Adenine In Aqueous Solution Research Articles

Multifunctional self-assembled gold nanorod monolayer/Ti3C2Tx nanocomposites based on interfacial electrostatic for highly sensitive SERS detection of organic dyes and adenine

Gold nanorods (Au NRs)/Ti 3 C 2 T x composites were prepared by self-assembly method as surface enhanced Raman scattering (SERS) substrates. Due to strong electrostatic interaction, Au NRs are evenly arranged on the surface of Ti 3 C 2 T x nanosheets, forming rich SERS hotspots. Au NRs/Ti 3 C 2 T x have high sensitivity and good reproducibility for the determination of organic dyes such as rhodamine 6G, crystal violet and malachite green. The detection limits were 1 × 10 −13 , 1 × 10 −13 and 1 × 10 −12 M, respectively. The relative standard deviations of samples in 40 areas were 4.57 %, 2.79 % and 3.47 %, respectively. The synthesized SERS substrate is sensitive to adenine. For adenine molecules in the range of 1 × 10 −5 –1 × 10 −9 M, SERS results show that the peak intensity is linear with adenine molecular concentration, and the detection limit can be as low as 1 × 10 −9 M. In addition, adenine in aqueous solution has good anti-interference ability to other nucleic acids with similar structure, such as guanine, cytosine and thymine. Therefore, Au NRs/Ti 3 C 2 T x are expected to become a potential substrate for unmarked, rapid and sensitive SERS detection of adenine in the field of bioanalysis. • A SERS substrate based on gold nanorods (Au NRs)/Ti 3 C 2 T x composites is proposed. • The Au NRs/Ti 3 C 2 T x substrate has high SERS sensitivity for adenine molecules. • It also has high sensitivity and good reproducibility in the determination of common organic dyes.

Effect of Inorganic Phosphate on the Photoproduction of Hydrogen Peroxide in Frozen Aqueous Solutions of Adenine Derivatives

The content of hydrogen peroxide in 2 × 10−4 M aqueous solutions of adenine (A), adenosine (Ado) and adenosine-5'-diphosphate (ADP) containing NaCl (0.1 M) irradiated with near-UV light at 77 K and identical solutions containing added inorganic phosphate (Pi) is determined. It is shown that introducing Pi into the solutions considerably improves the yield of H2O2. The results from detecting H2O2 in the studied systems are compared to estimates of the integral intensities of EPR signals (IntS) of the irradiated solutions before defrosting (and the estimates of content of different components of these spectra, obtained by modeling). It is concluded that the basic producers of H2O2 in the studied systems are aggregates of adenine derivatives that form upon the freezing of aqueous solutions.

Multi-hydrogen bond assisted SERS detection of adenine based on multifunctional graphene oxide/poly (diallyldimethyl ammonium chloride)/Ag nanocomposites

Nanocomposites of graphene oxide/poly (diallyldimethyl ammonium chloride)/Ag nanoparticles (GO/PDDA/Ag NPs) were constructed via a self–assembly process as a surface-enhanced Raman scattering (SERS) substrate, in which functional macromolecules PDDA were utilized to load GO and support Ag NPs. Fundamental SERS performance of this SERS substrate was evaluated using rhodamine 6G (R6G), which displayed excellent enhancement effect, transferable nature and high stability of the synthesized GO/PDDA/Ag NPs substrate. Furthermore, the synthesized SERS substrate was employed in the sensitive detection of adenine with a linear range of 0.05–1000 μM and low detection limit of 1 nM. Other than the large surface area of GO, multiple-hydrogen bond interactions between adenine and the modified PDDA were another important factor in capturing adenine molecules and enhancing SERS signal. The hydrogen bond interaction was calculated using quantum mechanical calculations. Moreover, determination of adenine in aqueous solutions was achieved with good anti-interference ability against other nucleic bases with similar structures, such as guanine, cytosine and thymine. Therefore, GO/PDDA/Ag can be anticipated to be a potential substrate for label-free, fast and sensitive SERS detection of adenine in the field of bioanalysis.

