Intermolecular hydrogen bonding in DNA base pairs interacting with different numbers of bare and hydrated Li+: NBO, QTAIM, and computational spectroscopic studies

In this study, the effect of different numbers of Li+ interacting with various sites of DNA base pairs (adenine-thymine (AT) and cytosine-guanine (GC)) on the base pair structures, the strength of hydrogen bonding between the bases, and spectroscopic properties (IR and absorption spectra) of the base pairs was investigated. Two quantum computational analyses, the natural bonding orbitals (NBO) and the quantum theory of atoms in molecules (QTAIM), were used to follow the change in the strength of hydrogen bonds between the bases in each pair. The type of base pair's site interacting with Li+ showed different effects on the change in the strength of the hydrogen bonds between the bases. The IR and absorption spectra of the lithiated base pairs were calculated and compared with those of bare base pairs. This comparison provided the changes in the spectra as a fingerprint for the structural identification of different lithiated base pairs. Also, the determination of the change in the strength of hydrogen bonds in the lithiated base pairs compared to their bare base pairs. In the other part of this study, the effect of the hydration of the attached Li+ in the structure of lithiated base pairs on the strength of their hydrogen bonds and spectra was investigated.

Resonance Hyper-Raman Spectroscopy of Nucleotides and Polynucleotides

We applied 532 nm-excited two-photon resonance hyper-Raman (RHR) spectroscopy to nucleotides (dA, dG, dT, and dC) to obtain fundamental knowledge about their spectral patterns. The RHR spectrum of each nucleotide exhibited various modes of the purine and pyrimidine rings, showing the ability to acquire the structural information on the chromophore. The band positions of the RHR spectrum and the 266 nm-excited one-photon UV-resonance Raman (UVRR) spectrum were identical, while the intensity patterns differed. The peak assignments of the RHR bands were given by analogy to the UVRR spectrum. In examining the polynucleotides, which form a double-stranded helix through intermolecular hydrogen bonds, some RHR bands were found to be available as structural markers. Moreover, several overtone and combination bands were detected above 2000 cm^-1. The frequencies of dA and dG were accounted for by considering the involvement of the vibration of dA at 1579 cm^-1 and that of dG at 1482 cm^-1, respectively. Multiple vibronically active modes were seen for dT and dC. HR spectroscopy offers unique information on the fundamental, combination, and overtone modes of dA and dG, of which the multiple electronic states are involved in the resonance process.

pH-Dependent Flavin Adenine Dinucleotide and Nicotinamide Adenine Dinucleotide Ultraviolet Resonance Raman (UVRR) Spectra at Intracellular Concentration

The ultraviolet resonance Raman spectra of the adenine-containing enzymatic redox cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide in aqueous solution of physiological concentration are compared with the aim of distinguishing between them and their building block adenine in potential co-occurrence in biological materials. At an excitation wavelength of 266 nm, the spectra are dominated by the strong resonant contribution from adenine; nevertheless, bands assigned to vibrational modes of the nicotinamide and the flavin unit are found to appear at similar signal strength. Comparison of spectra measured at pH 7 with data obtained pH 10 and pH 3 shows characteristic changes when pH is increased or lowered, mainly due to deprotonation of the flavin and nicotinamide moieties, and protonation of the adenine, respectively.

Development of Vibrational Frequency Maps for Nucleobases

Vibrational spectroscopy provides a powerful tool to probe the structure and dynamics of nucleic acids because specific normal modes, particularly the base carbonyl stretch modes, are highly sensitive to the hydrogen bonding patterns and stacking configurations in these biomolecules. In this work, we develop vibrational frequency maps for the C═O and C═C stretches in nucleobases that allow the calculations of their site frequencies directly from molecular dynamics simulations. We assess the frequency maps by applying them to nucleobase derivatives in aqueous solutions and nucleosides in organic solvents and demonstrate that the predicted infrared spectra are in good agreement with experimental measurements. The frequency maps can be readily used to model the linear and nonlinear vibrational spectroscopy of nucleic acids and elucidate the molecular origin of the experimentally observed spectral features.

