Adsorption Of Nucleotides Research Articles

Possible role of metal(II) octacyanomolybdate(IV) in chemical evolution: interaction with ribose nucleotides.

We have proposed that double metal cyanide compounds (DMCs) might have played vital roles as catalysts in chemical evolution and the origin of life. We have synthesized a series of metal octacyanomolybdates (MOCMos) and studied their interactions with ribose nucleotides. MOCMos have been shown to be effective adsorbents for 5'-ribonucleotides. The maximum adsorption level was found to be about 50% at neutral pH under the conditions studied. The zinc(II) octacyanomolybdate(IV) showed larger adsorption compared to other MOCMos. The surface area seems to important parameter for the adsorption of nucleotides. The adsorption followed a Langmuir adsorption isotherms with an overall adsorption trends of the order of 5'-GMP > 5'-AMP > 5'-CMP > 5'-UMP. Purine nucleotides were adsorbed more strongly than pyrimidine nucleotides on all MOCMos possibly because of the additional binding afforded by the imidazole ring in purines. Infrared spectral studies of adsorption adducts indicate that adsorption takes place through interaction between adsorbate molecules and outer divalent ions of MOCMos.

Effects of DNA nucleotide adsorption on the conductance of graphene nanoribbons from first principles

The effects of DNA nucleotide adsorption on the conductance of graphene nanoribbons are investigated through first-principles calculations. We find that, for the adsorption of a single nucleotide, the negatively charged phosphate produces conductance dips associated with quasibound states, reducing the hole conductance. The conductance of conduction electrons is also reduced by electron scattering at the Coulomb potential barriers produced by the phosphate, with no noticeable conductance dips near the Fermi level. Our results indicate that graphene nanoribbon is promising for the application to DNA sensor utilizing quantum carrier conductance.

Electrical properties of germanium-based insulator-semiconductor structures with an insulating layer of polynucleotides, and their monomer components on the surface

It is shown that adsorption of nucleic acid molecules and their monomeric components, i.e., nitrogenous bases, from aqueous solutions results in the formation of an insulating layer on the germanium surface. Comparatively small values of the insulator charge and the surface-state density point to promising applications of nucleotides for both the formation of germanium-based insulator-semiconductor structures with nanoscale insulating layers and low surface-state densities at the phase interface, and for germanium surface passivation. Changes in the electronic properties of the space-charge region of germanium during nucleotide adsorption on its surface can be used as a method for determining the nucleotide molecule concentration in aqueous solutions.

Adsorption of ribose nucleotides on manganese oxides with varied mn/o ratio: implications for chemical evolution.

Manganese exists in different oxidation states under different environmental conditions with respect to redox potential. Various forms of manganese oxides, namely, Manganosite (MnO), Bixbyite (Mn(2)O(3)), Hausmannite (Mn(3)O(4)) and Pyrolusite (MnO(2)) were synthesized and their possible role in chemical evolution studied. Adsorption studies of ribose nucleotides (5'-AMP, 5'-GMP, 5'-CMP and 5'-UMP) on these manganese oxides at neutral pH, revealed a higher binding affinity to manganosite (MnO) compared to the other manganese oxides. That manganese oxides having a lower Mn-O ratio show higher binding affinity for the ribonucleotides indirectly implies that such oxides may have provided a surface onto which biomonomers could have been concentrated through selective adsorption. Purine nucleotides were adsorbed to a greater extent compared to the pyrimidine nucleotides. Adsorption data followed Langmuir adsorption isotherms, and X( m ) and K( L ) values were calculated. The nature of the interaction and mechanism was elucidated by infrared spectral studies conducted on the metal-oxide and ribonucleotide-metal-oxide adducts.

