Adsorption Of Nucleic Acid Bases Research Articles

DFT and SERS Study of 15N Full-Labeled Adenine Adsorption on Silver and Gold Surfaces

Adsorption of nucleic acid bases on metal surface of nanoparticles has received much attention recently in bio- and nanotechnology, while it still remains a controversial problem in how adenine is adsorbed onto the metal surface. As the nitrogen in adenine plays an important role in the molecular recognition and interaction, the spectral feature related to the nitrogen is the key to analysis of the adsorption configurations. For this purpose, we employed density functional theory (DFT) calculations at B3LYP/6-311+G(d,p) level for the simulation of adsorption configurations, and in the meantime we checked the corresponding surface enhanced Raman spectroscopy (SERS) of 15N fully labeled adenine adsorbed on the surfaces of silver and gold nanoparticles both experimentally and theoretically. The agreement of spectral positions, intensities, and isotopic shifts of the SERS bands, suggests that adenine adsorbed on either silver or gold surface takes the same adsorption configuration in which N7H adenine interac...

Characterization of the Adsorption of Nucleic Acid Bases onto Ferrihydrite via Fourier Transform Infrared and Surface-Enhanced Raman Spectroscopy and X-ray Diffractometry.

Minerals could have played an important role in concentration, protection, and polymerization of biomolecules. Although iron is the fourth most abundant element in Earth's crust, there are few works in the literature that describe the use of iron oxide-hydroxide in prebiotic chemistry experiments. In the present work, the interaction of adenine, thymine, and uracil with ferrihydrite was studied under conditions that resemble those of prebiotic Earth. At acidic pH, anions in artificial seawater decreased the pH at the point of zero charge (pHpzc) of ferrihydrite; and at basic pH, cations increased the pHpzc. The adsorption of nucleic acid bases onto ferrihydrite followed the order adenine >> uracil > thymine. Adenine adsorption peaked at neutral pH; however, for thymine and uracil, adsorption increased with increasing pH. Electrostatic interactions did not appear to play an important role on the adsorption of nucleic acid bases onto ferrihydrite. Adenine adsorption onto ferrihydrite was higher in distilled water compared to artificial seawater. After ferrihydrite was mixed with artificial seawaters or nucleic acid bases, X-ray diffractograms and Fourier transform infrared spectra did not show any change. Surface-enhanced Raman spectroscopy showed that the interaction of adenine with ferrihydrite was not pH-dependent. In contrast, the interactions of thymine and uracil with ferrihydrite were pH-dependent such that, at basic pH, thymine and uracil lay flat on the surface of ferrihydrite, and at acidic pH, thymine and uracil were perpendicular to the surface. Ferrihydrite adsorbed much more adenine than thymine; thus adenine would have been better protected against degradation by hydrolysis or UV radiation on prebiotic Earth.

Adsorption of nucleic Acid bases, ribose, and phosphate by some clay minerals.

Besides having a large capacity for taking up organic molecules, clay minerals can catalyze a variety of organic reactions. Derived from rock weathering, clay minerals would have been abundant in the early Earth. As such, they might be expected to play a role in chemical evolution. The interactions of clay minerals with biopolymers, including RNA, have been the subject of many investigations. The behavior of RNA components at clay mineral surfaces needs to be assessed if we are to appreciate how clays might catalyze the formation of nucleosides, nucleotides and polynucleotides in the “RNA world”. The adsorption of purines, pyrimidines and nucleosides from aqueous solution to clay minerals is affected by suspension pH. With montmorillonite, adsorption is also influenced by the nature of the exchangeable cations. Here, we review the interactions of some clay minerals with RNA components.

Adsorption of nucleic acid bases on magnesium oxide (MgO)

AbstractThe adsorption of organic molecules on mineral matrices might have played a fundamental role in processes that led to the emergence of life. We investigated the adsorption properties of the nucleobases adenine, cytosine, uracil and hypoxanthine on magnesium oxide (MgO), determining the single solute batch equilibrium adsorption isotherms. Langmuir-type isotherms were fitted to data, assuming a rapid reversible equilibration of adsorption, demonstrated effectively through desorption experiments. The Langmuir equilibrium adsorption constantKand the amount of the solute per unit of adsorbent mass necessary to complete the monolayerbwere calculated. The results indicate that MgO is a good adsorbent for nucleobases (adenine > uracil > hypoxantine > cytosine), suggesting a role of metal oxides in concentrating biomolecules in prebiotic conditions that might have favoured the passage from geochemistry to biochemistry.

Adsorption of adenine, cytosine, thymine, and uracil on sulfide-modified montmorillonite: FT-IR, Mössbauer and EPR spectroscopy and X-ray diffractometry studies.