Metallic surface dynamics of genomic DNA and its nitrogenous bases: SERS assessment and theoretical considerations

The dynamics of genomic DNA and its nucleobases at a silver surface were explored using surface-enhanced Raman spectroscopy (SERS) and ab initio Verlet-type dynamics, respectively. The bands observed had full widths at half-maximum (FWHMs) in the wavenumber range 10-29 cm^-1. (Sub)picosecond molecular dynamics with global relaxation times of 0.37-1.06 ps were noted. Furthermore, the on-surface ab initio dynamics of the DNA bases were examined using DFT with a Verlet-type algorithm. The results attained for these ergodic dynamic systems describe real systems quite well and could therefore be correlated with corresponding experimental data.

Biocompatible organic-inorganic hybrid materials based on nucleobases and titanium developed by molecular layer deposition

We have constructed thin films of organic-inorganic hybrid character by combining titanium tetra-isopropoxide (TTIP) and the nucleobases thymine, uracil or adenine using the molecular layer deposition (MLD) approach. Such materials have potential as bioactive coatings, and the bioactivity of these films is described in our recent work [Momtazi, L.; Dartt, D. A.; Nilsen, O.; Eidet, J. R. J. Biomed. Mater. Res., Part A 2018, 106, 3090-3098. doi:10.1002/jbm.a.36499]. The growth was followed by in situ quartz crystal microbalance (QCM) measurements and all systems exhibited atomic layer deposition (ALD) type of growth. The adenine system has an ALD temperature window between 250 and 300 °C, while an overall reduction in growth rate with increasing temperature was observed for the uracil and thymine systems. The bonding modes of the films have been further characterized by Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy and X-ray diffraction, confirming the hybrid nature of the as-deposited films with an amorphous structure where partial inclusion of the TTIP molecule occurs during growth. The films are highly hydrophilic, while the nucleobases do leach in water providing an amorphous structure mainly of TiO₂ with reduced density and index of refraction.

Energetics and Vibrational Signatures of Nucleobase Argyrophilic Interactions

This study investigates the interactions of both purine (adenine and guanine) and pyrimidine (cytosine, thymine, and uracil) nucleobases with a pair of silver atoms (Ag2). Full geometry optimizations were performed on several structures of each nucleobase/Ag2 complex and the corresponding isolated monomers using the M06-2X density functional with a correlation consistent triple-ζ basis set augmented with diffuse functions on all atoms and a relativistic pseudopotential on Ag (aug-cc-pVTZ for H, C, N, and O and aug-cc-pVTZ-PP for Ag; denoted aVTZ). Harmonic vibrational frequency computations indicate that each optimized structure corresponds to a minimum on the M06-2X/aVTZ potential energy surface. Relative electronic energies for interactions between Ag2 and each nucleobase were compared to elucidate energetic differences between isomers. Further analysis of the changes in vibrational frequencies, infrared intensities, and Raman scattering activities reveals how different Ag2 binding sites might be differentiated spectroscopically. These results provide molecular-level insight into the interactions between nucleobases and silver, which may lead to better understanding and interpretation of surface-enhanced Raman spectroscopy experiments on nucleobases and related systems.

Influence of amine and thiol modifications at the 3' ends of single stranded DNA molecules on their adsorption on gold surface and the efficiency of their hybridization