Adsorption of nucleotides on the rutile (110) surface

Abstract The present study aims at the computer-aided design of suitably functionalized oxide surfaces for the integration of nanotubes into multi-purpose nano-electronic devices. The adsorption of the nucleotide cytidine monophosphate on the rutile (110) surface is investigated by density-functional-based tight-binding calculations. The nucleotide favors anchoring with two oxygen atoms of its phosphate part. Adsorption occurs preferentially at two neighboring five-fold coordinated Ti atoms along the [001] direction, thus opening a pathway to an ordered adsorption of nanotubes along [001]. The electronic densities of state show that the aromatic part of the cytidine residue remains unchanged upon adsorption on rutile. This implies that no significant changes occur in the nanotube binding capacity by -stacking of the aromatic part, hence, nucleotide-functionalized oxide surfaces are ideal substrates for the ordered, stable and electronically and chemically inert immobilization of nanotubes.

Study on the loss of nucleoside mono-, di- and triphosphates and phosphorylated peptides to a metal-free LC–MS hardware

In our earlier LC–MS experiments on the analysis of phosphocompounds like nucleotides (mono-, di- and triphosphate) and phosphopeptides and in literature, low sensitivity and severe losses of analyte to the instrumental setup were observed. Since we noticed that the stainless steel parts of the setup (e.g., the electrospray needle) adsorbed important quantities of the phosphorylated analytes, we made a LC–ESI setup without metallic surfaces. The first results were disappointing since also the fused silica surface of the LC-ESI coupler adsorbed part of the nucleotides and phosphopeptides injected in flow analysis experiments. We present experiments documenting the contribution of the different components of the setup. A number of potential solutions to the adsorption problem are proposed and tested. Only dimethyldichlorosilane deactivation of fused silica capillaries gave satisfactory results as adsorption of nucleotides and phosphopeptide was minimised.

Adsorption of Nucleic Acid Components on Rutile (TiO2) Surfaces

Nucleic acids, the storage molecules of genetic information, are composed of repeating polymers of ribonucleotides (in RNA) or deoxyribonucleotides (in DNA), which are themselves composed of a phosphate moiety, a sugar moiety, and a nitrogenous base. The interactions between these components and mineral surfaces are important because there is a tremendous flux of nucleic acids in the environment due to cell death and horizontal gene transfer. The adsorption of mono-, oligo-, and polynucleotides and their components on mineral surfaces may have been important for the origin of life. We have studied here interactions of nucleic acid components with rutile (TiO(2)), a mineral common in many terrestrial crustal rocks. Our results suggest roles for several nucleic acid functional groups (including sugar hydroxyl groups, the phosphate group, and extracyclic functional groups on the bases) in binding, in agreement with results obtained from studies of other minerals. In contrast with recent studies of nucleotide adsorption on ZnO, aluminum oxides, and hematite, our results suggest a different preferred orientation for the monomers on rutile surfaces. The conformations of the molecules bound to rutile surfaces appear to favor specific interactions, which in turn may allow identification of the most favorable mineral surfaces for nucleic acid adsorption.

Controlled and Efficient Hybridization Achieved with DNA Probes Immobilized Solely through Preferential DNA-Substrate Interactions

Quantitative and reproducible data can be obtained from surface-based DNA sensors if variations in the conformation and surface density of immobilized single-stranded DNA capture probes are minimized. Both the conformation and surface density can be independently and deterministically controlled by taking advantage of the preferential adsorption of adenine nucleotides (dA) on gold, as previously demonstrated using a model system in Opdahl, A.; Petrovykh, D. Y.; Kimura-Suda, H.; Tarlov, M. J.; Whitman, L. J. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 9-14. Here, we describe the immobilization and subsequent hybridization properties of a 15-nucleotide DNA probe sequence that has additional m adenine nucleotides, (dA)(m), at the 5' end. Quantitative analysis of immobilization and hybridization for these probes indicates that the (dA)(m) block preferentially adsorbs on gold, forcing the probe portion of the strand to adopt an upright conformation suited for efficient hybridization. In addition, a wide range of probe-to-probe lateral spacing can be achieved by coimmobilizing the probe DNA with a lateral spacer, a strand of k adenine nucleotides, (dA)(k). Altering either the length or relative concentration of the (dA)(k) spacers added during probe immobilization controls the average surface density of probes; the density of probes, in turn, systematically modulates their hybridization with solution targets.

