Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spectroscopic (UV/VIS, Raman) and Electrophoresis Study of Cytosine-Guanine Oligonucleotide DNA Influenced by Magnetic Field.

ABSTRACT: Studying the effect of a magnetic field on oligonucleotide DNA can provide a novel DNA manipulation technique for potential application in bioengineering and medicine. In this work, the optical and electrochemical response of a 100 bases oligonucleotides DNA, cytosine-guanine (CG100), is investigated via exposure to different magnetic fields (250, 500, 750, and 1000 mT). As a result of the optical response of CG100 to the magnetic field, the ultra-violet-visible spectrum indicated a slight variation in the band gap of CG100 of about 0.3 eV. Raman spectroscopy showed a significant deviation in hydrogen and phosphate bonds' vibration after exposure to the magnetic field. Oligonucleotide DNA mobility was investigated in the external electric field using the gel electrophoresis technique, which revealed a small decrease in the migration of CG100 after exposure to the magnetic field.

SUBMITTER: Banihashemian SM

PROVIDER: S-EPMC4801395 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Spectroscopic (UV/VIS, Raman) and Electrophoresis Study of Cytosine-Guanine Oligonucleotide DNA Influenced by Magnetic Field.

Banihashemian Seyedeh Maryam SM Periasamy Vengadesh V Boon Tong Goh G Abdul Rahman Saadah S

PloS one 20160321 3

Studying the effect of a magnetic field on oligonucleotide DNA can provide a novel DNA manipulation technique for potential application in bioengineering and medicine. In this work, the optical and electrochemical response of a 100 bases oligonucleotides DNA, cytosine-guanine (CG100), is investigated via exposure to different magnetic fields (250, 500, 750, and 1000 mT). As a result of the optical response of CG100 to the magnetic field, the ultra-violet-visible spectrum indicated a slight varia ...[more]

PMID: 26999445

Similar Datasets

Spectroscopic properties and molecular structure of copper phytate complexes: IR, Raman, UV-Vis, EPR studies and DFT calculations.

Project description:The copper phytate IP6Cu, IP6Cu2 and IP6Cu3 complexes were synthesized changing the phytate to metal mole ratio. The obtained products have been characterized by means of chemical and spectroscopic studies. Spectroscopic ATR/IR, FT-Raman, UV-Vis, EPR and magnetic measurements were carried out. The structures of these compounds have been proposed on the basis of the group theory and geometry optimization taking into account the shape and number of the bands corresponding to the stretching and bending vibrations of the phosphate group and metal-oxygen polyhedron. The role of the inter- and intra-hydrogen bonds in stabilization of the structure has been discussed. EPR studies showed that a local rhombic symmetry of copper ions appears in the studied phytates. Dominant interactions show antiferromagnetic properties depending on the content of paramagnetic ions.

| S-EPMC6394811 | biostudies-literature

Experimental isolation and spectroscopic characterization of squamocin acetogenin combining FT-IR, FT-Raman and UV-Vis spectra with DFT calculations.

Project description:Squamocin, an annonaceous acetogenin has been experimentally isolated and characterized in the solid state using the FT-IR and FT-Raman spectra and in methanol solution by UV-visible spectrum. The main bands observed were assigned combining the IR and Raman spectra with hybrid functional B3LYP/6-31G? calculations. Structural, electronic and topological properties were predicted at the same level of theory for the most stable conformer of squamocin in gas phase and methanol solution. A corrected solvation energy value of -147.54 kJ/mol was predicted for squamocin in methanol while the atomic population natural (NPA) charges evidence higher values on O atoms of R2 and R3 rings, as compared with the corresponding to lactone ring. Mapped MEP surfaces suggest that nucleophilic regions are located on the O atoms of three rings and of OH bonds belonging to side chain, in agreement with the higher charges values evidenced on these O atoms while electrophilic regions are predicted on the H atoms of OH groups. High stabilities of squamocin in both media was revealed by AIM studies while only in methanol solution by NBO calculations. The expansion of volume and the higher dipole moment in methanol suggest a clear solvation of squamocin by solvent molecules. Gap values have evidenced that squamocin is most reactive in methanol while that its large aliphatic chain produces an increases the reactivity of this ?-lactone, as compared with ascorbic acid lactone. Reasonable concordances among the predicted UV-visible and IR, Raman spectra with the corresponding experimental ones were found.

| S-EPMC7279733 | biostudies-literature

HF-EPR, Raman, UV/VIS light spectroscopic, and DFT studies of the ribonucleotide reductase R2 tyrosyl radical from Epstein-Barr virus.

