Vibrational analysis of nucleic acids. I. The phosphodiester group in dimethyl phosphate model compounds: (CH3O)2PO2-, (CD3O)2PO2-, and (13CH3O)2PO2-

Raman Probes for In Situ Molecular Analyses of Peripheral Nerve Myelination

The myelinating activity of living Schwann cells in coculture with neuronal cells was examined in situ in a Raman microprobe spectroscope. The Raman label-free approach revealed vibrational fingerprints directly related to the activity of Schwann cells' metabolites and identified molecular species peculiar to myelinating cells. The identified chemical species included antioxidants, such as hypotaurine and glutathione, and compartmentalized water, in addition to sphingolipids, phospholipids, and nucleoside triphosphates also present in neuronal and nonmyelinating Schwann cells. Raman maps at specific frequencies could be collected, which clearly visualized the myelinating action of Schwann cells and located the demyelinated ones. An important finding was the spectroscopic visualization of confined water in the myelin structure, which exhibited a quite pronounced Raman signal at ∼3470 cm^-1. This peculiar signal, whose spatial location precisely corresponded to a low-frequency fingerprint of hypotaurine, was absent in unmyelinating cells and in bulk water. Raman enhancement was attributed to frustration in the hydrogen-bond network as induced by interactions with lipids in the myelin sheaths. According to a generally accepted morphological model of myelin, an explanation was offered of the peculiar Raman scattering of water confined in intraperiod lines, according to an ordered hydrogen bonding structure. The possibility of concurrently mapping antioxidant molecules and compartmentalized water structure with high spectral accuracy and microscopic spatial resolution enables probing myelinating activity and might play a key-role in future studies of neuronal pathologies. Compatible with life, Raman microprobe spectroscopy with the newly discovered probes could be suitable for developing advanced strategies in the reconstruction of injured nerves and nerve terminals at neuromuscular junctions.

Cardiolipin Structure and Oxidation Are Affected by Ca2+ at the Interface of Lipid Bilayers

Ca²⁺-overload contributes to the oxidation of mitochondrial membrane lipids and associated events such as the permeability transition pore (MPTP) opening. Numerous experimental studies about the Ca²⁺/cardiolipin (CL) interaction are reported in the literature, but there are few studies in conjunction with theoretical approaches based on ab initio calculations. In the present study, the lipid fraction of the inner mitochondrial membrane was modeled as POPC/CL large unilamellar vesicles (LUVs). POPC/CL and, comparatively, POPC, and CL LUVs were challenged by singlet molecular oxygen using the anionic porphyrin TPPS4 as a photosensitizer and by free radicals produced by Fe²⁺-citrate. Calcium ion favored both types of lipid oxidation in a lipid composition-dependent manner. In membranes containing predominantly or exclusively POPC, Ca²⁺ increased the oxidation at later reaction times while the oxidation of CL membranes was exacerbated at the early times of reaction. Considering that Ca²⁺ interaction affects the lipid structure and packing, density functional theory (DFT) calculations were applied to the Ca²⁺ association with totally and partially protonated and deprotonated CL, in the presence of water. The interaction of totally and partially protonated CL head groups with Ca²⁺ decreased the intramolecular P-P distance and increased the hydrophobic volume of the acyl chains. Consistently with the theoretically predicted effect of Ca²⁺ on CL, in the absence of pro-oxidants, giant unilamellar vesicles (GUVs) challenged by Ca²⁺ formed buds and many internal vesicles. Therefore, Ca²⁺ induces changes in CL packing and increases the susceptibility of CL to the oxidation promoted by free radicals and excited species.

