Adsorption Of Nucleotides Research Articles

Exploration of DNA nucleotide adsorption on GeTe monolayer through DFT analysis

DNA nucleobase sensors provide crucial information for diagnosing diseases, analyzing genetics, and advancing biological research by detecting and identifying DNA sequences in real-time. This research examined how GeTe monolayer interact with DNA nucleobases through adsorption. The adsorption strengths of the four bases on the adsorbent surface followed the order of G > C > T > A. Analysis of electronic properties indicated that the interaction between nucleobases and GeTe primarily involves physical adsorption. Additionally, higher adsorption energies led to greater rearrangement of surface electrons and changes in the adsorbent's potential barrier, resulting in significant variations in the work function (WF) value. The desorption times at 498K were A (0.02 h), G (15.8 h), C (0.72 h), and T (0.43 h), indicating the potential of GeTe as a reusable material for nucleobase sensors. We can amplify the adsorption strength (30 %–45 %) and improve the discrimination between nucleobases (208 %–808 %) by employing solvents possessing higher dielectric constants. Comparisons with recent research validated the superior adsorption performance and selectivity of the material used in this study, highlighting the promising application of the GeTe monolayer in nucleobase sequencing technology.

Adsorption of nucleotides and nucleic acids on goethite nanoparticles: mode, sites and relationship with phosphate and non-phosphate structures

The impact of iron (hydr)oxide adsorption on nucleotides and nucleic acids (NNAs) in the environment varies.

Nucleotide Interaction with Nanocrystalline Ceria Surface

The adsorption of nucleotides on the surface of nanocrystalline cerium dioxide (pHpzc = 6.3) in NaCl solutions was investigated using multi-batch adsorption experiments over a wide range of pH. The obtained results were interpreted as a formation of outer and inner sphere surface complexes with the participation of phosphate moieties. The Basic Stern surface complexation model was applied to obtain quantitative equilibrium reaction constants.

Differential Surface Interactions and Surface Templating of Nucleotides (dGMP, dCMP, dAMP, and dTMP) on Oxide Particle Surfaces.

The fate of biomolecules in the environment depends in part on understanding the surface chemistry occurring at the biological-geochemical (bio-geo) interface. Little is known about how environmental DNA (eDNA) or smaller components, like nucleotides and oligonucleotides, persist in aquatic environments and the role of surface interactions. This study aims to probe surface interactions and adsorption behavior of nucleotides on oxide surfaces. We have investigated the interactions of individual nucleotides (dGMP, dCMP, dAMP, and dTMP) on TiO2 particle surfaces as a function of pH and in the presence of complementary and noncomplementary base pairs. Using attenuated total reflectance-Fourier transform infrared spectroscopy, there is an increased number of adsorbed nucleotides at lower pH with a preferential interaction of the phosphate group with the oxide surface. Additionally, differential adsorption behavior is seen where purine nucleotides are preferentially adsorbed, with higher surface saturation coverage, over their pyrimidine derivatives. These differences may be a result of intermolecular interactions between coadsorbed nucleotides. When the TiO2 surface was exposed to two-component solutions of nucleotides, there was preferential adsorption of dGMP compared to dCMP and dTMP, and dAMP compared to dTMP and dCMP. Complementary nucleotide base pairs showed hydrogen-bond interactions between a strongly adsorbed purine nucleotide layer and a weaker interacting hydrogen-bonded pyrimidine second layer. Noncomplementary base pairs did not form a second layer. These results highlight several important findings: (i) there is differential adsorption of nucleotides; (ii) complementary coadsorbed nucleotides show base pairing with a second layer, and the stability depends on the strength of the hydrogen bonding interactions and; (iii) the first layer coverage strongly depends on pH. Overall, the importance of surface interactions in the adsorption of nucleotides and the templating of specific interactions between nucleotides are discussed.

