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Results for “Spectroscopy, Fourier Transform Infrared”

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PubMed1997

RNA-diethylstilbestrol interaction studied by Fourier transform infrared difference spectroscopy.

Diethylstilbestrol (DES), a synthetic estrogen, is known to be a carcinogen in human and in animals. This study was designed to examine the interaction of DES with yeast RNA in aqueous solution at physiological pH with drug/RNA-phosphate (P) molar ratios of 1/80, 1/40, 1/20, 1/10, 1/4, and 1/2. Fourier transform infrared (FTIR) difference spectroscopy was used to determine the drug binding mode, the binding constant, the sequence selectivity, and RNA secondary structure in the RNA.DES complexes. Spectroscopic evidence showed that at low drug concentration (1/80 and 1/40), DES is intercalating through both Gua-Cyt and Ade-Urd base pairs with minor interaction with the backbone PO2 group (external binding). The calculated binding constant of K approximately 8.5 x 10(4) M-1 at a drug concentration of 3.12 x 10(-4) M shows that DES is a weaker intercalator than those of the methylene blue, acridine orange, and ethidium bromide. At high drug content (r > 1/40, where r represents the DES/RNA-phosphate molar ratio), a partial helix destabilization occurs with no alteration of RNA conformation upon drug complexation. However, a comparison with DNA.DES complexes showed that drug intercalation causes major reduction of the B-DNA structure in favor of A-DNA with no participation of the backbone PO2 group in the DES. DNA complexation.

DNA↗

PubMed2005

Phase correction of interferograms using digital all-pass filters.

A method for the phase correction of interferograms in Fourier transform infrared spectroscopy is presented. It is shown that phase error can be canceled to within an arbitrary angular precision by a low-order digital all-pass filter. Such a filter only modifies the phase of the Fourier transform of the interferogram and keeps the magnitude unchanged, like the Mertz method, for example. However, our method minimizes the asymmetric apodization that results in photometric errors when using the Mertz method alone. A practical example is provided in which phase correction over a frequency range of 800 cm(-1) to 4000 cm(-1) using a 9-pole all-pass filter resulted in a photometric error of <0.01%, much less than the 0.3% error of the Mertz method. An alternative and faster (approximately 100 ms) approach is to use an all-pass filter with lower angular precision followed by the Mertz method. Removing most of the phase error with the filter brings the interferogram to an optimal state so that the residual phase error can be completely removed with the Mertz procedure without introducing photometric error. The method can be used in most experiments, including emission spectroscopy, where conventional techniques are inadequate. A simple all-pass filter design algorithm is given.

Algorithms↗

PubMed2003

FTIR determination of ligand-induced secondary and tertiary structural changes in bovine plasminogen.

Human plasminogen undergoes a large tertiary structural change in the presence of lysine derivatives (e.g. epsilon-amino caproic acid, EACA). This change facilitates human plasminogen activation by human plasminogen activators, resulting in elevated blood plasmin levels. It is hypothesized that this structure-function relationship is similar for bovine plasminogen. The objectives of this study were to investigate the effect of the ligand EACA on the secondary structure of plasminogen (bovine, human, and rabbit) and the tertiary structure of bovine plasminogen using Fourier-transform infrared spectroscopy (FTIR). Spectra of plasminogen, EACA, and a mixture of plasminogen and EACA in water and deuterium were collected using FTIR. Fourier-self deconvoluted spectra in the amide I region (1700-1600 cm(-1)) were used to detect changes in secondary structure of plasminogen after EACA addition. Change in bovine plasminogen tertiary structure was determined by comparing ratios of amide II (1600-1500 cm(-1)) to amide I bond intensities over time for samples in deuterium. No differences in secondary structure were observed for any plasminogen in the presence of EACA; however, addition of EACA significantly changed tertiary structure of bovine plasminogen. This tertiary structural change indicates a transition from a folded to an unfolded state, which could be more easily converted to plasmin. These results are consistent with reported human plasminogen studies using neutron scattering (tertiary structure) and circular dichroism (secondary structure) methods.

Aminocaproic Acid↗

PubMed1996

FTIR monomer conversion analysis of UDMA-based dental resins.

The utility of the amide II absorption band at 1537 cm-1 as internal reference for calculation of monomer conversion in urethane dimethacrylates (UDMA)-based dental restorative materials and sealants by means of Fourier transform infrared spectroscopy (FTIR) is demonstrated in this paper.