DFT study of geometrical and vibrational features of a 3',5'-deoxydisugar-monophosphate (dDSMP) DNA model in the presence of counterions and solvent

The B3LYP/6-31++G* theoretical level was used to study the influence of various hexahydrated monovalent (Li⁺, Na⁺, K⁺) and divalent (Mg²⁺) metal counterions in interaction with the charged PO₂^- group, on the geometrical and vibrational characteristics of the DNA fragments of 3',5'-dDSMP, represented by four conformers (g⁺g⁺, g⁺t, g^-g^- and g^-t). All complexes were optimized through two solvation models [the explicit model (6H₂O) and the hybrid model (6H₂O/Continuum)]. The results obtained established that, in the hybrid model, counterions (Li⁺, Na⁺, K⁺, Mg²⁺) always remain in the bisector plane of the O1-P-O2 angle. When these counterions are explicitly hydrated, the smallest counterions (Li⁺, Na⁺) deviate from the bisector plane, while the largest counterions (K⁺ and Mg²⁺) always remain in the same plane. On the other hand, the present calculations reveal that the g⁺g⁺ conformer is the most stable in the presence of monovalent counterions, while conformers g⁺t and g^-t are the most stable in the presence of the divalent counterion Mg²⁺. Finally, the hybrid solvation model seems to be in better agreement with the available crystallographic and spectroscopic (Raman) experiments than the explicit model. Indeed, the six conformational torsions of the C4'-C3'-O3'-PO^-₂-O5'-C5'-C4' segment of all complexes of the g^-g^- conformer in 6H₂O/Continuum remain similar to the available experimental data of A- and B-DNA forms. The calculated wavenumbers of the g⁺g⁺ conformer in the presence of the monovalent counterion and of g^-t conformer in presence of the divalent counterion in the hybrid model are in good agreement with the Raman experimental data of A- and B-DNA forms. In addition, the maximum deviation between the calculated wavenumbers in the 6H₂O/Continuum for the g⁺g⁺ conformer and experimental value measured in an aqueous solution of the DMP-Na⁺ complex, is <1.07% for the PO₂^- (asymmetric and symmetric) stretching modes and <2.03% for the O5'-C5' and O3'-C3' stretching modes. Graphical abstract dDSMP-(OO)^- Mg²⁺/6W/Continuum.

Interaction of Na+, K+, Mg2+ and Ca2+ counter cations with RNA

Data on the location of alkaline and alkaline earth ions at RNA from crystallography, spectroscopy and computational modeling are reviewed.

Structural Changes Induced in Grapevine (Vitis vinifera L.) DNA by Femtosecond IR Laser Pulses: A Surface-Enhanced Raman Spectroscopic Study

In this work, surface-enhanced Raman spectra of ten genomic DNAs extracted from leaf tissues of different grapevine (Vitis vinifera L.) varieties, respectively, are analyzed in the wavenumber range 300–1800 cm⁻¹. Furthermore, structural changes induced in grapevine genomic nucleic acids upon femtosecond (170 fs) infrared (IR) laser pulse irradiation (λ = 1100 nm) are discussed in detail for seven genomic DNAs, respectively. Surface-enhanced Raman spectroscopy (SERS) signatures, vibrational band assignments and structural characterization of genomic DNAs are reported for each case. As a general observation, the wavenumber range between 1500 and 1660 cm⁻¹ of the spectra seems to be modified upon laser treatment. This finding could reflect changes in the base-stacking interactions in DNA. Spectral shifts are mainly attributed to purines (dA, dG) and deoxyribose. Pyrimidine residues seem to be less affected by IR femtosecond laser pulse irradiation. Furthermore, changes in the conformational properties of nucleic acid segments are observed after laser treatment. We have found that DNA isolated from Feteasca Neagra grapevine leaf tissues is the most structurally-responsive system to the femtosecond IR laser irradiation process. In addition, using unbiased computational resources by means of principal component analysis (PCA), eight different grapevine varieties were discriminated.

Structural effects of simvastatin on liver rat [corrected] tissue: Fourier transform infrared and Raman microspectroscopic studies

Simvastatin is one of the most frequently prescribed statins because of its efficacy in the treatment of hypercholesterolemia, reducing cardiovascular risk and related mortality. Determination of its side effects on different tissues is mandatory to improve safe use of this drug. In the present study, the effects of simvastatin on molecular composition and structure of healthy rat livers were investigated by Fourier transform infrared and Raman imaging. Simvastatin-treated groups received 50 mg/kg/day simvastatin for 30 days. The ratio of the area and/or intensity of the bands assigned to lipids, proteins, and nucleic acids were calculated to get information about the drug-induced changes in tissues. Loss of unsaturation, accumulation of end products of lipid peroxidation, and alterations in lipid-to-protein ratio were observed in the treated group. Protein secondary structure studies revealed significant decrease in α-helix and increase in random coil, while native β-sheet decreases and aggregated β-sheet increases in treated group implying simvastatin-induced protein denaturation. Moreover, groups were successfully discriminated using principal component analysis. Consequently, high-dose simvastatin treatment induces hepatic lipid peroxidation and changes in molecular content and protein secondary structure, implying the risk of liver disorders in drug therapy.

