Adsorption Of Adenine Research Articles

Rapid Thermal Drying Synthesis of Nonthiolated Spherical Nucleic Acids with Stability Rivaling Thiolated DNA

AbstractAttaching DNA oligonucleotides to gold nanoparticles (AuNPs) to prepare spherical nucleic acids (SNAs) has offered tremendous insights into surface chemistry with resulting bioconjugates serving as critical reagents in biosensors and nanotechnology. While thiolated DNA is generally required to achieve stable conjugates, we herein communicate that using a thermal drying method, a high DNA density and excellent SNA stability was achieved using nonthiolated DNA, rivaling the performance of thiolated DNA such as surviving 1 M NaCl, 2 month stability in 0.3 M NaCl and working in 50 % serum. A poly‐adenine block with as few as two consecutive terminal adenine bases is sufficient for anchoring on AuNPs. By side‐by‐side comparison with the salt‐aging method, the conjugation mechanism was attributed to competitive adenine adsorption at high temperature along with an extremely high DNA concentration upon drying. Bioanalytical applications of nonthiolated SNAs were validated in both solution and paper‐based sensor platforms, facilitating cost‐effective applications for SNAs.

Rapid Thermal Drying Synthesis of Nonthiolated Spherical Nucleic Acids with Stability Rivaling Thiolated DNA.

Attaching DNA oligonucleotides to gold nanoparticles (AuNPs) to prepare spherical nucleic acids (SNAs) has offered tremendous insights into biointerface chemistry with resulting bioconjugates serving as critical reagents in biosensors and nanotechnology. While thiolated DNA is generally required to achieve stable conjugates, we herein communicate that using a thermal drying method, a high DNA density and excellent SNA stability was achieved using nonthiolated DNA, rivaling the performance of thiolated DNA such as surviving 1 M NaCl, 2 month stability in 0.3 M NaCl and working in 50% serum. A poly-adenine block with as few as two consecutive terminal adenine bases is sufficient for anchoring on AuNPs. By side-by-side comparison with the salt-aging method, the conjugation mechanism was attributed to competitive adenine adsorption at high temperature along with an extremely high DNA concentration upon drying. Bioanalytical applications of the nonthiolated SNAs were validated in both solution and paper-based sensor platforms, facilitating cost-effective applications for SNAs.

Adenine Adsorption on Ag Doped Graphene : A Theoretical Insight

Adenine Adsorption on Ag Doped Graphene : A Theoretical Insight

Surface adsorption of adenine on pristine and B/N/O/P-doped coronene as a biosensing substrate for DNA detection- DFT study

Nucleobase detection is crucial for the exploration of specific nucleotide sequences. Inspired by the recent realization of two dimensional nanomaterials as DNA detectors as well as sensors, the interactions of pristine and B/N/O/P-doped coronenes with adenine nucleobase have been studied on the basis of Density Functional Theory. Optimal configurations, the corresponding adsorption energies, charge transfer and electrical properties have been calculated for each complex. The adsorption strength and charge transfer in doped coronene have been found larger than that in the pristine coronene. AIM-RDG study suggests that non-covalent interactions existing in the associated interactive region are responsible for the stability of the complexes. The change in electrical conductivity of coronenes after the adsorption indicates its sensitivity towards DNA bases. The predicted energy gap and the prolonged recovery time for adenine-coronene configurations imply that pristine/doped coronene has potential applications in DNA detection.

Adenine adsorption on Hf-doped graphene: A density functional theory investigation

We have used density functional theory to study how adenine molecules interact with the electrical structure of both pristine graphene (Gr) and hafnium doped graphene (GR-Hf). According to several measures, graphene doped with hafnium has favourable characteristics for use as an adsorbent for Adenine in biosensors. These include the adsorption energy, charge transfer mode, dipole moment, HOMO-LUMO energy, energy gap, and density of states (DOS).