Amides↗

PubMed2003

Stopped flow apparatus for time-resolved Fourier transform infrared difference spectroscopy of biological macromolecules in 1H2O.

Stopped flow spectroscopy is an established technique for acquiring kinetic data on dynamic processes in chemical and biochemical reactions, and Fourier transform infrared (FT-IR) techniques can provide particularly rich structural information on biological macromolecules. However, it is a considerable challenge to design an FT-IR stopped flow system with an optical path length low enough for work with aqueous (1H2O) solutions. The system presented here is designed for minimal sample volumes (approximately 5 microL) and allows simultaneous FT-IR rapid-scan and VIS measurements. The system employs a micro-structured diffusional mixer to achieve effective mixing on the millisecond time scale under moderate flow and pressure conditions, allowing measurements in a cell path length of less than 10 microns. This makes it possible to record spectra in 1H2O solutions over a wide spectral range. The system layout is also designed for a combination of kinetic and static measurements, in particular to obtain detailed information on the faster spectral changes occurring during the system dead time. A detailed characterization of the FT-IR stopped flow system is presented, including a demonstration of the alkaline conformational transition of cytochrome c as an example.

Biopolymers↗

PubMed2006

A molecular model for epsilon-caprolactam-based intercalated polymer clay nanocomposite: Integrating modeling and experiments.

In studying the morphology, molecular interactions, and physical properties of organically modified montmorillonite (OMMT) and polymer clay nanocomposites (PCNs) through molecular dynamics (MD), the construction of the molecular model of OMMT and PCN is important. Better understanding of interaction between various constituents of PCN will improve the design of polymer clay nanocomposite systems. MD is an excellent tool to study interactions, which require accurate modeling of PCN under consideration. Previously, the PCN models were constructed by different researchers on the basis of specific criteria such as minimum energy configuration, density of the polymer clay nanocomposite, and so forth. However, in this article we describe the development of models combining experimental and conventional molecular modeling to develop models, which are more representative of true intercalated PCN systems. The models were used for studying the morphological interactions and physical properties. These studies gave useful information regarding orientation of organic modifiers, area of coverage of organic modifiers over the interlayer clay surface, interaction of organic modifiers with clay in OMMT, interaction among different constituents of PCN, conformational and density change, and actual proportion of mixing of polymer with clay in PCN. We have X-ray diffraction and photoacoustic Fourier transform infrared spectroscopy to verify the model.

Aluminum Silicates↗

PubMed2001

Bacterial swarming: a biochemical time-resolved FTIR-ATR study of Proteus mirabilis swarm-cell differentiation.

Fourier transform infrared spectroscopy was applied to the study of the differentiation process undergone by Proteus mirabilis. This bacterium exhibits a remarkable dimorphism, allowing the cells to migrate on a solid substratum in a concerted manner yielding characteristic ring patterns. We performed an in situ noninvasive analysis of biochemical events occurring as vegetative cells differentiate into elongated, multinucleate, nonseptate, and hyperflagellated swarm cells. The major findings arising from this study are (i) the real-time monitoring of flagellar filament assembly, (ii) the evidence for de novo synthesis of qualitatively different lipopolysaccharides (LPS) and/or exopolysaccharides (EPS) constituting the slime into which bacteria swarm, and (iii) the alteration in the membrane fatty acid composition with a concomitant 10 degrees C decrease in the gel/liquid crystal phase transition resulting in an elevated membrane fluidity in swarm cells at the growth temperature. The time course of events shows that the EPS-LPS syntheses are synchronous with membrane fatty acid alterations and occur about 1 h before massive flagellar filament assembly is detected. This study not only provided a time sketch of biochemical events involved in the differentiation process but also led to the identification of the major spectral markers of both vegetative and swarm cells. This identification will allow to resolve the time-space structure of P. mirabilis colonies by using infrared microscopy.

Kinetics↗

PubMed2002

The two photocycles of photoactive yellow protein from Rhodobacter sphaeroides.