DNA Separation Using Zr(IV)-Loaded Resin through Ligand Exchange

Cleverly designed supports for the affinity separation based on ligand exchange draw much attention. We presented here the development of the material for convenient separation of nucleotides through the ligand exchange using Zr(IV)-loaded phosphonate-based cation exchange resin, Diaion CRP-200. Adsorption and desorption of nucleotides were evaluated by batchwise method. The binding processes of the nucleotides on the resin were reversible for the pH changes; the nucleotides adsorbed onto the resin at pH 3 from aqueous solution, and could be almost desorbed at pH 8. The binding capacity of double-stranded DNA was ca. 100 mg DNA per g of the resin, which is extremely higher than that of conventional adsorbent such as so-called glass milk. The resin could retrieve the DNA from agarose gel.

Interaction of ribose nucleotides with zinc oxide and relevance in chemical evolution

Metal oxides are the important constituents of the crusts of earth-like planets. Therefore, it is probable that metal oxides present on earth or in the primeval seas must have catalyzed different reactions in the course of chemical evolution and origin of life. The present report deals with the interaction of ribose nucleotides namely, 5′-AMP, 5′-GMP, 5′-CMP and 5′-UMP with zinc oxide. Adsorption of nucleotides on zinc oxide followed Langmuir adsorption isotherm. X m and K L values were calculated. Adsorption was found to be maximum in neutral medium as compared to acidic and basic medium. Infrared spectral studies of ribonucleotides, metal oxide and ribonucleotide–metal oxide adducts indicate that the nitrogen base and phosphate moiety of ribonucleotides interact with the positive charge surface of metal oxide. SEM studies were also done to support adsorption of nucleotides on zinc oxide. Results of the present study suggest the importance of metal oxides in concentrating the organic molecules from their dilute aqueous solutions in primeval seas.

Adsorption of nucleotides on β-cyclodextrin derivative grafted chitosan

A novel β-cyclodextrin derivative (CCD-C) was synthesized with chitosan and carboxymethyl-β-cyclodextrin. Its structure was characterized by elemental analysis, infrared spectra analysis, and X-ray diffraction analysis. The adsorption properties for guanosine 5′-monophosphate, cytidine 5′-monophosphate and uridine 5′-monophosphate were studied. Experimental results demonstrated that CCD-C had higher adsorption capability for guanosine 5′-monophosphate, and that the adsorption capacity for guanosine 5′-monophosphate was 74.20 mg/g. The adsorption capacity was greatly influenced by pH, time and temperature. The introduction of chitosan enhanced the adsorption ability and adsorption selectivity of β-cyclodextrin for guanosine 5′-monophosphate. This novel derivative of chitosan is expected to have wide applications in the separation, concentration and analysis of nucleotides in biological samples.

Adsorption of biopolymers at hydrophilic cellulose–water interface

The extent of adsorption (Gamma2(1)) of bovine serum albumin (BSA), beta-lactoglobulin, lysozyme, gelatin, and DNA from aqueous solution onto the hydrophilic surface of cellulose has been measured as function of biopolymer concentration at different temperatures, pHs, and ionic strengths, and in the presence of a high concentration of inorganic salts and denaturants. In all cases, the value of Gamma2(1) increases with the increase of biopolymer concentration (X2) in bulk and it attains a maximum value at a critical mole fraction concentration X2m. The value of Gamma2m depends upon the nature of protein, temperature, pH, and ionic strength, as well as the nature of neutral salts present in excess. Gamma2m for proteins at a fixed physicochemical condition stands in the following order: Gelatin>betalactoglobulin>lysozyme>BSA. The isotherms for adsorption of DNA nucleotides on cellulose surface at pH 4.0 have been compared at different temperatures and ionic strengths, and in the presence of high concentration of inorganic salts LiCl, NaCl, KCl, and Na2SO4. Values of Gamma2m for different systems have been evaluated and critically compared. At pH 6.0 and 8.0, Gamma2(1) values of DNA nucleotides on cellulose are all negative due to the excess positive hydration of cellulose. At pH 4.0, adsorption of nucleotides of acid, alkali, and heat-denatured DNA widely differ from each other and in the presence of excess concentration of urea becomes negative. The probable mechanisms of biopolymer-cellulose adsorption in terms of polymer hydration, steric interaction, London-van der Waals, hydrophobic, and other types of interactions have been discussed qualitatively. The standard free energy change for the adsorption of protein and DNA nucleotides on the cellulose surface at the state of adsorption saturation has been calculated in kJ per kg of cellulose using an integrated form of the Gibbs adsorption equation. The relation between DeltaG degrees and maximum affinities between biopolymers and the polysaccharide interface have been discussed for various systems.