Adsorption separation of guanosine 5′-Monophosphate and cytidine 5′-Monophosphate by mixed-mode Resin HD-1: Experimental study and mathematical modeling

The preparative separation of guanosine 5′-monophosphate (GMP) and cytidine 5′-monophosphate (CMP) on mixed-mode resin HD-1 was experimentally and theoretically investigated. The adsorption mechanisms of the two nucleotides were elucidated by analyzing adsorption equilibria and kinetics at different pH values. The adsorption dynamics of GMP and CMP in a fixed bed packed with resin HD-1 were studied. All nucleotide monovalent cations, zwitterions, and monovalent anions were adsorbed by the resin. Further, a general adsorption isotherm model was developed by considering the adsorption of different nucleotide species and the dissociation equilibrium behaviors of resin ligands. The model fit the adsorption isotherm data of GMP and CMP well. A modified liquid-film linear driving force model with the combined physical adsorption of nucleotides in different dissociation states and ion exchange of Na+ was established. The dissociation equilibria of resin ligands and nucleotides were considered. The model satisfactorily predicted the adsorption kinetic data at different pH values. The values of the efficient diffusion coefficients for GMP and CMP were not significantly influenced by the solution pH. A modified transport-diffusion model with pH gradient elution was proposed. The model accurately predicted the elution chromatographic peaks of GMP and CMP, as well as the pH at the outlet of the fixed bed packed with resin HD-1.

Nucleotide Interaction with a Chitosan Layer on a Silica Surface: Establishing the Mechanism at the Molecular Level.

The growing interest in gene therapy is coupled with the strong need for the development of safe and efficient gene transfection vectors. A composite based on chitosan and fumed silica has been found to be a prospective gene delivery carrier. This study presents an investigation of the nature of the bonds between a series of nucleotides with a chitosan layer deposited on a fumed silica surface. Experimentally measured surface complex formation constants (logK) of the nucleotides were found to be in the range of 2.69–4.02, which is higher than that for the orthophosphate (2.39). Theoretically calculated nucleotide complexation energies for chitosan deposited on the surface range from 11.5 to 23.0 kcal·mol–1, in agreement with experimental data. The adsorption of nucleotides was interpreted using their calculated speciation in an aqueous solution. Based on the structures of all optimized complexes determined from quantum-chemical PM6 calculations, electrostatic interactions between the surface-located NH3+ groups and −PO3H––/–PO32– fragments of the nucleotides were identified to play the decisive role in the adsorption mechanism. The saccharide fragment of monophosphates also plays an important role in the binding of the nucleotides to chitosan through the creation of hydrogen bonds.

Nucleotide Adsorption on Iron(III) Oxide Nanoparticle Surfaces: Insights into Nano-Geo-Bio Interactions Through Vibrational Spectroscopy.

Molecular processes at geochemical interfaces impact many environmental processes that are critical to the fate and transport of contaminants in water systems. Often these interfaces are coated with natural organic matter, oxyanions, or biological components, yet little is understood about these coatings. Herein, we are interested in better understanding the interaction of biological components with nanoscale iron oxide minerals. In particular, we use attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to investigate the adsorption behavior of deoxyadenosine monophosphate (dAMP) on hematite nanoparticle surfaces as a function of pH and in the presence and absence of adsorbed phosphate. These results show that fewer nucleotides adsorb at higher pH. Additionally, when phosphate anions are preadsorbed, nucleotide adsorption is significantly limited due to site-blocking by adsorbed inorganic phosphate. The pH dependence provides insights into the adsorption process and the importance of electrostatic interactions. Preadsorbed phosphate affects the binding mode of dAMP, suggesting synergistic interactions between the coadsorbates. Two-dimensional correlation spectroscopy was used to further analyze the infrared spectra. Based on this analysis, a dAMP adsorption pathway onto a preadsorbed phosphate-hematite surface was proposed, suggesting the displacement of adsorbed phosphate by dAMP. Overall, this study provides some insights into geochemical-biological interactions on nanoscale iron oxide surfaces using vibrational spectroscopy.