The absorption spectrum of the photoactive yellow protein from Rhodobacter sphaeroides (R-PYP) shows two maxima, absorbing at 360 nm (R-PYP(360)) and 446 nm (R-PYP(446)), respectively. Both forms are photoactive and part of a temperature- and pH-dependent equilibrium (Haker, A., Hendriks, J., Gensch, T., Hellingwerf, K. J., and Crielaard, W. (2000) FEBS Lett. 486, 52-56). At 20 degrees C, for PYP characteristic, the 446-nm absorbance band displays a photocycle, in which the depletion of the 446-nm ground state absorption occurs in at least three phases, with time constants of <30 ns, 0.5 micros, and 17 micros. Intermediates with both blue- and red-shifted absorption maxima are transiently formed, before a blue-shifted intermediate (pB(360), lambda(max) = 360 nm) is established. The photocycle is completed with a monophasic recovery of the ground state with a time constant of 2.5 ms. At 7 degrees C these photocycle transitions are slowed down 2- to 3-fold. Upon excitation of R-PYP(360) with a UV-flash (330 +/- 50 nm) a species with a difference absorption maximum at approximately 435 nm is observed that returns to R-PYP(360) on a minute time scale. Recovery can be accelerated by a blue light flash (450 nm). R-PYP(360) and R-PYP(446) differ in their overall protein conformation, as well as in the isomerization and protonation state of the chromophore, as determined with the fluorescent polarity probe Nile Red and Fourier Transform Infrared spectroscopy, respectively.

Bacterial Proteins↗

PubMedDate not supplied

Characterization of DNA immobilized on electrochemically prepared conducting polypyrrole-polyvinyl sulfonate films.

The article describes the adsorption characteristics of DNA onto electrochemically generated polypyrrole-polyvinyl sulfonate (PPY-PVS) films obtained as a function of pH. Adsorption on PPY doped with an anion proceeds by anion exchange, and since DNA possesses a fixed negative charge owing to PO4-, it favors a very strong binding displacing PVS with favorable energetic interactions. Characterization of adsorbed DNA onto the PPY-PVS films was carried out by ultraviolet-visible, Fourier transform infrared spectroscopy, and cyclic voltammetric studies.

Adsorption↗

PubMed2000

Effect of carbon coating on the properties of gamma irradiated ultra-high-molecular-weight polyethylene specimens.

We reported the effect of carbon coating on the changes in properties of the ultra-high-molecular-weight polyethylene standard material (Hospital for Special Surgery) alter gamma irradiation in air and storage for 2 years. The coating showed a slight improvement in crystallinity (X-ray) and tensile properties (under cyclic loading) over the uncoated and irradiated control group. The oxidation level as measured by Fourier- transform infrared spectroscopy was unaffected by coating.

Air↗

PubMedDate not supplied

Cyclopentadienyl iron dicarbonyl (eta 1-N-phthalimidato) complexes containing an isothiocyanate function: synthesis and application to protein side-chain selective labeling.

The two first transition metal carbonyl isothiocyanates were prepared in high yield within two steps from photolysis of CpFe(CO)2I and 3- or 4-aminophthalimide in the presence of diisopropylamine followed by reaction with thiophosgene/triethylamine. Their reaction with a model amino acid, i.e. beta-alanine, was performed and led to the expected thioureas. When reacted with bovine serum albumin in aqueous medium, conjugates bearing 6-10 iron-carbonyl fragments were obtained and characterized by Fourier transform infrared spectroscopy, thus demonstrating the usefulness of these reagents for the selective and covalent labeling of proteins.

Iron Compounds↗

PubMed2006

Self-assembly of well-defined polyacrylamide-polystyrene copolymer on fibrillar clays via ultrasonic-assisted surface-initiated atom transfer radical polymerization.

Well-defined polyacrylamide-polystyrene copolymers were grafted from the fibrillar clay, attapulgite, by a four-step self-assembly process: (i) the gamma-aminopropyltriethoxyl silane was self-assembled onto the surfaces of the attapulgite; (ii) the surface amino groups were amidated with bromoacetylbromide; (iii) the bromo-acetamide modified attapulgite was used as macro-initiator for the surface-initiated atom transfer radical polymerization of styrene with the catalyst of the complex of 1,10-phenanthroline and Cu(I)Br; (iv) the polystyrene grafted attapulgite was then used as macroinitiator for the polymerization of acrylamide. The two steps of the surface-initiated atom transfer radical polymerizations were all conducted under ultrasonic irradiation at room temperature. The product, polyacrylamide-polystyrene copolymers grafted attapulgite, had been characterized with elemental analysis, Fourier transform infrared spectroscopy, Thermogravimetric analysis (TGA), X-ray photoelectron spectroscopy, X-ray diffractometry, and transmission electron microscopy.

Acrylic Resins↗

PubMed2005

Microwave plasma treatment of polymer surface for irreversible sealing of microfluidic devices.