Poly oligonucleotides antifouling interface with highly specific response of multi-biomarkers in serum: Anti-fouling mechanisms and influencing factors

Quantifying trace markers in clinical samples with electrochemical impedance spectroscopy (EIS) biosensors is limited mainly by ubiquitous biofouling because traditional antifouling coatings suffer from low stability and unsatisfactory antifouling capability etc. Herein, a simple and effective strategy was constructed to achieve a highly specific EIS biosensing platform for quantifying protein and DNA in serum by using single-stranded oligonucleotides (ssDNA) as antifouling coating. To achieve the optimized antifouling capability of ssDNA coating, the influence factors of ssDNA structure are investigated by combining electrochemical experiments with theoretical calculations. The results demonstrated that the chemical adsorption of adenine on the Au surface is stronger than that of the other three bases, which endows the poly adenine-ssDNA (polyAn) coating with outstanding antifouling capability. Importantly, we found that the capture ligand structure and ssDNA length remarkably affected the antifouling capability of polyAn because of steric hindrance. As a proof of concept, EIS biosensors based on polyAn antifouling coating were developed to detect target DNA and nuclear factor kappa b p65 (NF-kB p65), respectively, exhibiting outstanding capability of detecting DNA and NF-kB p65 in human serum with low interference and good accuracy. Overall, the presented work may contribute to a deeper understanding of the influence factors of ssDNA-based antifouling coating and holds great insight into the construction of highly specific biosensors for quantifying disease markers in clinical samples.

Theoretical study of DNA base adenine adsorption on cadmium doped graphene for biosensor applications

We reported the mechanism of DNA base adenine adsorption on Cadmium doped Graphene by implementing density functional theory (DFT). Our theoretical investigation reveals the structural and electrical features of the complicated, complex, biological system of Graphene-Adenine (Gr-A) depending on the Cadmium (Cd) atom. The DNA chemical base Adenine is adsorbed on pristine Graphene; However, significant chemisorption is observed on Cd-doped Graphene. We successfully reported the transfer of charge, Highest Occupied Molecular Orbital -Lowest Unoccupied Molecular Orbital (HOMO-LUMO), and Density of State (DOS). The findings showed that the reduction in the HOMO-LUMO gap values had rosined the electrical conductivity values of the Cd-doped Graphene following the adsorption of the Adenine base. The current study revealed that the graphene adsorption capacity for Adenine could be enhanced by doping the Cadmium (Cd) dopant. As a result, Cd-doped graphene was introduced as a strong adsorbent for biosensor applications in various fields.

Adenine adsorption in different pH acetate buffer

Adenine adsorption in different pH acetate buffer

Interaction between adenine and Cu2+ and Fe3+-montmorillonites: a prebiotic chemistry experiment

AbstractThe modification of minerals with metals can promote changes in their surface and, consequently, in their physicochemical properties. Minerals could have played an important role in the origin of life as they can protect molecules against degradation by radiation and hydrolysis, pre-concentrate molecules from dilute solutions and catalyse the formation of polymers. Thus, the current work studied the modification of montmorillonite with Cu2+ and Fe3+ ions. These modified montmorillonites were used to study the interaction with adenine dissolved in distilled water and artificial seawater 4.0 Gy (Gy = billion years ago). The most important result of this work is that the adsorption of adenine onto modified montmorillonites is a complex interaction among adenine, salts in seawater and Cu2+/Fe3+-montmorillonite (Cu2+/Fe3+-Mont) . The adsorption of Cu2+ and Fe3+ onto montmorillonite decreased its surface area and pore volume. The Sips isotherm model showed the best fit of the data and n values indicate that the adenine adsorption process was homogeneous. The highest adenine adsorption was obtained in artificial seawater 4.0 Gy onto Fe3+-Mont at 60°C and the lowest in distilled water or artificial seawater 4.0 Gy onto montmorillonite [montmorillonite washed with distilled water (Mont-STD)] at 60°C. Adenine adsorption onto Mont-STD/montmorillonite modified with 500 ml of 0.1 mol l−1 of CuCl2 and Fe3+-Mont was an exothermic process and an endothermic process, respectively. For all adsorptions ΔG was negative. The adsorption of adenine onto Fe3+-Mont was ruled out by entropy and the other samples by enthalpy and entropy, being a major contribution for Gibbs free energy from enthalpy. The Fourier transform-infrared data indicate that the interaction of adenine with minerals may occur through the NH2 functional group.