Surface-enhanced Raman spectroscopy of genomic DNA from in vitro grown tomato (Lycopersicon esculentum Mill.) cultivars before and after plant cryopreservation

In this work the surface-enhanced Raman scattering (SERS) spectra of five genomic DNAs from non-cryopreserved control tomato plants (Lycopersicon esculentum Mill. cultivars Siriana, Darsirius, Kristin, Pontica and Capriciu) respectively, have been analyzed in the wavenumber range 400-1800 cm(-1). Structural changes induced in genomic DNAs upon cryopreservation were discussed in detail for four of the above mentioned tomato cultivars. The surface-enhanced Raman vibrational modes for each of these cases, spectroscopic band assignments and structural interpretations of genomic DNAs are reported. We have found, that DNA isolated from Siriana cultivar leaf tissues suffers the weakest structural changes upon cryogenic storage of tomato shoot apices. On the contrary, genomic DNA extracted from Pontica cultivar is the most responsive system to cryopreservation process. Particularly, both C2'-endo-anti and C3'-endo-anti conformations have been detected. As a general observation, the wavenumber range 1511-1652 cm(-1), being due to dA, dG and dT residues seems to be influenced by cryopreservation process. These changes could reflect unstacking of DNA bases. However, not significant structural changes of genomic DNAs from Siriana, Darsirius and Kristin have been found upon cryopreservation process of tomato cultivars. Based on this work, specific plant DNA-ligand interactions or accurate local structure of DNA in the proximity of a metallic surface, might be further investigated using surface-enhanced Raman spectroscopy.

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.

Reaction mechanism of adenylyltransferase DrrA from Legionella pneumophila elucidated by time-resolved fourier transform infrared spectroscopy

Modulation of the function of small GTPases that regulate vesicular trafficking is a strategy employed by several human pathogens. Legionella pneumophila infects lung macrophages and injects a plethora of different proteins into its host cell. Among these is DrrA/SidM, which catalyzes stable adenylylation of Rab1b, a regulator of endoplasmatic reticulum to Golgi trafficking, and thereby alters the function and interactions of this small GTPase. We employed time-resolved FTIR-spectroscopy to monitor the DrrA-catalyzed AMP-transfer to Tyr77 of Rab1b. A transient complex between DrrA, adenylylated Rab1b, and the pyrophosphate byproduct was resolved, allowing us to analyze the interactions at the active site. Combination of isotopic labeling and site-directed mutagenesis allowed us to derive the catalytic mechanism of DrrA from the FTIR difference spectra. DrrA shares crucial residues in the ATP-binding pocket with similar AMP-transferring enzymes such as glutamine synthetase adenylyltransferase or kanamycin nucleotidyltransferase, but provides the complete active site on a single subunit. We determined that Asp112 of DrrA functions as the catalytic base for deprotonation of Tyr77 of Rab1b to enable nucleophilic attack on the ATP. The study provides detailed understanding of the Legionella pneumophila protein DrrA and of AMP-transfer reactions in general.