Adsorption of molecules of DNA (deoxyribonucleic acid) or modified DNA on gold surfaces is often the first step in construction of many various biosensors, including biosensors for detection of DNA with a particular sequence. In this work we study the influence of amine and thiol modifications at the 3' ends of single stranded DNA (ssDNA) molecules on their adsorption on the surface of gold substrates and on the efficiency of hybridization of immobilized DNA with the complementary single stranded DNA. The characterization of formed layers has been carried out using infrared spectroscopy and atomic force microscopy. As model single stranded DNA we used DNA containing 20 adenine bases, whereas the complementary DNA contained 20 thymine bases. We found that the bands in polarization modulation-infrared reflection-adsorption spectroscopy (PM-IRRAS) spectra of layers formed from thiol-modified DNA are significantly narrower and sharper, indicating their higher regularity in the orientation of DNA on gold surface when using thiol linker. Also, hybridization of the layer of thiol-modified DNA containing 20 adenine bases with the respective DNA containing thymine bases leads to formation of much more organized structures than in the case of unmodified DNA or DNA with the amine linker. We conclude that the thiol-modified ssDNA is more promising for the preparation of biosensors, in comparison with the amine-modified or unmodified ssDNA. We have also found that the above-mentioned modifications at the 3' end of ssDNA significantly influence the IR spectrum (and hence the structure) of polycrystalline films formed from such compounds, even though adsorbed fragments contain less than 5% of the DNA chain. This effect should be taken into account when comparing IR spectra of various polycrystalline films formed from modified and unmodified DNA.

Sub-picosecond proton tunnelling in deformed DNA hydrogen bonds under an asymmetric double-oscillator model

We present a model of proton tunnelling across DNA hydrogen bonds, compute the characteristic tunnelling time (CTT) from donor to acceptor and discuss its biological implications. The model is a double oscillator characterised by three geometry parameters describing planar deformations of the H bond, and a symmetry parameter representing the energy ratio between ground states in the individual oscillators. We discover that some values of the symmetry parameter lead to CTTs which are up to 40 orders of magnitude smaller than a previous model predicted. Indeed, if the symmetry parameter is sufficiently far from its extremal values of 1 or 0, then the proton's CTT under any physically realistic planar deformation is guaranteed to be below one picosecond, which is a biologically relevant time-scale. This supports theories of links between proton tunnelling and biological processes such as spontaneous mutation.

Raman spectroscopy and quantum-mechanical analysis of tautomeric forms in cytosine and 5-methylcytosine on gold surfaces

Spectral differences between cytosine (Cyt) and 5-methylcytosine (5MC) were investigated by means of Raman spectroscopy with a combination of density functional theory (DFT) calculations. Surface-enhanced Raman scattering (SERS) revealed discriminating peaks of 5MC from those of Cyt upon adsorption on gold nanoparticles (AuNPs). Among the notable features, the multiple bands between 850 and 700cm^-1 for the ring-breathing modes of 5MC and Cyt could be correlated well with the simulated spectra based on the DFT calculations of the adsorbates on the gold cluster atoms. The relative energetic stabilities of the enol/keto and the amino/imino tautomeric forms of Cyt and 5MC have been estimated using DFT calculations, before and after binding six atom gold clusters. Among the six tautomeric forms, the 7H keto amino and the 4H imino trans forms are expected to be predominant in binding gold atoms, whereas the enol trans/cis conformers would coexist in the free gas phase. Our approach may provide useful theoretical guidelines for identifying 5MC from Cyt by analyzing Raman spectra on gold surfaces on the basis of quantum-mechanical calculations.

Cooperative vibrational properties of hydrogen bonds in Watson–Crick DNA base pairs

For the AT pair, Symst and Strech peaks further shift toward the red, giving the H-bonds an amplified effect (orange arrows).

Avoiding Ethanol Presence in DNA Samples Enhances the Performance of Ultraviolet Resonance Raman Spectroscopy Analysis

Ethanol is an essential chemical reagent in DNA preparation as its use increases the yield of extraction. All methodologies for DNA isolation involve the use of ethanol in order to prevent DNA dissolution in water and to optimize the binding of DNA to chromatographic membranes. In this note, we show how the presence of ethanol traces in DNA aqueous solution affects ultraviolet Raman spectra, leading to possible misinterpretations. We report a simple method to remove the ethanol Raman features from the spectra, based on heating the DNA sample at 80 ℃, followed by a slow cooling procedure.

Cooperative hydrogen-bonding of the adenine–thymine pair as a strategy for lowering the limit of detection of thymine by surface-enhanced Raman spectroscopy

The formation of cooperative hydrogen bonds between the thymine–adenine pair was used to indirectly determine thymine by SERS, improving the limit of detection values up to two orders of magnitude.