Thermosensitive N-isopropylacrylamide-vinylphenyl boronic acid copolymer latex particles for nucleotide isolation

Abstract In this study, thermosensitive N-isopropylacrylamide-4-vinylphenylboronic acid copolymer latex, poly(NIPA-co-VPBA) particles were obtained by dispersion polymerization. A nucleotide isolation procedure was proposed by using the latex particles as the sorbent. As a model nucleotide, β-nicotiamide adenine dinucleotide (β-NAD) was adsorbed onto the latex particles at a low temperature (i.e. +4 °C) via the interaction between boronic acid groups of particles and diol groups of β-NAD. The equilibrium β-NAD adsorption capacities up to 40 mg/g were obtained by the proposed sorbent. The equilibrium β-NAD adsorption capacity of the latex particles significantly decreased with increasing temperature and nearly zero nucleotide adsorption was observed at the temperatures higher than 30 °C. On the other hand, poly(NIPA-co-VPBA) latex particles forming a stable aqueous suspension in the temperature range of 4–25 °C exhibited a thermoflocculation behavior at the temperatures higher than 30 °C. The effects of temperature both on the β-NAD adsorption capacity and the colloidal stability of the particles were used for β-NAD recovery. After adsorption of β-NAD onto the stable latex particles at +4 °C, the particles were flocculated by elevating the temperature to 37 °C and β-NAD was desorbed from the flocculating particles simultaneously. Hence, β-NAD was recovered in the clear supernatant. Therefore, the desorption of β-NAD to a medium at any ionic strength and at any pH could be achieved by using temperature as an on-off switch controlling the adsorption/desorption behavior.

Nucleotide adsorption–desorption behaviour of boronic acid functionalized uniform-porous particles

In this study, nucleotide adsorption–desorption behaviour of boronic acid-carrying uniform, porous particles was investigated. The particles were produced by a “multi-step microsuspension polymerization” in the form of poly(styrene–vinylphenyl boronic acid–divinylbenzene) terpolymer. In the first step of the production method, uniform polystyrene latex particles (6.2 μm in size) were obtained by dispersion polymerization. These particles were first swollen by a low molecular mass organic agent (i.e. dibutylphthalate, DBP) and then by a monomer mixture including styrene (S), 4-vinylphenyl boronic acid (VPBA) and divinylbenzene (DVB). The particle uniformity was protected in both swelling stages by adjusting DBP/polystyrene latex and monomer mixture/polystyrene latex ratios. Polymerization of the monomer mixture in the swollen seed particles provided boronic acid-carrying uniform, porous particles 11–12 μm in size. To have uniform particles with different porosities and boronic acid contents, the feed concentration of boronic acid-carrying monomer and the monomer/seed latex ratio were changed. The particles were tried as sorbent for the adsorption of a model nucleotide (i.e., β-nicotinamide adenine dinucleotide, β-NAD). In the β-NAD adsorption experiments, the maximum equilibrium adsorption was obtained at pH 8.5 which was very close to p K a of boronic acid. The incorporation of boronic acid functionality provided a significant increase in the β-NAD adsorption. In contrast to plain poly(styrene- co-divinylbenzene) particles, four-fold higher β-NAD adsorption was obtained with the boronic acid functionalized particles. β-NAD was desorbed from the particles with the yields higher than 90% by weight.

Dietary fiber suppresses elevations of uric acid and allantoin in serum and urine induced by dietary RNA and increases its excretion to feces in rats.