Facile electrochemical hydrogenation and chlorination of glassy carbon to produce highly reactive and uniform surfaces for stable anchoring of thiolated molecules

Carbon is a highly adaptable family of materials and is one of the most chemically stable materials known, providing a remarkable platform for the development of tunable molecular interfaces. Herein, we report a two-step process for the electrochemical hydrogenation of glassy carbon followed by either chemical or electrochemical chlorination to provide a highly reactive surface for further functionalization. The carbon surface at each stage of the process is characterized by AFM, SEM, Raman, attenuated total reflectance (ATR) FTIR, X-ray photoelectron spectroscopy (XPS), and electroanalytical techniques. Electrochemical chlorination of hydrogen-terminated surfaces is achieved in just 5 min at room temperature with hydrochloric acid, and chemical chlorination is performed with phosphorus pentachloride at 50 °C over a three-hour period. A more controlled and uniform surface is obtained using the electrochemical approach, as chemical chlorination is observed to damage the glassy carbon surface. A ferrocene-labeled alkylthiol is used as a model system to demonstrate the genericity and potential application of the highly reactive chlorinated surface formed, and the methodology is optimized. This process is then applied to thiolated DNA, and the functionality of the immobilized DNA probe is demonstrated. XPS reveals the covalent bond formed to be a C-S bond. The thermal stability of the thiolated molecules anchored on the glassy carbon is evaluated, and is found to be far superior to that on gold surfaces. This is the first report on the electrochemical hydrogenation and electrochemical chlorination of a glassy carbon surface, and this facile process can be applied to the highly stable functionalization of carbon surfaces with a plethora of diverse molecules, finding widespread applications.

Ab initio molecular dynamics of Na⁺ and Mg²⁺ countercations at the backbone of RNA in water solution

The interactions between sodium or magnesium ions and phosphate groups of the RNA backbone represented as dinucleotide fragments in water solution have been studied using ab initio Born-Oppenheimer molecular dynamics. All systems have been simulated at 300 and 320 K. Sodium ions have mobility higher than that of the magnesium ions and readily change their position with respect to the phosphate groups, from directly bonded to completely solvated state, with a rough estimate of the lifetime of bonded Na(+) of about 20-30 ps. The coordination number of the sodium ions frequently changes in irregular intervals ranging from several femtoseconds to about 10 ps with the most frequently encountered coordination number five, followed by six. The magnesium ion is stable both as directly bonded to an oxygen atom from the phosphate group and completely solvated by water. In both states the Mg(2+) ion has exactly six oxygen atoms in the first coordination shell; moreover, during the whole simulation of more than 100 ps no exchange of ligand in the first coordination shells has been observed. Solvation of the terminal phosphate oxygen atoms by water molecules forming hydrogen bonds in different locations of the ions is also discussed. The stability of the system containing sodium ions essentially does not depend on the position of the ions with respect to the phosphate groups.

Ultrafast energy migration pathways in self-assembled phospholipids interacting with confined water

Phospholipids self-assembled into reverse micelles in benzene are introduced as a new model system to study elementary processes relevant for energy transport in hydrated biological membranes. Femtosecond vibrational spectroscopy gives insight into the dynamics of the antisymmetric phosphate stretching vibration ν(AS)(PO(2))(-), a sensitive probe of local phosphate-water interactions and energy transport. The decay of the ν(AS)(PO(2))(-) mode with a 300-fs lifetime transfers excess energy to a subgroup of phospholipid low-frequency modes, followed by redistribution among phospholipid vibrations within a few picoseconds. The latter relaxation is accelerated by adding a confined water pool, an efficient heat sink in which the excess energy induces weakening or breaking of water-water and water-phospholipid hydrogen bonds. In parallel to vibrational relaxation, resonant energy transfer between ν(AS)(PO(2))(-) oscillators delocalizes the initial excitation.

In situ ATR-IR spectroscopic and electron microscopic analyses of settlement secretions of Undaria pinnatifida kelp spores

Knowledge about the settlement of marine organisms on substrates is important for the development of environmentally benign new methods for control of marine biofouling. The adhesion to substrates by spores of Undaria pinnatifida, a kelp species that is invasive to several countries, was studied by scanning electron and transmission electron microscopies (SEM/TEM) as well as by in situ attenuated total reflection infrared (ATR-IR) spectroscopy. The IR spectra showed that adhesive secretion began approximately 15 min after initial settlement and that the adhesive bulk material contained protein and anionic polysaccharides. Energy dispersive X-ray microanalysis of the adhesive identified sulphur and phosphorus as well as calcium and magnesium ions, which facilitate the gelation of the anionic polysaccharides in the sea water. The adhesive may be secreted from Golgi bodies in the spore, which were imaged by TEM of spore thin sections. Additionally, an in situ settlement study on TiO(2) particle film by ATR-IR spectroscopy revealed the presence of phosphorylated moieties directly binding the substrate. The presence of anionic groups dominating the adhesive suggests that inhibition of spore adhesion will be favoured by negatively charged surfaces.