Adenine Adsorption in Different pH Acetate Buffer

The research results facilitate the description of adenine adsorption on the mercury electrode with reference to the pH of the supporting electrolyte which was the acetate buffer with pH of 3, 4, 5 and 6. The thermodynamic analysis indicates that the curves of the differential volume of the studied systems with adenine do not overlap with the curves for the supporting electrolyte – the acetate buffer. This indicates the occurrence of adsorption of the studied compound on the mercury electrode within the whole range of applied concentrations in the case of every tested pH value of the acetate buffer. Adsorption energy and interaction constants were determined using the Frumkin isotherm and the viral isotherm. It was demonstrated that a adenine molecule is adsorbed on the mercury electrode in a buffer with pH 4, 5 and 6 through the negative pole, whereas in a buffer with pH 3 through the positive pole. Physical adsorption was observed in the studied systems. This is indicated by the occurrence of a typical maximum on the curve of the relation the relative surface excess amounts and the potential of the electrode; crossed curves of the following relation surface charge of the electrode from its potential (surface charge of the electrode from its potential σ = f(E)) at one point and, thus, the possibility of determining electrical parameters characterizing maximum adsorption as well as the absence of linearity of the function free energy of adsorption as a function of electrode potential ∆G0 = f(E).

Adsorption structure of adenine on cerium oxide

The adsorption of adenine on the CeO2(111)/Cu(111) surface in vacuum was studied by photoelectron spectroscopy, resonant photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy, and the present work describes in detail the bonding of the molecule to the ordered stoichiometric cerium dioxide film. The experimental findings were supported by density functional theory (DFT + U) analysis of different adsorption geometries of adenine on CeO2(111). The phase with adenine lying flat on the surface dominates on CeO2(111) up to 0.1 monolayer (ML) of adenine coverage. The mobility of single molecules was apparently sufficiently high to allow diffusion and formation of chain structures, which were observed to be stable in the temperature range from 25 to 250 °C. Beyond 0.1 ML, adenine molecules adsorb predominantly in an upright orientation. This phase, stable up to 120 °C, is according to theory stabilised via N3/Ce4+ and N9H/O2–. It was further complemented by experimental findings demonstrating free N10H2 groups in adsorbed molecules. Thus, the saturation coverage of adenine on CeO2(111), 0.23 ML, is most likely characterised by a combination of parallel and upright bound molecules.

Adenine Adsorbed onto Montmorillonite Exposed to Ionizing Radiation: Essays on Prebiotic Chemistry

Most adsorption and radiolysis experiments related to prebiotic chemistry studies are performed in distilled water or sodium chloride solutions. However, distilled water and sodium chloride solutions do not represent the composition of the primitive seas of Earth. In this work, an artificial seawater with ion abundances Mg2+ > Ca2+ >> Na+ ≈ K+ and SO42- >> Cl- was used, one that is different from the average composition of seawater today. This artificial seawater is named seawater 4.0 Ga, since it better represents the composition of the major constituents of seawater of primitive Earth. The radiolysis of adenine adsorbed onto montmorillonite was studied. The most important result is that adenine is adsorbed onto montmorillonite, when it is dissolved in artificial seawater 4.0 Ga, and the clay protects adenine against gamma radiation decomposition. However, desorption of adenine from montmorillonite was possible only with 0.10 mol L-1 of KOH. This result indicates that adenine was strongly bonded to montmorillonite. Fourier transform infrared spectroscopy showed that NH2 group and electrostatic interactions, between negatively charged montmorillonite and positively charged adenine, are responsible for adsorption of adenine onto montmorillonite. In addition, X-ray diffractograms showed that adenine enters in the interlayer space of montmorillonite.