Microwave plasma was generated in a glass bottle containing 2-3 Torr of oxygen for plasma treatment of a polymer surface. A "kitchen microwave oven" and a dedicated microwave digestion oven were used as the power source. Poly(dimethylsiloxane)(PDMS) slabs treated by a 30 W plasma for 30-60 s sealed irreversibly to form microfluidic devices that can sustain solution flow of an applied pressure of 42 psi without leaking. Experimental set up and conditions for the production of a homogeneous plasma to activate the PDMS surface for irreversible sealing are described in detail. The surface of a microwave plasma-treated PDMS slab was characterized using atomic force microscopy (AFM) and attenuated total reflection-Fourier Transform infrared spectroscopy (ATR-FTIR). The plasma-treated surface bears silica characteristics.

Dimethylpolysiloxanes↗

PubMed1994

Evidence of possible carcinogenesis during conformational changes in bladder mucosa induced by bladder outlet obstruction.

Fourier transform infrared spectroscopy with attenuated total reflectance technique was applied to determine the mucosa on the surface of the rabbit urinary bladder wall before and after obstruction. Several abnormal spectra related to the hydrogen bonding in nucleic acids of protein, previously found in the colon malignant tissues, appeared in the infrared spectra of the obstructed bladder mucosa, which could not be found in normal bladder mucosa. Urinary bladder outlet obstruction seemed to induce carcinogenesis in the obstructed bladder mucosa by forming several infrared spectral abnormalities.

Animals↗

PubMed2005

Ion translocation by the Escherichia coli NADH:ubiquinone oxidoreductase (complex I).

The energy-converting NADH:ubiquinone oxidoreductase, also known as respiratory complex I, couples the transfer of electrons from NADH to ubiquinone with the translocation of ions across the membrane. It was assumed that the complex exclusively works as a proton pump. Recently, it has been proposed that complex I from Klebsiella pneumoniae and Escherichia coli work as Na+ pumps. We have used an E. coli complex I preparation to determine the type of ion(s) translocated by means of enzyme activity, generation of a membrane potential and redox-induced Fourier-transform infrared spectroscopy. We did not find any indications for Na+ translocation by the E. coli complex I.

Biological Transport↗

PubMed2006

Synthesis and characterization of new biodegradable hyaluronan alkyl derivatives.

Several new biocompatible and degradable materials were prepared by chemical modification of sodium hyaluronate. The method of activation of hyaluronate by cyanogen bromide was used and subsequent reaction with nucleophile led to the formation of carbamate. This modification of hydroxyl groups of glycosaminoglycans preserves the carboxyl groups and retains properties of polyelectrolyte. This method affords derivatives easily and the reaction condition correlates with degree of substitution. The experimental results show the effect of reaction conditions (reaction time, ratio of reactants) and effect of substitution on biodegradability. The obtained materials were characterized by nuclear magnetic resonance and Fourier transform infrared spectroscopy.

Animals↗

PubMed2000

Illuminating folding intermediates.

Time-resolved Fourier transform infrared spectroscopy provides evidence of non-native antiparallel beta-sheet structural elements in the folding intermediates of alpha-lactalbumin.

Hydrogen-Ion Concentration↗

PubMed1997

Detachment of linking film bacteria from enamel surfaces by oral rinses and penetration of sodium lauryl sulphate through an artificial oral biofilm.

The biofilm mode of growth protects plaque micro-organisms against environmental attacks, such as from antimicrobials or detergents. Dental plaque is linked to enamel through the adhesion of initial colonizers. Once this link is disrupted, the entire plaque mass adhering to it detaches. Experiments in a parallel-plate flow chamber demonstrated that bacteria adhering to saliva-coated enamel could not be stimulated to detach by perfusion of the flow chamber with two traditional mouthrinses (Corsodyl and Scope), whereas perfusion with a prebrushing rinse (Plax) or its detergent components stimulated detachment from saliva-coated enamel of a wide variety of bacterial strains. Following perfusion of the flow chamber with the mouthrinses, little additional detachment of adhering bacteria by the passage of a liquid-air interface occurred. After perfusion with the prebrushing rinse, however, significant numbers of still-adhering bacteria could be stimulated to detach by passage of a liquid-air interface, indicating that Plax had weakened their adhesive bond. The ability of Plax or its detergent components to detach plaque bacteria is not always obvious from in vivo experiments, and reports on its clinical efficacy are inconsistent. Likely, antimicrobials or detergents are unable to penetrate the plaque and reach the linking film bacteria, as demonstrated here by Fourier transform infrared spectroscopy.

Animals↗