Deconvolution of Raman spectroscopic signals for electrostatic, H-bonding, and inner-sphere interactions between ions and dimethyl phosphate in solution

Quantitative analysis of metal ion-phosphodiester interactions is a significant experimental challenge due to the complexities introduced by inner-sphere, outer-sphere (H-bonding with coordinated water), and electrostatic interactions that are difficult to isolate in solution studies. Here, we provide evidence that inner-sphere, H-bonding and electrostatic interactions between ions and dimethyl phosphate can be deconvoluted through peak fitting in the region of the Raman spectrum for the symmetric stretch of non-bridging phosphate oxygen (ν(s)PO(2)(-)). An approximation of the change in vibrational spectra due to different interaction modes is achieved using ions capable of all or a subset of the three forms of metal ion interaction. Contribution of electrostatic interactions to ion-induced changes to the Raman ν(s)PO(2)(-) signal could be modeled by monitoring attenuation of ν(s)PO(2)(-) in the presence of tetramethylammonium, while contribution of H-bonding and inner-sphere coordination could be approximated from the intensities of altered ν(s)PO(2)(-) vibrational modes created by an interaction with ammonia, monovalent or divalent ions. A model is proposed in which discrete spectroscopic signals for inner-sphere, H-bonding, and electrostatic interactions are sufficient to account for the total observed change in ν(s)PO(2)(-) signal due to interaction with a specific ion capable of all three modes of interaction. Importantly, the quantitative results are consistent with relative levels of coordination predicted from absolute electronegativity and absolute hardness of alkali and alkaline earth metals.

A quantitative Raman spectroscopic signal for metal-phosphodiester interactions in solution

Accurate identification and quantification of metal ion-phosphodiester interactions are essential for understanding the role of metal ions as determinants of three-dimensional folding of large RNAs and as cofactors in the active sites of both RNA and protein phosphodiesterases. Accomplishing this goal is difficult due to the dynamic and complex mixture of direct and indirect interactions formed with nucleic acids and other phosphodiesters in solution. To address this issue, Raman spectroscopy has been used to measure changes in bond vibrational energies due to metal interactions. However, the contributions of inner-sphere, H-bonding, and electrostatic interactions to the Raman spectrum of phosphoryl oxygens have not been analyzed quantitatively. Here, we report that all three forms of metal ion interaction result in attenuation of the Raman signal for the symmetric vibration of the nonbridging phosphate oxygens (nu(s)PO(2)(-)), while only inner-sphere coordination gives rise to an apparent shift of nu(s)PO(2)(-) to higher wavenumbers (nu(s)PO(2)(-)M) in solution. Formation of nu(s)PO(2)(-)M is shown to be both dependent on metal ion identity and an accurate measure of site-specific metal ion binding. In addition, the spectroscopic parameter reflecting the energetic difference between nu(s)PO(2)(-) and nu(s)PO(2)(-)M (DeltanuM) is largely insensitive to changes in phosphodiester structure but strongly dependent on the absolute electronegativity and hardness of the interacting metal ion. Together, these studies provide strong experimental support for the use of nu(s)PO(2)(-)M and DeltanuM as general spectroscopic features for the quantitative analysis of metal binding affinity and the identification of metal ions associated with phosphodiesters in solution.