Adsorption of nucleotides on clay surfaces: Effects of mineral composition, pH and solution salts

In the context of the origin of life, clays have been proposed as possible materials to adsorb, protect and potentially foster the formation of complex bio molecules. In the present study, the adsorption of nucleotides onto clay surfaces has been tackled through classical molecular dynamics calculations. Various parameters have been varied by modelling the deoxyguanosine mono phosphate molecule at the basal surface of two clay minerals: montmorillonite and nontronite, at pH = 3 and 7, and in a 0.5 M NaCl solution in presence or absence of Ca2+ divalent cations. It has been firstly observed that counter cations in solution adopts a three-layers structure above the mineral basal surfaces which can be modified by the mineral composition, the location of the surface charge, and results in substantial effects on nucleotide adsorption. For montmorillonite, for which the charge is located in the octahedral (inner) layer, the two closest counter cations layers above the mineral surface are less populated while the third layer comprises the largest cations density. For nontronite, for which the negative charge is located on the surface oxygen atoms of the tetrahedral layer in contact with the aqueous solution, the first two counter cations layers are the most populated. The negative charge on the surface is thus screened by the first two layers above nontronite surface, and by only the third layer for montmorillonite. As a result, the negatively charged phosphate moiety of nucleotides can approach closer to the surface of nontronite by coordinating with the first two layers cations and the nucleobase adsorb on the surface in a parallel orientation maximizing Van der Walls interactions. On montmorillonite, the phosphate coordinates the cations of the third layer and thus remains rather far from the surface, which does not allow the nucleobase parallel binding. These theoretical results explain experimental results on the effect of mineral and solution composition on the adsorption of nucleotides on the surface of swelling clays.

Adsorption Complexes of Purine Nucleotides on a Titanium Dioxide Surface

It has been shown that the adsorption of purine nucleotides from aqueous solutions on the surface of nanocrystalline titanium dioxide results in the formation of outer-sphere electrostatic complexes. Stability constants have been calculated for the adsorption complexes, in which anionic forms of nucleotides are bonded to protonated groups of titanium dioxide.

Transition Metals Enhance the Adsorption of Nucleotides onto Clays: Implications for the Origin of Life

The chemical evolution of early life requires the concentration of monomers to polymerize from the diluted primordial ocean. Transition metals such as Fe, Mn, and Zn, could have reached considerable levels in the early seawater and/or hydrothermal fluid but their influences on the adsorption of biomolecules have not been clearly addressed yet. In this study, we conducted batch adsorption experiments to explore effects of various metal cations (Li, Mg, Ca, Zn, Ni, and Mn) on the adsorption of selected nucleotides (dGMP, dAMP, and AMP) and adenosine onto nontronite and montmorillonite. We also varied the concentration of the cations and pH of the solutions to evaluate their effects. Our results show that Zn and to some extent Ni increase the adsorption of nucleotides and adenosine compared with Na, Mg, and Ca which are major salts in modern seawater. This increased adsorption is primarily attributed to the mediating role of transition metals between the clays and nucleotides and adenosine. The enhancing eff...

Adsorption of Pyrimidine Nucleotides on a Titanium Dioxide Surface

The adsorption of pyrimidine mononucleotides from aqueous solutions on the surface of nanocrystalline titanium dioxide is studied. The interaction of the nucleotides with hydroxyl groups of titanium dioxide is interpreted in terms of the surface complexation theory. The results of an experimental study of the dependence of adsorption on the pH and ionic strength of solutions are used to calculate the stability constants of the outer-sphere adsorption complexes, which result from the electrostatic interaction of protonated groups with anionic forms of nucleotides.

Effects of salinity on the adsorption of nucleotides onto phyllosilicates.

