence labeled with methylene blue (MB) molecules near 5′ end and Glucose Oxidase (GOx) at 3′ end, has a self-hybridization and then forms a duplex-like structure which makes MB and GOx approach the AuNPs/C-dots modified electrode. MB units can then act as a relay that electrically contacts GOx with the AuNPs/C-dots modified electrode and activate the bioelectrocatalyzed oxidation of glucose to glucose acid. In consequence, based on the bioelectrocatalyzed signal amplification on the AuNPs/C-dots platform, Ag+ could be quantitatively detected in the range of 10−11–10−5M with a low detection limit of 3pM. Also, there is an excellent selectivity against other interferential metal ions. The detection of Ag+ ions was realized by Ag+ self-induced conformational change of DNA scaffold which involved only one oligonucleotide showing its convenience and availability.

SERS Study and DFT Simulation of the Interaction of Cytosine with Copper Electrode

Abstract In order to obtain a deeper insight into the interaction between cytosine and copper electrode, a surface-enhanced Raman scattering (SERS) study and density functional theory (DFT) simulation have been used. The experimental result shows that a decrease of relative intensity of the band at around 1315 cm−1 is accompanied by a considerable increase of relative intensity of the bands in the 1490∼1600 cm−1 region when the potential is below −0.7 V, and it is explained by the chemical effect (CE). Simultaneously, the geometry and Raman spectra of neutral and cationic Cu-cytosine complexes are calculated and simulated using the B3LYP/lanl2dz basis. The simulation shows that the relative intensities of Raman spectra depend strongly on the molecular active sites involved in the interaction between the copper electrode and the cytosine molecule. Combining the experimental results with theoretical calculations, we conclude that the adsorptive orientation of cytosine on the copper electrode occurs on the N3 site and the carbonyl site when the potential is above and below −0.7 V, respectively. This study also indicates that a combination of SERS and DFT simulations is a valuable tool for studying interactions of biomolecules with metal.

The replacement of chlorides by cytosines in copper(II) complexes containing guanidine derivatives

Two copper(II) chloride complexes of amidino-O-methylurea (L1), [Cu(L1)Cl2] (1), and (N-benzyl)-amidino-O-methylurea (L2), [Cu(L2)Cl2] (2), were prepared and characterized by elemental analysis, infrared, diffuse reflectance, electron spin resonance and electrospray ionization mass spectra. Their cytosine binding abilities has been studied and found that two cytosine molecules are able to coordinate with the copper centers by replacing the chloride ligands to yield the bifunctional binding adducts [Cu(L1)(cyt)2]Cl2 (1c) and [Cu(L2)(cyt)2]Cl2 (2c), respectively. The shift of the CO band of cytosine in both cytosine-bound products to higher energy suggested that the N(3)–cytosine atom coordinates to the copper center. The large blue shifts of the d–d absorbance maxima and the nine superhyperfine splitting from the CuN4 chromophore were also observed in their electronic and EPR spectra. Their thermal decompositions have also supported the interaction of cytosine with complexes 1 and 2. Density functional calculations have also been performed and revealed that square planar coordination geometry is more stable for both 1c and 2c. The binding energy of 1c is found to be ∼20% lower than that of 2c, indicative of the higher binding potential of 1c.

Structure of Cytosine on Cu(110): a Scanned-Energy Mode Photoelectron Diffraction Study

The local adsorption structure formed by the interaction of cytosine with a Cu(110) surface, following adsorption at ∼300 K and annealing to ∼420 K, has been investigated by O 1s and N 1s scanned-energy mode photoelectron diffraction (PhD). Initial characterization by soft-X-ray photoelectron spectroscopy and O K-edge near-edge X-ray absorption fine structure (NEXAFS) indicates that chemisorption leads to dehydrogenation of the NH species in the molecular ring and indicates that the molecular plane is perpendicular to the surface and close to the [110] azimuth. The PhD results confirm this orientation and show that the molecule bonds to the surface through the deprotonated N atom and the O atom, both of which occupy off-atop sites. The associated Cu−N and Cu−O bondlengths are 1.94(+0.07/−0.03) A and 1.94(+0.06/−0.04) A, respectively. Density functional theory calculations provide further support for this local structure and provide information on the possible role of intermolecular interaction. Possible ...

Probing differential Ag+–nucleobase interactions with isothermal titration calorimetry (ITC): Towards patterned DNA metallization

DNA has been successfully used as a scaffold for the fabrication of metallic nanowires, primarily based on the electrostatic complexation and reduction of the metal cations on the negatively charged sugar-phosphate backbone. Here, we probe the differential binding affinities of nucleobases for silver ions using sensitive isothermal titration calorimetry (ITC) measurements of the reaction enthalpies, which go in order: C > G > A > or = T. Using the disparity between the interaction of cytosine (strong binding) and thymine (weak binding) with silver ions, we have successfully generated silver nanoparticle doublets and triplets on custom-made oligonucleotides, C(30)-T(40)-C(30) and C(20)-T(20)-C(20)-T(20)-C(20), respectively. Thus, a new and simple method of generating metallized DNA wires is presented, based entirely on the nucleotide sequence of DNA. The concept could be extended to other cations and complex DNA sequences in order to achieve intricately patterned DNA constructs.