A computational study of dsDNA pairs and vibrational resonance in separating water

This article investigates the relationship between molecular sequence and dependent interacting behavior of molecular segment pairs and secondly, sequence dependent, vibrational resonance in surrounding normal saline, protein-free water. The development of a molecular model to explore these systems phenomena, the results of several nanoscale molecular dynamics simulations, and analysis of behavior of interacting ΦX174 double-stranded DNA segment pair models in various configurations are presented. Fourier analysis revealed intriguing vibration frequencies within the solvent plane between the segments, while subsequent frequency domain transformation of the time domain waveforms revealed statistically significant resonating harmonic signals in the THz range.

A Prebiotic Chemistry Experiment on the Adsorption of Nucleic Acids Bases onto a Natural Zeolite

There are currently few mechanisms that can explain how nucleic acid bases were synthesized, concentrated from dilute solutions, and/or protected against degradation by UV radiation or hydrolysis on the prebiotic Earth. A natural zeolite exhibited the potential to adsorb adenine, cytosine, thymine, and uracil over a range of pH, with greater adsorption of adenine and cytosine at acidic pH. Adsorption of all nucleic acid bases was decreased in artificial seawater compared to water, likely due to cation complexation. Furthermore, adsorption of adenine appeared to protect natural zeolite from thermal degradation. The C=O groups from thymine, cytosine and uracil appeared to assist the dissolution of the mineral while the NH2 group from adenine had no effect. As shown by FT-IR spectroscopy, adenine interacted with a natural zeolite through the NH2 group, and cytosine through the C=O group. A pseudo-second-order model best described the kinetics of adenine adsorption, which occurred faster in artificial seawaters.

Oxidative damage in DNA bases revealed by UV resonant Raman spectroscopy

We report on the use of the UV Raman technique to monitor the oxidative damage of deoxynucleotide triphosphates (dATP, dGTP, dCTP and dTTP) and DNA (plasmid vector) solutions.

Quantum chemical and spectroscopic investigations of 3-methyladenine

FTIR, FT-Raman and UV-Vis spectra of 3-methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.

An experimental and theoretical vibrational study of interaction of adenine and thymine with artificial seawaters: A prebiotic chemistry experiment

Nucleic acid bases play important roles in living beings. Thus, their interaction with salts the prebiotic Earth could be an important issue for the understanding of origin of life. In this study, the effect of pH and artificial seawaters on the structure of adenine and thymine was studied via parallel determinations using FT-IR, Raman spectroscopy and theoretical calculations. Thymine and adenine lyophilized in solutions at basic and acidic conditions showed characteristic bands of the enol-imino tautomer due to the deprotonation and the hydrochloride form due to protonation, respectively. The interaction of thymine and adenine with different seawaters representative of different geological periods on Earth was also studied. In the case of thymine a strong interaction with Sr(2+) promoted changes in the Raman and infrared spectra. For adenine changes in infrared and Raman spectra were observed in the presence of salts from all seawaters tested. The experimental results were compared to theoretical calculations, which showed structural changes due to the presence of ions Na(+), Mg(2+), Ca(2+) and Sr(2+) of artificial seawaters. For thymine the bands arising from C4=C5 and C6=O stretching were shifted to lower values, and for adenine, a new band at 1310cm(-1) was observed. The reactivity of adenine and thymine was studied by comparing changes in nucleophilicity and energy of the HOMO orbital.

Experimental and first-principles study of guanine adsorption on ZnO clusters

Electronic structure for interaction of guanine with Zn₂O₂ cluster and the most preferred N1-site to form a stable G–Zn₂O₂ model.