In the context of the origin of life, phyllosilicate surfaces might favor the adsorption, concentration and reactivity of otherwise diluted prebiotic molecules. The primitive oceanic seafloor was certainly rich in Fe-Mg-rich phyllosilicates. The salinity of the primitive seawater remains largely unknown. Values ranging from 1 to 15 times modern salinity have been proposed and the salt composition of the primitive ocean also remains elusive although it may have played a role in the interactions between nucleotides and mineral surfaces. Therefore we studied the adsorption of 5'-monophosphate deoxyguanosine (dGMP) as a model nucleotide onto a Fe-rich swelling clay, i.e. nontronite, and an Al-rich phyllosilicate, i.e. pyrophyllite, for comparison. Experiments were carried out at atmospheric pressure, 25 °C and natural pH, with a series of salts NaCl, MgCl2, CaCl2, MgSO4, NaH2PO4 and LaCl3 in order to evaluate the effect of cations and anions on dGMP adsorption. The present study shows that nucleotides are adsorbed on both phyllosilicates via a ligand exchange mechanism. The phosphate group of the nucleotide is adsorbed on the lateral metal hydroxyls of the broken edges of phyllosilicates. The presence of divalent cations or molecular anions, such as phosphate or sulfate, tends to inhibit this interaction on mineral surfaces. However, in the presence of divalent cations, cationic bridging on the basal surfaces of the swelling clay also occurs and could induce a higher retention capacity of the swelling clays compared to non-swelling phyllosilicates in primitive and modern natural environments.

In Ukrainian

The adsorption of adenine nucleotides with different phosphate chains from aqueous solutions onto nanocrystalline ceria surface was investigated. The adsorption dependences of pH and ionic strength are interpreted in terms of surface complexation theory.  The equilibrium reaction constants of  the formation of outer-sphere electrostatic complexes are calculated with using basic Stern model for double electric layer.

Prebiotic RNA polymerisation: energetics of nucleotide adsorption and polymerisation on clay mineral surfaces.

We measured the binding energy and bonding parameters between model nucleotide functional groups and model clay mineral surfaces in solutions of acidic pH. We demonstrate that basal surfaces of clay minerals interact most strongly with nucleobases and show that the adsorption of the phosphate group to clay edges could facilitate polymerisation. Our results suggest that Al- and Fe-rich edge sites behave similarly in nucleotide polymerisation through change of the phosphodiester bond strength. We present an internally consistent set of thermodynamic parameters that represent the nucleotide-clay mineral system.

Adsorption of nucleotides onto ferromagnesian phyllosilicates: Significance for the origin of life

The concentration of prebiotic organic building blocks may have promoted the formation of biopolymers in the environment of the early Earth. We therefore studied the adsorption of RNA monomers AMP, GMP, CMP, and UMP, and DNA monomers dGMP, dCMP, and TMP, on minerals that were abundant in the early Earth environment as the result of aqueous or hydrothermal alteration of the primitive oceanic crust. We focused our study on swelling clays, i.e. nontronite and montmorillonite, and non-swelling phyllosilicates, i.e. pyrophyllite, chlorite, lizardite and chrysotile suspended in an aqueous saline solution analog to seawater. In this reference study, adsorption experiments were carried out under standard conditions of pressure and temperature and controlled pH. Under such conditions, this work is also relevant to the preservation of nucleic acids in Fe–Mg-rich terrestrial and Martian soils. We compared the adsorption of the different monomers on individual minerals, as well as the adsorption of single monomers on the whole suite of minerals. We found that DNA monomers adsorb much more strongly than RNA monomers, and that any monomer containing the G nucleobase adsorbed more strongly than one containing the C nucleobase. At high surface loadings (greater than about 1mM monomer in aqueous solution) we also found a dramatic increase in the slope of adsorption isotherm on the swelling clays, leading to large increases in the amounts adsorbed. Data were processed in order to understand the adsorption mechanism of nucleotides onto mineral surfaces. We infer that all nucleotides behave as homologous molecules in regard to their adsorption onto the studied mineral surfaces. At low to moderate surface loadings, their adsorption is best explained by a single mechanism common to the suite of minerals of the present study. At pH 7, adsorption certainly proceeds by ligand exchange between the phosphate group and the hydroxyls of the broken edges of phyllosilicates leading to the saturation of lateral surfaces. Below pH 4, swelling clays also adsorb nucleotides through cation exchange on basal surfaces, whereas non-swelling phyllosilicates do not. However, at high surface loadings an additional mechanism stabilizing adsorption occurs. Given the proposed adsorption mechanisms, the possibility of a favorable polymerization at the mineral–water interface is discussed. We propose that Fe–Mg rich phyllosilicates tightly bind nucleotides, under ambient conditions, and concentrate them up to 1000 times the solution concentration upon saturation. Nontronites have the most diverse and favorable adsorption behaviors and could have helped to the concentration and polymerization of nucleotides under primitive Earth-like conditions.