Magnetic Core-shell nanoparticles with molecularly imprinted polymers for selective adsorption and separation of adenine

Magnetic Core-shell nanoparticles coated with an adenine-imprinted polymer layer were successfully synthesized. The morphology of the nanoparticles was characterized by transmission electron microscopy (TEM). The nanoparticles have a definite core-shell structure and an imprinted polymer layer. The adsorption, recognition and reusability of the molecularly imprinted nanoparticles were analyzed by static/dynamic adsorption, competitive adsorption and reproducibility experiment. The magnetic molecularly imprinted nanoparticles exhibit fast adsorption, high adsorption capacity, strong specificity and satisfactory recovery.

Adsorption of adenine on mercury electrode in acetate buffer at pH 5 and pH 6 and its effect on electroreduction of zinc ions

The measurements of double-layer differential capacitance, zero charge potential, and surface tension at that potential allowed us to examine the adsorption properties of adenine on the mercury surface from the neat buffer solution, i.e., the acetate buffer at pH 5 and pH 6. The systems obtained at such pH values were close to physiological fluids in their characteristics. The adsorption energy and interaction constants were determined using Frumkin isotherm and virial isotherm. It was shown that the adenine molecule is adsorbed on the mercury electrode with its negative pole against the electrode surface. Using the cyclic voltammetry technique and measuring Faraday impedance, an increasing effect of adenine on the kinetics of zinc ion electroreduction was found. In both buffer solutions, the neutral adenine molecules can form on the surface of the working electrode, an unstable active complex with depolarizer ions, facilitating electron exchange.Graphical abstract

Beryllium oxide (BeO) nanotube provides excellent surface towards adenine adsorption: A dispersion-corrected DFT study in gas and water phases

Zigzag (5, 0) BeO nanotube (BeONT) has been examined in detail towards adsorption properties of adenine nucleobase on its surface via D2-DFT calculation method in the gas and water phases. A detailed surface study reveals that there are four orientations for nucleobase adsorption that none of the vibrational spectrums demonstrated imaginary frequency, recognizing that all of the relaxed structures are at the minimum of energy. The minimum and maximum adsorption energies are both in chemisorption regime with calculated values of −140 (−118 BSSE corrected) and −191 (−168 BSSE corrected) in the gas phase, and −181 and −310 kJ/mol in the water phase, using meta-hybrid functional (ꞷB97XD) and 6-31G** basis set. For all positions, BeONT showed p-type semiconducting property because of receiving electronic charge from adenine molecule. Our findings suggest that BeONT could be used as a possible strong carrier for adenine molecule in practical applications.

The Effect of Adenine Adsorption on Zn (II) Electroreduction in Acetate Buffer

The paper presents the thermodynamic analysis of adenine adsorption on a mercury electrode in an acetate buffer at pH 3 and pH 4. Adsorption energy and constants were determined using the Frumkin isotherm and the virial isotherm. Stronger adsorption in the buffer at pH 3 was observed in comparison to the buffer at pH 4. Using cyclic voltammetry and Faraday impedance measurement, an inhibitory effect of adenine on the kinetics of Zn (II) ion electro-reduction was observed.

Salinity Effects on the Adsorption of Nucleic Acid Compounds on Na-Montmorillonite: a Prebiotic Chemistry Experiment.

Any proposed model of Earth's primitive environments requires a combination of geochemical variables. Many experiments are prepared in aqueous solutions and in the presence of minerals. However, most sorption experiments are performed in distilled water, and just a few in seawater analogues, mostly inconsistent with a representative primitive ocean model. Therefore, it is necessary to perform experiments that consider the composition and concentration of dissolved salts in the early ocean to understand how these variables could have affected the absorption of organic molecules into minerals. In this work, the adsorption of adenine, adenosine, and 5'AMP onto Na+montmorillonite was studied using a primitive ocean analog (4.0Ga) from experimental and computational approaches. The order of sorption of the molecules was: 5'AMP > adenine > adenosine. Infrared spectra showed that the interaction between these molecules and montmorillonite occurs through the NH2 group. In addition, electrostatic interaction between negatively charged montmorillonite and positively charge N1 of these molecules could occur. Results indicate that dissolved salts affect the sorption in all cases; the size and structure of each organic molecule influence the amount sorbed. Specifically, the X-ray diffraction patterns show that dissolved salts occupy the interlayer space in Na-montmorillonite and compete with organic molecules for available sites. The adsorption capacity is clearly affected by dissolved salts in thermodynamic terms as deduced by isotherm models. Indeed, molecular dynamic models suggest that salts are absorbed in the interlamellar space and can interact with oxygen atoms exposed in the edges of clay or in its surface, reducing the sorption of the organic molecules. This research shows that the sorption process could be affected by high concentration of salts, since ions and organic molecules may compete for available sites on inorganic surfaces. Salt concentration in primitive oceans may have strongly affected the sorption, and hence the concentration processes of organic molecules on minerals.