Geometrical and vibrational features of phosphate, phosphorothioate and phosphorodithioate linkages interacting with hydrated cations: a DFT study

The effect of hexahydrated monovalent and divalent cations on the geometrical and vibrational features of dimethyl phosphate, dimethyl phosphorothioate and dimethyl phosphorodithioate anions (simple suitable model compounds representing the anionic moieties of natural and some modified nucleic acids) was studied. For this purpose, density functional theory (DFT) calculations were carried out at the B3LYP/6-31++G* level. Our results indicate that only K(+) and Mg(2+) prefer to be located in the bisector plane of the PO(2)(-) angle, whereas Li(+) and Na(+) deviate from this plane. Monovalent and divalent cations are slightly deviated from the OPS(-) bisector plane and are found closer to the free oxygen atom. Moreover, the present calculations have shown that in contrast to the general belief, the g(-)g(-) conformer (with respect to the torsion angles defined around the P-O ester bonds) is not always the energetically most favorable. For instance, the g(-)t conformer presents the lowest energy in the case of dimethyl phosphorothioate. The calculated vibrational wavenumbers obtained for dimethyl phosphate and dimethyl phosphorothioate interacting with hydrated sodium counterion, were compared with those previously recorded by Raman scattering and infrared absorption (IR) in aqueous solutions. It has been evidenced that the use of explicit solvent versus dielectric continuum, considerably improves the agreement between the theoretical and observed characteristic wavenumbers.

Monitoring the redox and protonation dependent contributions of cardiolipin in electrochemically induced FTIR difference spectra of the cytochrome bc(1) complex from yeast

Biochemical studies have shown that cardiolipin is essential for the integrity and activity of the cytochrome bc(1) complex and many other membrane proteins. Recently the direct involvement of a bound cardiolipin molecule (CL) for proton uptake at center N, the site of quinone reduction, was suggested on the basis of a crystallographic study. In the study presented here, we probe the low frequency infrared spectroscopy region as a technique suitable to detect the involvement of the lipids in redox induced reactions of the protein. First the individual infrared spectroscopic features of lipids, typically present in the yeast membrane, have been monitored for different pH values in micelles and vesicles. The pK(a) values for cardiolipin molecule have been observed at 4.7+/-0.3 and 7.9+/-1.3, respectively. Lipid contributions in the electrochemically induced FTIR spectra of the bc(1) complex from yeast have been identified by comparing the spectra of the as isolated form, with samples where the lipids were digested by lipase-A(2). Overall, a noteworthy perturbation in the spectral region typical for the protein backbone can be reported. Interestingly, signals at 1159, 1113, 1039 and 980 cm(-1) have shifted, indicating the perturbation of the protonation state of cardiolipin coupled to the reduction of the hemes. Additional shifts are found and are proposed to reflect lipids reorganizing due to a change in their direct environment upon the redox reaction of the hemes. In addition a small shift in the alpha band from 559 to 556 nm can be seen after lipid depletion, reflecting the interaction with heme b(H) and heme c. Thus, our work highlights the role of lipids in enzyme reactivity and structure.

Ca2+-dimethylphosphate complex formation: providing insight into Ca2+-mediated local dehydration and membrane fusion in cells

Earlier studies using X-ray diffraction, light scattering, photon correlation spectroscopy, and atomic force microscopy, strongly suggest that SNARE-induced membrane fusion in cells proceeds as a result of calcium bridging opposing bilayers. The bridging of phospholipid heads groups in the opposing bilayers by calcium leads to the release of water from hydrated Ca(2+) ions as well as the loosely coordinated water at PO-lipid head groups. Local dehydration of phospholipid head groups and the calcium, bridging opposing bilayers, then leads to destabilization of the lipid bilayers and membrane fusion. This hypothesis was tested in the current study by atomistic molecular dynamic simulations in the isobaric-isothermal ensemble using hydrated dimethylphosphate anions (DMP(-)) and calcium cations. Results from the study demonstrate, formation of DMP-Ca(2+) complexes and the consequent removal of water, supporting the hypothesis. Our study further demonstrates that as a result of Ca(2+)-DMP self-assembly, the distance between anionic oxygens between the two DMP molecules is reduced to 2.92A, which is in close agreement with the 2.8A SNARE-induced apposition established between opposing bilayers, reported earlier from X-ray diffraction measurements.