Adsorption of nucleotides on biomimetic apatite: The case of adenosine 5⿲ triphosphate (ATP)

ATP is a well-known energy supplier in cells. The idea to associate ATP to pharmaceutical formulations/biotechnological devices to promote cells activity by potentially modulating their microenvironment thus appears as an appealing novel approach. Since biomimetic nanocrystalline apatites have shown great promise for biomedical applications (bone regeneration, cells diagnostics/therapeutics, ⿦), thanks to a high surface reactivity and an intrinsically high biocompatibility, the present contribution was aimed at exploring ATP/apatite interactions. ATP adsorption on a synthetic carbonated nanocrystalline apatite preliminarily characterized (by XRD, FTIR, Raman, TG-DTA and SEM-EDX) was investigated in detail, pointing out a good agreement with Sips isothermal features. Adsorption characteristics were compared to those previously obtained on monophosphate nucleotides (AMP, CMP), unveiling some specificities. ATP was found to adsorb effectively onto biomimetic apatite: despite smaller values of the affinity constant KS and the exponential factor m, larger adsorbed amounts were reached for ATP as compared to AMP for any given concentration in solution. m<1 suggests that the ATP/apatite adsorption process is mostly guided by direct surface bonding rather than through stabilizing intermolecular interactions. Although standardοGads° was estimated to only ⿿4kJ/mol, the large value of Nmax led to significantly negative effective οGads values down to ⿿33kJ/mol, reflecting the spontaneous character of adsorption process. Vibrational spectroscopy data (FTIR and Raman) pointed out spectral modifications upon adsorption, confirming chemical-like interactions where both the triphosphate group of ATP and its nucleic base were involved. The present study is intended to serve as a basis for future research works involving ATP and apatite nanocrystals/nanoparticles in view of biomedical applications (e.g. bone tissue engineering, intracellular drug delivery, ⿦).

Hydrophilic interaction chromatography coupled to tandem mass spectrometry in the presence of hydrophilic ion-pairing reagents for the separation of nucleosides and nucleotide mono-, di- and triphosphates

A fast and efficient method for the simultaneous separation of highly polar compounds, in this case nucleosides and nucleotide mono-, di- and triphosphates, using hydrophilic interaction chromatography coupled with tandem mass spectrometry (HILIC–MS/MS) is proposed. This new separation method revealed the possibilities of the formation of hydrophilic ion-pairing compounds.Three stationary phases (HILIC XBridge-Amide, HILIC-CoreShell and ZIC-HILIC) were assayed for the separation of 20 target analytes, and a detailed study of the composition of the mobile phase was made using different salts at different concentrations in a organic-rich mobile phase. We report that in order to prevent the adsorption of nucleotides on the LC–MS setup and to enhance their retention on the HILIC stationary phase, a mobile phase containing hexafluoro-2-propanol and different cations should be used. Four cations were evaluated: ammonium, diethylammonium, triethylammonium and tetrabutylammonium. The results revealed the formation of an ionic-association compound between the phosphorylated analytes and the cationic ion-pairing reagents, whose retention increased with the polarity of the cationic ion-pairing reagent.HILIC XBridge-Amide was found to be the most suitable column for the separation of these analytes, and the optimized mobile phase consisted of an ACN/UHQ water mixture (3min of isocratic elution using 82:18%, v/v and then a fast gradient from 18% to 22% of water) with 100mM hexafluoro-2-propanol and 50mM diethylamine (wwpH 9–wspH 10). In a total analysis time of 8min, good results were achieved in terms of resolution. Under these optimum conditions, a further comprehensive study of the retention mechanism was carried out.