An experimental and theoretical study of adenine adsorption on Au(111).

A model study of adenine adsorption on the Au(111) surface is reported for molecular adlayers prepared by evaporation in vacuum and deposition from saturated aqueous solution. The electronic structure and adsorption geometry of the molecular films were studied experimentally by X-ray photoelectron spectroscopy and near edge X-ray absorption fine structure spectroscopy. Adsorption models are proposed for the adlayers arising from the different preparation methods. Density functional theory calculations were used to examine both parallel and upright adenine adsorption geometries, supply additional information on the bond strength, and identify which atom is involved in bonding to Au(111). In the case of deposition in vacuum, the adenine molecule is bound via van der Waals forces to Au(111) with the molecular plane parallel to the surface, consistent with the published scanning tunneling microscopy data on this system. The most stable parallel adenine configuration was found to have an adsorption energy of ca. -1.1 eV using the optB86b-vdW functional. For adenine deposition from aqueous solution, the adlayer is disordered, with molecules in an upright geometry, and with an adsorption energy of ca. -1.0 eV, coordinated via the imino N3 nitrogen atom. The present study contributes to the substantial literature of model studies of adenine on Au(111), complementing the existing knowledge with information on electronic structure, bonding geometry and adsorption energy of this system.

Thermally Controlled Bonding of Adenine to Cerium Oxide: Effect of Substrate Stoichiometry, Morphology, Composition, and Molecular Deposition Technique

The adsorption of adenine, one of the structural units of DNA and RNA, on nanostructured cerium oxide was studied using synchrotron radiation based techniques: photoelectron and X-ray absorption spectroscopies. Using a systematic approach, we studied this biomolecule’s bonding to the inorganic surface and examined the effects of different stoichiometry, morphology and composition of cerium oxide films, as well as two methods of molecular deposition (evaporation in vacuum and deposition from aqueous solution). The adenine molecule chemisorbs on the stoichiometric (IV) cerium oxide intact via nitrogen atoms, independent of the oxide morphology and deposition technique. Annealing of the adenine adlayer at 250 °C causes CeO2 surface partial reduction, along with the partial deprotonation of the nitrogen. The reaction of adenine with ex situ prepared CeO2 films (nanostructured compact and porous) activates Ce4+ cation reduction not only on the surface but also in the subsurface layers accompanied by water deso...

Study on the electronic structure of Cr- and Ni-doped fullerenes upon adsorption of adenine: A comprehensive DFT calculation

Density functional theory (DFT) method has been employed to study the adsorption behavior of adenine as a purine nucleobase on the surface of Cr-doped C20 fullerene (C19Cr) and Ni-doped C20 fullerene (C19Ni). The binding energies, interactions distances, natural bond orbital (NBO) analysis, thermochemical parameters, dipole moments, and frontier molecular orbitals are calculated to profoundly understand the impacts of adenine adsorption on the electronic and chemical properties of C19Cr and C19Ni nanoclusters. It is discovered that adenine is adsorbed on the surface of C19Cr and C19Ni nanoclusters in three different configurations denoted as a, b, and c. The highest binding energy for adenine adsorption on C19Cr (C19Ni) is −205.0 (−200.6) kJ/mol for b geometry, demonstrating the capability of C19Cr and C19Ni nanoclusters toward adenine chemisorption. Notably, the binding energy of adenine on the aforementioned nanoclusters is slightly affected by changing the adsorption orientation.