Project description:Epstein-Barr virus (EBV) belongs to the gamma subfamily of herpes viruses, among the most common pathogenic viruses in humans worldwide. The viral ribonucleotide reductase small subunit (RNR R2) is involved in the biosynthesis of nucleotides, the DNA precursors necessary for viral replication, and is an important drug target for EBV. RNR R2 generates a stable tyrosyl radical required for enzymatic turnover. Here, the electronic and magnetic properties of the tyrosyl radical in EBV R2 have been determined by X-band and high-field/high-frequency electron paramagnetic resonance (EPR) spectroscopy recorded at cryogenic temperatures. The radical exhibits an unusually low g₁-tensor component at 2.0080, indicative of a positive charge in the vicinity of the radical. Consistent with these EPR results a relatively high C-O stretching frequency associated with the phenoxyl radical (at 1508 cm⁻¹) is observed with resonance Raman spectroscopy. In contrast to mouse R2, EBV R2 does not show a deuterium shift in the resonance Raman spectra. Thus, the presence of a water molecule as a hydrogen bond donor moiety could not be identified unequivocally. Theoretical simulations showed that a water molecule placed at a distance of 2.6 Å from the tyrosyl-oxygen does not result in a detectable deuterium shift in the calculated Raman spectra. UV/VIS light spectroscopic studies with metal chelators and tyrosyl radical scavengers are consistent with a more accessible dimetal binding/radical site and a lower affinity for Fe²⁺ in EBV R2 than in Escherichia coli R2. Comparison with previous studies of RNR R2s from mouse, bacteria, and herpes viruses, demonstrates that finely tuned electronic properties of the radical exist within the same RNR R2 Ia class.

| S-EPMC3181257 | biostudies-literature

Surface-Enhanced Hyper-Raman Spectra of Adenine, Guanine, Cytosine, Thymine, and Uracil.

Project description:Using picosecond excitation at 1064 nm, surface-enhanced hyper-Raman scattering (SEHRS) spectra of the nucleobases adenine, guanine, cytosine, thymine, and uracil with two different types of silver nanoparticles were obtained. Comparing the SEHRS spectra with SERS data from the identical samples excited at 532 nm and with known infrared spectra, the major bands in the spectra are assigned. Due to the different selection rules for the one- and two-photon excited Raman scattering, we observe strong variation in relative signal strengths of many molecular vibrations obtained in SEHRS and SERS spectra. The two-photon excited spectra of the nucleobases are found to be very sensitive with respect to molecule-nanoparticle interactions. Using both the SEHRS and SERS data, a comprehensive vibrational characterization of the interaction of nucleobases with silver nanostructures can be achieved.

| S-EPMC5215682 | biostudies-literature

Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV-Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer).

Project description:For many decades, uracil has been an antineoplastic agent used in combination with tegafur to treat various human cancers, including breast, prostate, and liver cancer. Therefore, it is necessary to explore the molecular features of uracil and its derivatives. Herein, the molecule's 5-hydroxymethyluracil has been thoroughly characterized by NMR, UV-Vis, and FT-IR spectroscopy by means of experimental and theoretical analysis. Density functional theory (DFT) using the B3LYP method at 6-311++G(d,p) was computed to achieve the optimized geometric parameters of the molecule in the ground state. For further investigation and computation of the NLO, NBO, NHO analysis, and FMO, the improved geometrical parameters were utilized. The potential energy distribution was used to allocate the vibrational frequencies using the VEDA 4 program. The NBO study determined the relationship between the donor and acceptor. The molecule's charge distribution and reactive regions were highlighted using the MEP and Fukui functions. Maps of the hole and electron density distribution in the excited state were generated using the TD-DFT method and PCM solvent model in order to reveal electronic characteristics. The energies and diagrams for the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) were also provided. The HOMO-LUMO band gap estimated the charge transport within the molecule. When examining the intermolecular interactions in 5-HMU, Hirshfeld surface analysis was used, and fingerprint plots were also produced. The molecular docking investigation involved docking 5-HMU with six different protein receptors. Molecular dynamic simulation has given a better idea of the binding of the ligand with protein.

| S-EPMC10004125 | biostudies-literature

PES, molecular structure, spectroscopic (FT-IR, FT-Raman), electronic (UV-Vis, HOMO-LUMO), quantum chemical and biological (docking) studies on a potent membrane permeable inhibitor: dibenzoxepine derivative.

Project description:The dibenzoxepines derivatives have found a broad application in biological and pharmaceutical fields as new prospective drugs. So, the molecule (3aS,12bS)-5-Chlor-2-methyl-2,3,3a,12b-tetrahydro-1H-dibenzo[2,3:6,7]oxepino[4,5-c]pyrrol has been characterized by DFT (Density Functional Theory) approach to predict the important properties of it. The minimum energy conformer has been found by PES (Potential Energy Surface) and then the structure is optimized. Further, the structure is characterized spectroscopically by FT-IR and FT-Raman techniques to know the functional group and chemically active atoms. The geometrical parameters, PED (Potential Energy Distribution) assignments have also been reported. The electronic properties of the title compound have been explained by UV-Vis and HOMO-LUMO analyses that describe the charge transfer between the atoms of the molecule. Molecular Electrostatic Potential (MEP), Electron Localization Function (ELF) and Localized Orbital Locator (LOL) have been depicted to know the chemically active regions. The electrophilic and nucleophilic regions have been shown by Fukui functions. The Non-Linear Optics (NLO) for non-linear optical effects and the Natural Bond Orbital (NBO) for charge delocalization were studied. To study the biological activity of the title compound, molecular docking has been performed which suggests that the title molecule may act as a membrane permeable inhibitor.

| S-EPMC7452420 | biostudies-literature

UV-Vis and ATR-FTIR spectroscopic investigations of postmortem interval based on the changes in rabbit plasma.