Adsorption of nucleotides on biomimetic apatite: The case of adenosine 5′ monophosphate (AMP)

This work investigates the interaction between the nucleotide adenosine 5′ monophosphate molecule (AMP) and a biomimetic nanocrystalline carbonated apatite as a model for bone mineral. The analogy of the apatite phase used in this work with biological apatite was first pointed out by complementary techniques. AMP adsorption isotherms were then investigated. Obtained data were fitted to a Sips isotherm with an exponent greater than one suggesting positive cooperativity among adsorbed molecules. The data were compared to a previous study relative to the adsorption of another nucleotide, cytidine monophosphate (CMP) onto a similar substrate, evidencing some effect of the chemical nature of the nucleic base. An enhanced adsorption was observed under acidic (pH 6) conditions as opposed to pH 7.4, which parallels the case of DNA adsorption on biomimetic apatite. An estimated standard Gibbs free energy associated to the adsorption process (ΔG°ads≅−22kJ/mol) intermediate between “physisorption” and “chemisorption” was found. The analysis of the solids after adsorption pointed to the preservation of the main characteristics of the apatite substrate but shifts or enhancements of Raman bands attributed to AMP showed the existence of chemical interactions involving both the phosphate and adenine parts of AMP. This contribution adds to the works conducted in view of better understanding the interaction of DNA/RNA and their constitutive nucleotides and the surface of biomimetic apatites. It could prove helpful in disciplines such as bone diagenesis (DNA/apatite interface in aged bones) or nanomedicine (setup of DNA- or RNA-loaded apatite systems). Also, the adsorption of nucleic acids on minerals like apatites could have played a role in the preservation of such biomolecules in the varying conditions known to exist at the origin of life on Earth, underlining the importance of dedicated adsorption studies.

Adsorption of nucleotides on biomimetic apatite: The case of cytidine 5′ monophosphate (CMP)

The chemical interaction between DNA macromolecules and hard tissues in vertebrate is of foremost importance in paleogenetics, as bones and teeth represent a major substrate for the genetic material after cell death. Recently, the empirical hypothesis of DNA “protection” over time thanks to its adsorption on hard tissues was revisited from a physico-chemical viewpoint. In particular, the existence of a strong interaction between phosphate groups of DNA backbone and the surface of apatite nanocrystals (mimicking bone/dentin mineral) was evidenced on an experimental basis. In the field of nanomedicine, DNA or RNA can be used for gene transport into cells, and apatite nanocarriers then appear promising. In order to shed some more light on interactions between DNA molecules and apatite, the present study focuses on the adsorption of a “model” nucleotide, cytidine 5′ monophosphate (CMP), on a carbonated biomimetic apatite sample. The follow-up of CMP kinetics of adsorption pointed out the rapidity of interaction with stabilization reached within few minutes. The adsorption isotherm could be realistically fitted to the Sips model (Langmuir–Freundlich) suggesting the influence of surface heterogeneities and adsorption cooperativity in the adsorption process. The desorption study pointed out the reversible character of CMP adsorption on biomimetic apatite. This contribution is intended to prove helpful in view of better apprehending the molecular interaction of DNA fragments and apatite compounds, independently of the application domain, such as bone diagenesis or nanomedicine. This study may also appear informative for researchers interested in the origins of life on Earth and the occurrence and behavior of primitive biomolecules.

Adsorption of nucleotides onto Fe–Mg–Al rich swelling clays

Mineral surfaces may have played a role in the origin of the first biopolymers, by concentrating organic monomers from a dilute ocean. Swelling clays provide a high surface area for the concentration of prebiotic monomers, and have therefore been the subject of numerous investigations. In that context, montmorillonite, the most abundant swelling clay in modern environments, has been extensively studied with regard to adsorption and polymerization of nucleic acids. However, montmorillonite was probably rather marginal on the primitive ocean floor compared to iron–magnesium rich phyllosilicates such as nontronite that results from the hydrothermal alteration of a mafic or ultramafic oceanic crust. In the present paper, we study the adsorption of nucleotides on montmorillonite and nontronite, at various pH and ionic strength conditions plausible for Archean sea-water. A thorough characterization of the mineral surfaces shows that nucleotide adsorb mainly on the edge faces of the smectites by ligand exchange between the phosphate groups of the nucleotides and the –OH groups from the edge sites over a wide pH range (4–10). Nontronite is more reactive than montmorillonite. At low pH, additional ion exchange may play a role as the nucleotides become positively charged.