Understanding membrane fusion combining experimental and simulation studies

Target membrane proteins, SNAP-25 and syntaxin (t-SNARE), and secretory vesicle-associated membrane protein (v-SNARE), are part of the conserved protein complex involved in fusion of opposing bilayers in biological systems in the presence of calcium. It is known that SNARE interaction allows opposing bilayers to come close within a distance of approximately 2.8 A, enabling calcium to drive membrane fusion. X-ray diffraction studies and light scattering measurements performed in SNARE-reconstituted liposomes demonstrate that when reconstituted t-SNARE- and v-SNARE-vesicles are allowed to interact prior to calcium addition, membrane fusion fail to occur. These results suggest that hydrated calcium ions are too large (approximately 6 A) to fit between the SNARE-apposed bilayer space, and as a result, unable to induce membrane fusion. In the presence of calcium, however, t-SNARE vesicles interact with v-SNARE vesicles, allowing formation of calcium-phosphate bridges between the opposing bilayers, resulting in the expulsion of coordinated water at the phosphate of the phospholipid head-groups, and due to disruption of the water shell around the calcium ion, enabling lipid mixing and membrane fusion. This hypothesis when tested using atomistic molecular dynamic simulations in the isobaric-isothermal ensemble using hydrated dimethylphosphate anions (DMP(-)) and calcium cations, demonstrate formation of DMP-Ca(2+) complexes and the consequent removal of water, supporting the hypothesis. As a result of Ca(2+)-DMP self-assembly, the distance between anionic oxygens between the two DMP molecules is reduced to 2.92 A, which is in agreement with the 2.8 A SNARE-induced apposition established between opposing lipid bilayers, reported from X-ray diffraction measurements.

Potential of surface-enhanced Raman spectroscopy for the rapid identification of Escherichia coli and Listeria monocytogenes cultures on silver colloidal nanoparticles

Surface-enhanced Raman (SERS) spectra of various batches of bacteria adsorbed on silver colloidal nanoparticles were collected to explore the potential of the SERS technique for rapid and routine identification of E. coli and L. monocytogenes cultures. Relative standard deviation (RSD) of SERS spectra from silver colloidal suspensions and ratios of SERS peaks from small molecules (K(3)PO(4)) were used to evaluate the reproducibility, stability, and binding effectiveness of citrate-reduced silver colloids over batch and storage processes. The results suggested consistent reproducibility of silver colloids over batch process and also stability and consistent binding effectiveness over an eight-week storage period. A variety of mixtures of E. coli/L. monocytogenes cultures with different colloidal batches revealed that, despite large variations in relative intensities and positions of SERS active bands, characteristic and unique bands at 712 and 390 cm(-1) were consistently observed and were the strongest in E. coli and L. monocytogenes cultures, respectively. Two specific bands were used to develop simple algorithms in the evaluation of binding effectiveness of silver colloids over storage and further to identify E. coli and L. monocytogenes cultures with a 100% success. A single spectrum acquisition took 5 approximately 6 min, and a minimum of 25 microL silver colloid was directly mixed with 25 microL volume of incubated bacterial culture. The short acquisition time and small volume of incubated bacterial culture make silver colloidal nanoparticle based SERS spectroscopy ideal for potential use in the routine and rapid screening of E. coli and L. monocytogenes cultures on large scales. This is the first report of the development of simple and universal algorithms for bacterial identification from the respective exclusive SERS peaks.

A library of IR bands of nucleic acids in solution

This review presents a compilation and discussion of infrared (IR) bands characteristic of nucleic acids in various conformations. The entire spectral range 1800-800 cm(-1) relevant for DNA/RNA in aqueous solution has been subdivided into four sections. Each section contains descriptions of bands appearing from group specific parts of nucleic acid structure, such as nucleobase, base-sugar, sugar-phosphate and sugar moiety. The approach allows comparisons of information obtained from one spectral region with another. The IR band library should facilitate detailed and unambiguous assignment of structural changes, ligand binding, etc. in nucleic acids from IR spectra. is aimed at highlighting specific features that are useful for following major changes in nucleic acid structures. also concerns some recent results, where IR spectroscopy has been used to obtain semi-quantitative information on coexisting modes of sugar pucker in oligonucleotides.