In the present work the interactions of nucleic acid bases with and adsorption on clays were studied at two pHs (2.00, 7.00) using different techniques. As shown by Mössbauer and EPR spectroscopies and X-ray diffractometry, the most important finding of this work is that nucleic acid bases penetrate into the interlayer of the clays and oxidize Fe(2+) to Fe(3+), thus, this interaction cannot be regarded as a simple physical adsorption. For the two pHs the order of the adsorption of nucleic acid bases on the clays was: adenine ≈ cytosine > thymine > uracil. The adsorption of adenine and cytosine on clays increased with decreasing of the pH. For unaltered montmorillonite this result could be explained by electrostatic forces between adenine/cytosine positively charged and clay negatively charged. However for montmorillonite modified with Na(2)S, probably van der Waals forces also play an important role since both adenine/cytosine and clay were positively charged. FT-IR spectra showed that the interaction between nucleic acid bases and clays was through NH(+) or NH (2) (+) groups. X-ray diffractograms showed that nucleic acid bases adsorbed on clays were distributed into the interlayer surface, edge sites and external surface functional groups (aluminol, silanol) EPR spectra showed that the intensity of the line g ≈ 2 increased probably because the oxidation of Fe(2+) to Fe(3+) by nucleic acid bases and intensity of the line g = 4.1 increased due to the interaction of Fe(3+) with nucleic acid bases. Mössbauer spectra showed a large decreased on the Fe(2+) doublet area of the clays due to the reaction of nucleic acid bases with Fe(2+).

Adsorption of Nucleic Acid Bases and Amino Acids on Single-Walled Carbon and Boron Nitride Nanotubes: A First-Principles Study

We study the adsorptions of nucleic acid bases adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) and four amino acids phenylalanine, tyrosine, tryptophan, alanine on the single-walled carbon nanotubes (SWCNTs) and boron nitride nanotubes (SWBNNTs) by using density functional theory. We find that the aromatic content plays a critical role in the adsorption. The adsorptions of nucleic acid bases and amino acids on the (7, 7) SWBNNT are stronger than those on the (7, 7) SWCNT. Oxidative treatment of SWCNTs favors the adsorption of biomolecules on nanotubes.

Adsorption of nucleic acid bases on clays: an investigation using Langmuir and Freundlich isotherms and FT-IR spectroscopy

In the present paper, the adsorption of nucleic acid bases (A, adenine; C, cytosine; U, uracil; and T, thymine) on clays (bentonite, kaolinite, and montmorillonite) was studied at different pH (2.00 and 7.20). It should be pointed out there is no reported study of adsorption of nucleic acid bases on clays using seawater (with the major elements), and a wide range of pH. The main finding of this study was that the ratio of A and T adsorbed on clays ranged from 4.68 to 25.1, much higher than the ratio of their occurrence in organisms ranging from 0.95 to 1.05. The weaker adsorption of U and T on clays raises the question of the possibility of a genetic code based on purines only. The FT-IR spectra at pH 2.00 showed that the interaction of A, C, T, and U with the clays occurs through positively charged, protonated groups.

Determination of the rate control step of purin and pyrimidine bases adsorption on cobalt(II)–CDAE-sporopollenin

In this work, adsorption kinetics of nucleic acid bases and nucleosides as ligands on cobalt(II)–carboxylated diaminoethyl sporopollenin (CDAE-sporopollenin) have been performed using continuous column runs. Adsorption rate measurements were carried out by using a UV-Vis spectrophotometer, and rate control step of the adsorption process was determined. The adsorption of nucleic acid bases and nucleosides from solutions of different initial concentrations onto resin was measured as a function of time at 25 °C. The results show that type of ligand has a great effect on ligand adsorption behaviour. External ligand concentrations play a significant role on adsorption rate of nucleic acid bases. The homogeneous diffusion model (HDM) is applied to the experimental breakthrough data. In all of the concentration range of adenine and uracil (nucleic acid bases), the graphs of −ln[1− U ( α )] versus t were a straight line, which suggests that fractional attainment of equilibrium adsorption under film diffusion control is observed. On the contrary, adenosine and uridin (nucleosides), the graphs were not a straight line and have underwent adsorption under particle diffusion control.

An impedance study of the adsorption of nucleic acid bases at glassy carbon electrodes

Electrochemical impedance has been used to study the adsorption at glassy carbon electrodes of guanine, its corresponding nucleoside, guanosine, and adenine. Impedance studies at different concentrations and applied potentials show clearly that all three bases are adsorbed on the electrode, blocking the surface. Irradiating the electrode with low-frequency (20 kHz) ultrasound whilst recording the impedance spectra increased transport of molecules to the electrode surface with cavitation cleaning the surface and removing strongly adsorbed molecules of bases. In this way, sonoelectrochemical experiments enabled the electrode processes to be studied in the absence of adsorption.