This study was performed to examine the effects of several kinds of dietary fibers (DF) with different physical properties on dietary RNA metabolism. Male Wistar strain rats, 4 wk old, were fed diets with or without a 3% yeast RNA and a 5% DF (cellulose, chitin, chitosan, inulin, and xanthan gum) for 20 d (Experiment 1) or 5 d (Experiment 2). Feeding DF tested lowered the serum uric acid and allantoin concentrations and the urinary excretions of their compounds and increased the amount of RNA excreted into the feces compared with fiber-free. The water-holding capacity and nucleotide adsorption of chitin and chitosan in acidic solutions were higher than those of cellulose. The digestion rate of RNA by RNase A in vitro was found to be lower in the DF tested than in fiber-free. The decrease was remarkable in chitosan and xanthan gum. The uptakes of 14C-labeled adenosine and adenosine 5'-monophosphate (5'-AMP) in the rat jejunum were markedly decreased in regard to chitosan and xanthan gum in comparison with the fiber-free. These phenomena suggest that DF with high viscosity is more strongly associated with the suppression of RNA digestion by RNase A and the depression of the uptake of purine compounds to jejunum. The present results reveal that the elevation of serum uric acid concentration induced by dietary RNA can be suppressed by DF in rats.

Boronic acid-functionalized HEMA-based gels for nucleotide adsorption

A gel matrix that could be used as a sorbent for the specific adsorption of nucleotides was prepared by the radical copolymerization of 2-hydroxyethylmethacrylate (HEMA) with a relatively new boronic acid–functionalized monomer (4-vinylphenylboronic acid, VPBA). The synthesis of a gel could be achieved at a reasonably low temperature (+4°C) by using potassium persulfate and tetramethylethylenediamine as the redox system and methylenebisacrylamide (MBA) as the crosslinker. To increase the diol binding affinity of boronic acid–carrying gels, two different amine-containing monomers [N-3-(dimethylamino)propylmethacrylamide, DMAPM and 2-(dimethylamino)ethylmethacrylate, DMAEM) were also included in the gel-formation recipe. Then HEMA–VPBA–DMAPM and HEMA–VPBA–DMAEM terpolymer gels were obtained. The boronic acid–functionalized gel matrices with different swelling properties were produced by changing the feed concentrations of VPBA and of the amine-containing monomers (DMAPM and DMAEM). To test the usability of produced gels as a sorbent in the nucleotide adsorption, β-nicotinamide adenine dinucleotide (β-NAD) was selected as a model compound. The results of adsorption experiments indicated that the β -NAD adsorption capacity of HEMA-based gels increased with increasing VPBA feed concentration. Equilibrium adsorption capacities up to 33 mg β-NAD/g dry gel could be achieved with the DMAPM-containing boronic acid–functionalized HEMA-based gels. An increase in the feed concentration of DMAPM resulted in an increase in the β-NAD adsorption capacity of gels, while a decrease was observed with an increasing feed concentration of the other amine-containing monomer (DMAEM). © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 78: 268–277, 2000

Thermally reversible VPBA–NIPAM copolymer gels for nucleotide adsorption

A thermosensitive gel matrix was prepared by free radical copolymerization of Nisopropylacrylamide (NIPAM) with a boronic acid-carrying monomer (i.e. 4-vinylphenylboronic acid, VPBA). The synthesis of the gel was performed at 70°C in an alcohol-water mixture, using azobisisobutyronitrile and methylenebisacrylamide as the initiator and the crosslinker, respectively. Toproduce thermosensitive gels with a higher diol-binding affinity, an amino-containing comonomer, N-[3-(dimethylamino)propyl]methacrylamide (DMAPM) was included in the gel formation recipe. Thermally reversible VPBA-NIPAM and VPBA-DMAPM-NIPAM gels with different swelling properties were obtained by changing the feed concentrations of VPBA and DMAPM. To test the usability of the produced gels as sorbents in nucleotide adsorption, β-nicotinamide adenine dinucleotide (β-NAD) was selected as a model biomolecule. Then the adsorption isotherm for β-NAD was obtained at +4°C in HEPES buffer medium with a pH of 8.5. The support material was in a highly swollen form under these conditions, due to its thermosensitive character. This property was then used to enhance β-NAD adsorption onto the gel matrix. Equilibrium adsorption capacities up to 70 mg β-NAD/g dry gel could be achieved with the thermosensitive support prepared with the 12.9 mol% VPBA feed. The gels produced with higher VPBA and DMAPM feed concentrations exhibited higher equilibrium adsorption capacities for β-NAD.