One-step synthesis of acriflavine-based carbon dots for adenine detection and a theoretical study on the detection mechanism

Adenine detection is important in biomedicine. Here, we report acriflavine-based carbon dots prepared via a one-step synthesis that can detect adenine in aqueous solution via fluorescence. Titration experiments show that the fluorescence intensity of carbon dots increases by up to 35% as the concentration of adenine increases. High-resolution transmission electron microscopy images show that carbon dots have a recognizable lattice structure. Based on this, we built a theoretical model using the DFT method to explain the mechanism by which adenine enhances fluorescence on the carbon dots.

Mechanisms of Metabolite Amyloid Formation: Computational Studies for Drug Design against Metabolic Disorders.

Ordered self-organization of polypeptides into fibrillar assemblies has been associated with a number of pathological conditions linked to degenerative diseases. Recent experimental observations have demonstrated that even small-molecule metabolites can aggregate into supramolecular arrangements with structural and functional properties reminiscent of peptide-based amyloids. The molecular determinants of such mechanisms, however, are not clear yet. Herein, we examine the process of formation of ordered aggregates by adenine in aqueous solution by molecular dynamics simulations. We also investigate the effects of an inhibiting polyphenol, namely, epigallocatechin gallate (EGCG), on this mechanism. We show that, while adenine alone is able to form extended amyloid-like oligomers, EGCG interferes with the supramolecular organization process. Interestingly, acetylsalicylic acid is shown not to interfere with ordered aggregation, consistent with experiments. The results of these mechanistic studies indicate the main pharmacophoric determinants that a drug-like inhibitor should possess to effectively interfere with metabolite amyloid formation.

Surface-enhanced infrared attenuated total reflection spectroscopy via carbon nanodots for small molecules in aqueous solution.

In this study, carbon nanodots (CNDs) with excellent aqueous dispersibility, narrow size distribution, and oxygen-rich functional groups have been prepared via a green electrochemical method. Graphite electrodes were directly electrolyzed at ambient temperatures to form uniform CNDs in deionized water, which is free from additional oxidant/reductant. As-synthesized CNDs have been applied to coat an attenuated total reflection (ATR) waveguide enabling surface-enhanced infrared absorption (SEIRA) spectroscopic studies for detecting a variety of analytes in aqueous phase with remarkably enhanced IR band intensities. Finally, the proposed ATR-SEIRA strategy enabled quantitatively analyzing adenine in aqueous solution after optimizing the amount of CNDs, the solution pH, and potential CND aggregation. Graphical abstract.

UV Absorption and Magnetic Circular Dichroism Spectra of Purine, Adenine, and Guanine: A Coupled Cluster Study in Vacuo and in Aqueous Solution.

The absorption and magnetic circular dichroism (MCD) spectra of purine and of the purine nucleobases adenine and guanine have been calculated in gas phase at the Coupled Cluster Singles and Doubles (CCSD) and Resolution-of-Identity Singles and Approximate Doubles (RI-CC2) levels of theory. Exploiting a new development in the TURBOMOLE program package for computing vertical excitation energies and Faraday [Formula: see text] terms in an implicit solvent approximated by the conductor-like screening model (COSMO) at the CC2 level, we have investigated the solvent effects on the relative positions of the ππ* and nπ* electronic transitions in these three molecules and compared them to the corresponding vacuum results. In the case of adenine, we also included specific solvent effects with a small water cluster. The spectra obtained with the implicit model COSMO are in qualitative agreement with those obtained with explicit water molecules both with and without the inclusion of the bulk solvent effects via the continuum solvent model. This suggests that the inclusion of the electrostatic contributions of the solvent can provide a sufficiently accurate description of the absorption spectra for adenine. The results for purine, adenine, and guanine show that, after the inclusion of bulk solvation, the ππ* states shift to lower energies while at the same time nπ* states show a reversed behavior. The computed MCD spectra show the characteristic bisignate profile found experimentally in all cases, despite, for adenine, remarkable differences in the origin of the individual peaks for different computational methods. Therefore, the ability (or inability) of MCD to determine the relative stability of the La and Lb states is critically reassessed. According to our best estimate for adenine in aqueous solution, the La state is more stable than Lb.