Project description:Estimating PMI is of great importance in forensic investigations. Although many methods are used to estimate the PMI, a few investigations focus on the postmortem redistribution. In this study, ultraviolet-visible (UV-Vis) measurement combined with visual inspection indicated a regular diffusion of hemoglobin into plasma after death showing the redistribution of postmortem components in blood. Thereafter, attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy was used to confirm the variations caused by this phenomenon. First, full-spectrum partial least-squares (PLS) and genetic algorithm combined with PLS (GA-PLS) models were constructed to predict the PMI. The performance of GA-PLS model was better than that of full-spectrum PLS model based on its root mean square error (RMSE) of cross-validation of 3.46 h (R2 = 0.95) and the RMSE of prediction of 3.46 h (R2 = 0.94). The investigation on the similarity of spectra between blood plasma and formed elements also supported the role of redistribution of components in spectral changes in postmortem plasma. These results demonstrated that ATR-FTIR spectroscopy coupled with the advanced mathematical methods could serve as a convenient and reliable tool to study the redistribution of postmortem components and estimate the PMI.

| S-EPMC5533326 | biostudies-literature

Near UV-Vis and NMR Spectroscopic Methods for Rapid Screening of Antioxidant Molecules in Extra-Virgin Olive Oil.

Project description:Several spectroscopic techniques have been optimized to check extra-virgin olive oil quality and authenticity, as well as to detect eventual adulterations. These methods are usually complementary and can give information about different olive oil chemical components with bioactive and antioxidant properties. In the present work, a well-characterized set of extra-virgin olive oil (cultivar Frantoio) samples from a specific area of Tuscany (Italy) were investigated by combining near UV-Vis absorption spectroscopy, 1H and 13C nuclear magnetic resonance (NMR) to identify and quantify different chemical components, such as pigments, secoiridoids and squalene, related to the nutritional and quality properties of olive oils. Moreover, the pigmentation index of olives, organoleptic and sensory properties, total phenolic compound contents and the lipidic fractions of olive oils were investigated. The results obtained are, finally, compared and discussed in order to correlate several properties of both olives and olive oils with specific features of the cultivation area.

| S-EPMC7764626 | biostudies-literature

An integrated transcriptomics and metabolomics study of the immune response of newly hatched chicks to the cytosine-phosphate-guanine oligonucleotide stimulation.

Project description:The immunological immaturity of the innate immune system during the first-week post-hatch enables pathogens to infect chickens, leading to the death of the animals. Current preventive solutions to improve the resistance of chicks to infections include vaccination, breeding, and sanitation. Other prophylactic solutions have been investigated, such as the stimulation of animal health with immunostimulants. Recent studies showed that administration of immune-modulators to one-day-old chicks, or in ovo, significantly reduces mortality in experimental bacterial or viral infection challenge models. Owing to a lack of molecular biomarkers required to evaluate chicken immune responses and assess the efficacy of vaccines or immune-modulators, challenge models are still used. One way to reduce challenge experiments is to define molecular signatures through omics approaches, resulting in new methodologies to rapidly screen candidate molecules or vaccines. This study aims at identifying a dual transcriptomics and metabolomics blood signature after administration of CpG-ODN (cytosine-phosphate-guanine oligodeoxynucleotides), a reference immune-stimulatory molecule. A clinical study was conducted with chicks and transcriptomics and metabolomics analyses were performed on whole-blood and plasma samples, respectively. Differentially expressed genes and metabolites with different abundance were identified in chicks treated with CpG-ODN. The results showed that CpG-ODN activated the innate immune system, within hours after administration, and its effect lasted over time, as metabolomics and transcriptomics profiles still varied 6 D after administration. In conclusion, through an integrated clinical omics approach, we deciphered in part the mode of action of CpG-ODN in post-hatch chicks.

| S-EPMC7598132 | biostudies-literature

Elucidating the Mechanism of Working SnO<sub>2</sub> Gas Sensors Using Combined Operando UV/Vis, Raman, and IR Spectroscopy.

Project description:SnO2 is the most widely used metal oxide gas-sensing material but a detailed understanding of its functioning is still lacking despite its relevance for applications. To gain new mechanistic insight into SnO2 gas sensors under working conditions, we have developed an operando approach based on combined UV/Vis, Raman, and FTIR spectroscopy, allowing us for the first time to relate the sensor response to the concentration of oxygen vacancies in the metal oxide, the nature of the adsorbates, and the gas-phase composition. We demonstrate with the example of ethanol gas sensing that the sensor resistance is directly correlated with the number of surface oxygen vacancies and the presence of surface species, in particular, acetate and hydroxy groups. Our operando results enable an assessment of mechanistic models proposed in the literature to explain gas sensor operation. Owing to their fundamental nature, our findings are of direct relevance also for other metal oxide gas sensors.

| S-EPMC6856817 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data