Spectroscopic probe on N-H⋯N, N-H⋯O and controversial C-H⋯O contact in A-T base pair: a DFT study

DNA base pair A-T has been investigated by IR and NMR spectroscopy using DFT methods. The results have been analyzed in terms of infrared vibrational frequencies and (1)H NMR chemical shifts. Different types of interactions N-H⋯N, N-H⋯O and C-H⋯O types have been investigated in DNA base pairs. Although, previous reports argued about the third C-H⋯O type interaction in A-T base pair, such typical interaction has been analyzed thoroughly by IR and NMR spectroscopy using DFT methods. Our results show that the CH⋯O interaction in the A-T base pair is a weak interaction compared to normal hydrogen bond interactions.

Understanding oligonucleotide-templated nanocrystals: growth mechanisms and surface properties

We describe studies of nanoparticle synthesis using oligonucleotides as capping ligands. The oligonucleotides nucleate, grow, and stabilize near-infrared fluorescent, approximately uniform PbS nanocrystals in an aqueous environment. The properties of the resulting particles strongly depend upon the sequences as well as synthesis conditions. Fourier Transform infrared measurements suggest that functional groups on the nucleobases such as carbonyl and amine moieties are responsible for surface passivation, while the phosphate backbone is strained to accommodate nucleobase bonding, preventing irreversible aggregation and thereby stabilizing the colloids. Our theoretical model indicates that oligonucleotide-mediated particle growth relies on the chemical reactivity of the oligonucleotide ligands that saturate dangling bonds of growing clusters, and favorable sequences are those that have the highest surface reactivity with growing particles. The oligonucleotide template approach is facile and versatile, offering a route to produce a range of material compositions for other chalcogenide semiconductor quantum dots and metal oxide nanoparticles.

Absolute cross sections for vibrational excitations of cytosine by low energy electron impact

The absolute cross sections (CSs) for vibrational excitations of cytosine by electron impact between 0.5 and 18 eV were measured by electron-energy loss (EEL) spectroscopy of the molecule deposited at monolayer coverage on an inert Ar substrate. The vibrational energies compare to those that have been reported from IR spectroscopy of cytosine isolated in Ar matrix, IR and Raman spectra of polycrystalline cytosine, and ab initio calculation. The CSs for the various H bending modes at 142 and 160 meV are both rising from their energy threshold up to 1.7 and 2.1 × 10(-17) cm(2) at about 4 eV, respectively, and then decrease moderately while maintaining some intensity at 18 eV. The latter trend is displayed as well for the CS assigned to the NH(2) scissor along with bending of all H at 179 meV. This overall behavior in electron-molecule collision is attributed to direct processes such as the dipole, quadrupole, and polarization contributions, etc. of the interaction of the incident electron with a molecule. The CSs for the ring deformation at 61 meV, the ring deformation with N-H symmetric wag at 77 meV, and the ring deformations with symmetric bending of all H at 119 meV exhibit common enhancement maxima at 1.5, 3.5, and 5.5 eV followed by a broad hump at about 12 eV, which are superimposed on the contribution due to the direct processes. At 3.5 eV, the CS values for the 61-, 77-, and 119-meV modes reach 4.0, 3.0, and 4.5 × 10(-17) cm(2), respectively. The CS for the C-C and C-O stretches at 202 meV, which dominates in the intermediate EEL region, rises sharply until 1.5 eV, reaches its maximum of 5.7 × 10(-17) cm(2) at 3.5 eV and then decreases toward 18 eV. The present vibrational enhancements, correspond to the features found around 1.5 and 4.5 eV in electron transmission spectroscopy (ETS) and those lying within 1.5-2.1 eV, 5.2-6.8 eV, and 9.5-10.9 eV range in dissociative electron attachment (DEA) experiments with cytosine in gas phase. While the ETS features are ascribed to shape resonances associated with the electron occupation of the second and third antibonding π-orbitals of the molecule in its ground state, the correspondence with DEA features suggests the existence of common precursor anion states decaying with certain probabilities into the vibrationally excited ground state.