In-Situ Self-Assembly of Zinc/Adenine Hybrid Nanomaterials for Enzyme Immobilization

In this study, a one-step and facile immobilization of enzymes by self-assembly of zinc ions and adenine in aqueous solution with mild conditions was reported. Enzymes, such as glucose oxidase (GOx) and horseradish peroxidase (HRP), could be efficiently encapsulated in Zn/adenine coordination polymers (CPs) with high loading capacity over 90%. When the enzyme was immobilized by CPs, it displayed high catalytic efficiency, high selectivity and enhanced stability due to the protecting effect of the rigid framework. As a result, the relative activity of Zn/adenine nano-CP-immobilized GOx increased by 1.5-fold at pH 3 and 4-fold at 70 to 90 °C, compared to free GOx. The immobilized GOx had excellent reusability (more than 90% relative activity after being reused eight times). Furthermore, the use of this system as a glucose biosensor was also demonstrated by co-immobilization of two enzymes, detecting glucose down to 1.84 µM with excellent selectivity. The above work indicated that in-situ self-assembly of Zn/adenine CPs could be a simple and efficient method for biocatalyst immobilization.

Photochemical decoration of silver nanoparticles on magnetic microspheres as substrates for the detection of adenine by surface-enhanced Raman scattering

In this work, silver nanoparticles (AgNPs) decorated magnetic microspheres (MMs) are prepared as surface-enhanced Raman scattering (SERS) substrate for the analysis of adenine in aqueous solutions. To prepare these substrates, magnetic particles were first synthesized by coprecipitation of Fe(II) and Fe(III) with ammonium hydroxide. A thin layer of cross-linked polymer was formed on these magnetic particles by polymerization through suspension of magnetic particles into a solution of divinyl benzene/methyl methacrylate. The resulted polymer protected magnetic particles are round in shape with a size of 80μm in diameter. To form AgNPs on these MMs, photochemical reduction method was employed and the factors in photochemical reduction method were studied and optimized for the preparation of highly sensitive and stable AgNPs on MMs substrates (abbreviated as AgMMs substrates). By dispersing the AgMMs in aqueous samples, cylindrical magnet was used to attract the AgMMs for SERS detections. The observed enhancement factor of AgMMs reached 7 orders in magnitude for detection of adenine with a detection limit approaching to few hundreds of nanomolar.

Photosensitized formation of peroxyl radicals in aqueous solutions of adenine at 77 K

Conditions for the formation of peroxyl radicals photosensitized by near-UV irradiation in frozen aqueous solutions of adenine containing 0.1 M NaCl (pH 4–7) are studied. Analysis of the EPR spectra shows that the systems under study contain two types of peroxyl radicals presumably classified earlier as O2−· and HO2··. The effect of freezing methods on the production of the radicals is shown. The signal from O2−· predominates in the spectra of samples with open surfaces and is likely due to the reduction of adsorbed O2 molecules with photoejected electrons. The signal from HO2· could be due to photoinduced interaction between the sensitizer and solvent. Possible mechanisms of these processes are considered.

Effect of inorganic salts on free radicals production by near UV irradiation of frozen aqueous solutions of adenine and its derivatives

The addition of Na and Ca chlorides to adenine (A), adenosine (Ado) and adenosine diphosphate solutions at pH 5.3 has been shown to result in intensification of EPR signals in samples irradiated by near UV at 77 K and appearance of signals of Cl2-* and peroxyl radicals. The peroxyl radicals contribution can exceed 30% of total amount of paramagnetic products. The addition of inorganic phosphate reduces the contribution of peroxyl radicals. Possible mechanisms of the processes involved are discussed.