Adsorption of Aqueous Nucleobases, Nucleosides, and Nucleotides on Humic Acids. 3. Adsorption of Uracil, Uridine, and Uridine-5‘-Monophosphate on a German Peat-Derived Humic Acid and Its Tightly Bound Mercury(II) Form

Aqueous nucleic acid constituents uracil, uridine, and uridine-5‘-monophosphate are selectively adsorbed by a solid German peat-derived humic acid (GHA) and its tightly bound mercury(II) form (MGHA). Adsorption isotherms with GHA and MGHA adsorbents were obtained at 19 solute concentrations from 0 to 1.20 mM and seven fixed temperatures from 5.0 to 35.0 °C. Langmuir data analysis indicates that adsorption occurs in sequential steps A, B, and C, depending on the solute and experimental conditions. MGHA very strongly adsorbs low concentrations of uracil and site capacity vA for uracil adsorption on MGHA in step A increases with increasing temperature. The last steps of adsorption of relatively high concentrations of uridine, and uridine-5‘-monophosphate on MGHA are S-curves ascribed to increasing site capacity with increasing solute concentration. Comparison of the new data for adsorbents GHA and MGHA with data for adsorption of uracil, uridine, and uridine-5‘-monophosphate on compost-derived humic acid (CHA) from part 1 reveals similarities and differences. Nevertheless, linear plots of adsorption enthalpies vs entropies in all detected steps with CHA, GHA, and MGHA as adsorbents indicate that selective adsorption of nucleic acid constituents on different HAs is free energy buffered by similar mechanisms.

ChemInform Abstract: A “Site Creation” Model for Specific Adsorption of Aqueous Nucleobases, Nucleosides, and Nucleotides on Compost‐Derived Humic Acid.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

A “Site Creation” Model for Specific Adsorption of Aqueous Nucleobases, Nucleosides, and Nucleotides on Compost-Derived Humic Acid

Aqueous nucleic acid constituent solutes cytosine (1), cytidine (2), cytidine 5‘-monophosphate (3), thymine (4), thymidine (5), thymidine 5‘-monophosphate (6), uracil (7), uridine (8), uridine 5‘-monophosphate (9), adenine (10), adenosine (11), adenosine 5‘-monophosphate (12), guanosine (13), and guanosine 5‘-monophosphate (14) adsorb on compost-derived humic acid in sequential steps A, B, and C. Langmuir analysis of the isotherms gives a site capacity vi and equilibrium constant Ki for a given solute and adsorption step i that increases vA < vB < vC and decreases KA > KB > KC at 25.0 °C. Data at six temperatures in the range 10.0−40.0 °C indicate that structurally related solutes like 7, 8, and 9 adsorb through their nucleobase units. Adsorption of a solute in step A, B, or C can be endothermic, thermoneutral, or exothermic. This paper uses the site capacity vi at 25.0 °C, the average site capacity over the experimental temperature range 〈vi〉, the adsorption equilibrium constant Ki at 25.0 °C, and the adsorption enthalpy ΔHi and entropy ΔSi for each solute to propose a model consisting of four components for each step i = A or B or C: (a) solute adsorption on a specific HA site A, B, or C involved in respective step A, B, or C; (b) as a result of primary adsorption on site A or B or C for many solutes, freeing up or “creation” of more sites A or B or C, respectively, from interactions A ... X, Y, etc. with other humic acid (HA) structural components X, Y, etc.; (c) solute adsorption at the newly available sites A or B or C; and (d) site hydration by water. The model accounts for the wide range of measured adsorption enthalpies and entropies. Among several conclusions is that adenine has an outstanding ability to interact with A and B sites of compost-derived HA and that B sites are harder for other solutes to access than A and C sites. Humic acids change their dimensions and state of aggregation to suit their environment. It now appears that selectivity for a solute is related to HA's ability to make more adsorption sites available near the point of primary solute interaction.