Differential adsorption of nucleic acid bases: Relevance to the origin of life.

The adsorption of organic molecules onto the surfaces of inorganic solids has long been considered a process relevant to the origin of life. We have determined the equilibrium adsorption isotherms for the nucleic acid purine and pyrimidine bases dissolved in water on the surface of crystalline graphite. The markedly different adsorption behavior of the bases describes an elutropic series: guanine > adenine > hypoxanthine > thymine > cytosine > uracil. We propose that such differential properties were relevant to the prebiotic chemistry of the bases and may have influenced the composition of the primordial genetic architecture.

The Adsorption of Nucleic Acid Bases by Raney-nickel, -cobalt, and -copper

Abstract The order of the relative affinity of adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) to Raney-nickel, Raney-cobalt and Raney-copper was determined in an alkaline solution by means of a columnchromatographic method. These bases could be placed in these orders: G>A>C>U>T for Raney-nickel, G>C>A>T∼U for Raney-cobalt, and A∼G∼C>T∼U for Raney-copper. It was also found that these Raney-metals could be placed in the following order as to ability to distinguish those bases: Raney-nickel>>Raney-cobalt>Raney-copper.

375 — Structural effects of nucleic acid bases, nucleosides and nucleotides on their adsorption at a gold electrode studied by specular reflectivity measurement

The adsorption of nucleic acid bases (adenine, guanine, thymine, cytosine), their deoxy-nucleosides and deoxynucleotides has been investigated at a gold electrode by specular reflectivity measurements in 0.1 M NaClO 4. Reflectivity—potential curves of these compounds exhibited a decrease in reflectivity caused by their adsorption. All compounds are adsorbed in the potential range around the point of zero charge (p.z.c.). Adenine and guanine begin to be adsorbed at a more negative potential than thymine and cytosine, suggesting a larger adsorptivity of purine bases than pyrimidine. The adsorption of guanine and cytosine at high concentrations may accompany the reorientation and/or the dimer formation. Deoxynucleosides and deoxynucleotides, except deoxythymidine and dTMP, show a somewhat larger adsorptivity in the positive potential region than the corresponding bases, due to the participation of deoxyribose and phosphate groups. The results obtained from an analysis of the adsorption isother of adenine, thymine and their derivatives suggests that they are oriented with their base moieties flat to the negatively charged electrode surface.

Reactions of nucleic acid bases with inorganic soil constituents

The adsorption at pH's 4, 6 and 8 of adenine, guanine, cytosine, thymine and uracil on clays (montmorillonite, illite and kaolinite), Fe- and Al-oxides (goethite, hematite and gibbsite), a soil, and on a laboratory-prepared fulvic acid-montmorillonite complex was investigated. Portions of the clays and soil were saturated with H +, Fe 3+ and Ca 2+. Quantitatively, the extent of adsorption of nucleic acid bases by the clays was proportional to their exchange capacities, but the nature of the dominant cation had only minor effects. By contrast, the adsorption was strongly affected by pH, tending to decrease with increase in pH. Adsorption on goethite and gibbsite was lower than that on clays, while adsorption of nucleic acid bases on soils was slightly lower than that on oxides. The fulvic acid-montmorillonite complex adsorbed substantial, although smaller amounts of purines and pyrimidines, than did montmorillonite alone. The main adsorption mechanism at pH 4 appeared to be cation exchange whereas at pH 8 complex formation between the nucleic acid bases and cations on inorganic surfaces seemed to occur. The results of this and earlier work show that both inorganic and organic soil constituents adsorb nucleic acid bases. Which adsorption reaction predominates will depend on the clay and organic matter content and on the pH.

Structural effects of nucleic acid bases, nucleosides and nucleotides on their adsorption at a gold electrode studied by specular reflectivity measurement

The adsorption of nucleic acid bases (adenine, guanine, thymine, cytosine), their deoxynucleosides and deoxynucleotides has been investigated at a gold electrode by specular reflectivity measurements in 0.1 M NaClO4. Reflectivity-potential curves of these compounds exhibited a decrease in reflectivity caused by their adsorption. All compounds are adsorbed in the potential range around the point of zero charge (p.z.c.). Adenine and guanine begin to be adsorbed at a more negative potential than thymine and cytosine, suggesting a larger adsorptivity of purine bases than pyrimidine. The adsorption of guanine and cytosine at high concentrations may accompany the reorientation and/or the dimer formation. Deoxynucleosides and deoxynucleotides, except deoxythymidine and dTMP, show a somewhat larger adsorptivity in the positive potential region than the corresponding bases, due to the participation of deoxyribose and phosphate groups. The results obtained from an analysis of the adsorption isotherm of adenine, thymine and their derivatives suggests that they are oriented with their base moieties flat to the negatively charged electrode surface.