Gas-phase spectroscopy of protonated adenine, adenosine 5′-monophosphate and monohydrated ions

Microsolvation of chromophore ions commonly has large effects on their electronic structure and as a result on their optical absorption spectra. Here spectroscopy of protonated adenine (AdeH(+)) and its complex with one water molecule isolated in vacuo was done using a home-built mass spectrometer in combination with a tuneable pulsed laser system. Experiments also included the protonated adenosine 5'-monophosphate nucleotide (AMPH(+)). In the case of bare AdeH(+) ions, one-photon absorption leads to four dominant fragment ions corresponding to ammonium and ions formed after loss of either NH3, HCN, or NH2CN. The yields of these were measured as a function of the wavelength of the light from 210 nm to 300 nm, and they were combined to obtain the total photoinduced dissociation at each wavelength (i.e., action spectrum). A broad band between 230 nm and 290 nm and the tail of a band with maximum below 210 nm (high-energy band) are seen. In the case of AdeH(+)(H2O), the dominant dissociation channel after photoexcitation in the low-energy band was simply loss of H2O while photodissociation of protonated AMP revealed two dominant dissociation channels associated with the formation of either AdeH(+) or loss of H3PO4. The action spectra of AdeH(+), AdeH(+)(H2O), and AMPH(+) are almost identical in the 230-290 nm region, and they resemble the absorption spectrum of protonated adenine in aqueous solution recorded at low pH. Hence from our work it is firmly established that the lowest-energy transitions are independent of the surroundings.

Probing Ultrafast Dynamics in Adenine With Mid-UV Four-Wave Mixing Spectroscopies

Heterodyne-detected transient grating (TG) and two-dimensional photon echo (2DPE) spectroscopies are extended to the mid-UV spectral range in this investigation of photoinduced relaxation processes of adenine in aqueous solution. These experiments are the first to combine a new method for generating 25 fs laser pulses (at 263 nm) with the passive phase stability afforded by diffractive optics-based interferometry. We establish a set of conditions (e.g., laser power density, solute concentration) appropriate for the study of dynamics involving the neutral solute. Undesired solute photoionization is shown to take hold at higher peak powers of the laser pulses. Signatures of internal conversion and vibrational cooling dynamics are examined using TG measurements with signal-to-noise ratios as high as 350 at short delay times. In addition, 2DPE line shapes reveal correlations between excitation and emission frequencies in adenine, which reflect electronic and nuclear relaxation processes associated with particular tautomers. Overall, this study demonstrates the feasibility of techniques that will hold many advantages for the study of biomolecules whose lowest-energy electronic resonances are found in the mid-UV (e.g., DNA bases, amino acids).

Photophysics and photostability of adenine in aqueous solution: A theoretical study

The sequential Monte Carlo/CASPT2 approach was employed to investigate deactivation and emission processes from the lowest-lying ππ∗ and nπ∗ excited states of 9H-adenine in aqueous solution. It is found that conical intersections connecting the ππ∗ and nπ∗ states with the ground state are also present in solution, whereas the barriers for the deactivation paths are significantly smaller on solvated conditions. The large destabilization of the nπ∗ state found in solution possibly prevents its involvement in the deactivation photophysics and explains the change from a bi- to a mono-exponential decay for the molecule in the gas phase and solution, respectively.

On the existence of the H3 tautomer of adenine in aqueous solution. Rationalizations based on hybrid quantum mechanics/molecular mechanics predictions

The (15)N NMR spectrum of adenine in aqueous solution has been modeled using high-level combined density functional theory/molecular mechanics techniques coupled to a dynamical averaging scheme. The explicit consideration of the three lowest-energy tautomers of adenine-H9, H7 and H3-allows for a well-founded comparison to experimental data. Based on a very good agreement between the predicted and measured (15)N NMR spectrum of adenine, we have estimated the populations of the H9 and H7 tautomers to be around 83 and 17%, respectively-in good agreement with experimental data-and thus concluded that the H3 tautomer is likely not to be formed in aqueous solution. In addition to the (15)N NMR spectrum we have also predicted the (13)C NMR spectrum and (2)J((15)N-H) indirect spin-spin coupling constants. Finally we have calculated and rationalized the general shape of the low-resolution UV absorption spectrum of adenine in water.