Unexpected bilayer formation in Langmuir films of nucleolipids

Langmuir monolayers have been extensively investigated by various experimental techniques. These studies allowed an in-depth understanding of the molecular conformation in the layer, phase transitions, and the structure of the multilayer. As the monolayer is compressed and the surface pressure is increased beyond a critical value, usually occurring in the minimal closely packed molecular area, the monolayer fractures and/or folds, forming multilayers in a process referred to as collapse. Various mechanisms for monolayer collapse and the resulting reorganization of the film have been proposed, and only a few studies have demonstrated the formation of a bilayer after collapse and with the use of a Ca(2+) solution. In this work, Langmuir isotherms coupled with imaging ellipsometry and polarization modulation infrared reflection absorption spectroscopy were recorded to investigate the air-water interface properties of Langmuir films of anionic nucleolipids. We report for these new molecules the formation of a quasi-hexagonal packing of bilayer domains at a low compression rate, a singular behavior for lipids at the air-water interface that has not yet been documented.

Guanine: A Combined Study Using Vibrational Spectroscopy and Theoretical Methods

The present paper reports a conformational study of solid-state anhydrous guanine, using vibrational spectroscopy techniques—infrared, Raman, and inelastic neutron scattering—coupled to quantum mechanical methods at the DFT level, both for the isolated molecule and the condensed state. In both cases, the 7H-keto-amino tautomer was found to be the prevalent form, contrary to aqueous solutions and hydrated polycrystalline guanine, where the 9H-keto-amino tautomer is the most favoured species. This paper is a significant contribution for the existing spectroscopic characterization of this purine base, by unambiguously assigning its vibrational spectra.

Ag cluster-aptamer hybrid: specifically marking the nucleus of live cells

Silver cluster-aptamer hybrids were mineralized via an artificially designed aptamer. The hybrids gave red emission when excited by light, and they successfully targeted the nucleus of live cells. This method is an effective approach to make cell target probes.

Raman spectral study of metal-cytosine complexes: a density functional theoretical (DFT) approach

The fluctuation of surface-enhanced Raman scattering (SERS) spectra has been an obstacle to the analysis of the adsorbate on the metal surface. In this paper, we aim at using the density functional theory (DFT) to study the fluctuant Raman spectra of the cytosine molecule which interacts with a coinage metal atom or cation via N1 and N3 sites. The results show that the adsorption site strongly influences the Raman spectral property of cytosine molecule, especially the relative intensity of some bands. In addition, the SERS spectra of cytosine which is adsorbed on the gold, silver, and copper electrodes are measured, and the possible orientation and adsorption site of the cytosine molecule adsorbed on metal electrodes surface are proposed with the help of DFT simulations.

Localization and anharmonicity of the vibrational modes for GC Watson-Crick and Hoogsteen base pairs

We present an ab initio study of the vibrational properties of cytosine and guanine in the Watson-Crick and Hoogsteen base pair configurations. The results are obtained by using two different implementations of the DFT method. We assign the vibrational frequencies to cytosine or to guanine using the vibrational density of states. Next, we investigate the importance of anharmonic corrections for the vibrational modes. In particular, the unusual anharmonic effect of the H(+) vibration in the case of the Hoogsteen base pair configuration is discussed.

SERS Study and DFT Simulation of the Interaction of Cytosine with Copper Electrode

In order to obtain a deeper insight into the interaction between cytosine and copper electrode, a surface-enhanced Raman scattering (SERS) study and density functional theory (DFT) simulation have been used. The experimental result shows that a decrease of relative intensity of the band at around 1315 cm−1 is accompanied by a considerable increase of relative intensity of the bands in the 1490∼1600 cm−1 region when the potential is below −0.7 V, and it is explained by the chemical effect (CE). Simultaneously, the geometry and Raman spectra of neutral and cationic Cu-cytosine complexes are calculated and simulated using the B3LYP/lanl2dz basis. The simulation shows that the relative intensities of Raman spectra depend strongly on the molecular active sites involved in the interaction between the copper electrode and the cytosine molecule. Combining the experimental results with theoretical calculations, we conclude that the adsorptive orientation of cytosine on the copper electrode occurs on the N3 site and the carbonyl site when the potential is above and below −0.7 V, respectively. This study also indicates that a combination of SERS and DFT simulations is a valuable tool for studying interactions of biomolecules with metal.