Partial Molar Volumes of Uracil, Thymine, Adenine in Water and of Adenine in Aqueous Solutions of Uracil and Thymine

The partial molar volumes of uracil, thymine and adenine in water and adenine in aqueous solutions of uracil and thymine, at fixed composition, were determined over a range of temperatures. The partial molar volumes of adenine in aqueous uracil and thymine are less than in pure water.

NMR Solvent Shifts of Adenine in Aqueous Solution from Hybrid QM/MM Molecular Dynamics Simulations

We present first principles calculations of the NMR solvent shift of adenine in aqueous solution. The calculations are based on snapshots sampled from a molecular dynamics simulation, which were obtained via a hybrid quantum-mechanical/mechanical modeling approach, using an all-atom force field (TIP3P). We find that the solvation via the strongly fluctuating hydrogen bond network of water leads to nontrivial changes in the NMR spectra of the solutes regarding the ordering of the resonance lines. Although there are still sizable deviations from experiment, the overall agreement is satisfactory for the 1H and 15N NMR shifts. Our work is another step toward a realistic first-principles prediction of NMR chemical shifts in complex chemical environments.

Stacking Conformation of 9-[ω-(Thymin-1-yl)alkyl]adenine in Aqueous Solution

An intramolecular stacking between adenine and thymine rings of 9-[ω-(thymin-1-yl)alkyl]adenine was investigated by means of NMR and UV spectroscopy. The stacking conformation was presumed on the basis of the temperature dependence on the chemical shifts of the adenine and thymine ring protons in the buffer solution at pD 7.0.

Adenine, deoxyadenosine and deoxyadenosine 5 ′-monophosphate studied by femtosecond fluorescence upconversion spectroscopy

Aqueous solutions of adenine (A), deoxyadenosine (dA) and deoxyadenosine 5 ′-monophosphate (dAMP) were studied in room temperature by femtosecond fluorescence upconversion. The fluorescence decays cannot be described by single exponentials. They consist of an ultrafast component (230 fs for A, <100 fs for dA and dAMP) and a slower one (8 ps for A, 0.5 ps for dA and dAMP). The slow component constitutes 95% of the total fluorescence (time-integrated) for the base while only 24% for the nucleoside or the nucleotide. The initial fluorescence anisotropy is 0.30±0.03 for A, 0.25±0.05 for dA and dAMP. The anisotropy of the A fluorescence partially decays during its lifetime due to rotational diffusion.

Raman spectroscopy study of acid-base and structural properties of 9-[2-(phosphonomethoxy)ethyl]adenine in aqueous solutions.

The acid-base properties of the acyclic antiviral nucleotide analogue 9- [2-(phosphonomethoxy)ethyl] adenine (PMEA) in aqueous solutions are studied by means of Raman spectroscopy in a pH range of 1-11 and compared with the properties of its common adenosine monophosphate counterparts (5'-AMP, 3'-AMP, and 2'-AMP). Factor analysis is used to separate the spectra of pure ionic species (PMEA2-, HPMEA-, H2PMEA, H3PMEA+) in order to determine their abundance, sites of protonation, and corresponding spectroscopic pK(a) values. The characteristic Raman features of the neutral adenine moiety in PMEA2- and HPMEA- species resemble those of neutral adenine in the AMPs, whereas significant differences are observed between the Raman spectra of the N1-protonated adenine of the solute zwitterionic H2PMEA and its N1-protonated AMP counterparts. On the contrary, the spectrum of crystalline H2PMEA, adopting an "anti-like" conformation, is found to be similar to the N1-protonated AMPs in solution. To explain peculiar Raman features a "syn-like" conformation is suggested for N1-protonated PMEA species in aqueous solutions instead of an anti-like one adopted by H2PMEA in crystals or by common AMPs in aqueous solutions. A physical mechanism of the anti-like to syn-like conformational transition of the solute PMEA that is due to adenine protonation and the flexibility of the (phosphonomethoxy)ethyl group is proposed and discussed.