Correlation between normal modes in the 20-200 cm-1 frequency range and localized torsion motions related to certain collective motions in proteins

In certain biologically relevant collective motions, such as protein domain motions and sub-domain motions, large amplitude movements are localized in one or a few flexible regions consisting of a small number of residues. This paper explores the possible use of normal mode analysis in probing localized vibrational torsion motions in these flexible regions that may be related to certain collective motions. The normal modes of 10 structures of five proteins in different conformation (TRP repressor, calmodulin, calbindin D(9k), HIV-1 protease and troponin C), known to have shear or hinge domain or sub-domain motion, respectively, are analyzed. Our study identifies, for each structure, unique normal modes in the 20-200 cm-1 frequency range, whose corresponding motions are primarily concentrated in the region where large amplitude torsion movements of a known domain or sub-domain motion occur. This suggests possible correlation between normal modes at 20-200 cm-1 frequency range and initial fluctuational motions leading to localized collective motions in proteins, and thus the potential application of normal mode analysis in facilitating the study of biologically important localized motions in biomolecules.

Structural effects of cytosine methylation on DNA sugar pucker studied by FTIR

This FTIR investigation concerns structural consequences of 5-methylation of cytosine in a DNA decamer in solution. Methylation of DNA is an important functional signal in transcription, but its effect on DNA structure is variable and not fully understood. Here, single and multiple 5-methylcytosine substitutions are introduced into the self-complementary sequence d(CCGGCGCCGG)(2). No major structural effect of methylation on the DNA duplex in solution is seen in the IR spectra: The overall B-form character of the backbone and S-type of sugar puckering are maintained in all the studied sequences, in agreement with previous literature. However, certain significant effects are detected in the IR regions sensitive to sugar pucker and glycosidic torsional angle. A single or multiple 5-methylcytosine substitution in d(CCGGCGCCGG)(2) leads to a doublet splitting of the S-type 840-820 cm(-1) sugar conformational band. The results suggest the coexistence of two different major sugar puckers within the S-conformational family, with an increased relative contribution of the C2'-endo type of sugar in the methylated sequences. In addition, a partial or full downshift of the guanosine/anti marker band at 1,375 cm(-1) in the methylated sequences reflects a change in the value of the dihedral angle chi of guanosine upon methylation. The IR spectra are interpreted in terms of localized transitions between the BI and BII subconformational states of the B-DNA backbone caused by the methylation. An increased amount of the BII subconformer in the methylated sequences should give rise to a structurally more rigid conformation, in agreement with earlier observations on DNA backbone dynamics and bending flexibility in methylated DNA.

Conformation and interactions of the packaged double-stranded DNA genome of bacteriophage T7

The structure of the packaged double-stranded DNA genome of bacteriophage T7 was compared to that of unpackaged T7 DNA using digital difference Raman spectroscopy. Spectral data were obtained at 25 degrees C from native T7 virus (100 mg/mL), empty T7 capsids (50 mg/mL), and purified T7 DNA (40 mg/mL) in buffer containing 200 mM NaCl, 10 mM MgCl2, and 10 mM Tris at pH 7.5. At these conditions, the local conformation of T7 DNA was not affected by packaging. Specifically, the local B-form secondary structure of unpackaged T7 DNA, including furanose C2'-endo pucker, anti glycosyl torsion, Watson-Crick base pairing, and base stacking, were essentially fully (> 98%) retained when the genome was condensed within the viral capsid. However, the average electrostatic environment of T7 DNA phosphates was altered dramatically by packaging as revealed by large perturbations in the Raman bands associated with localized vibrations of the DNA phosphate groups. The change in the phosphate environment was attributed to Mg2+ ions that were packaged with the genomic DNA, and the observed Raman perturbations of genomic DNA were equivalent to those generated by a 50-100-fold increase in Mg2+ concentration in aqueous phosphodiester model compounds. The T7 data were qualitatively and quantitatively similar to those observed previously for packaged DNA of bacteriophage P22 and imply that genomic DNAs of T7 and P22 are both organized in a similar fashion within their respective capsids. The results show that the condensed genome does not contain kinks or folds that would disrupt the local B conformation by more than 2%. The present findings are discussed in relation to previously proposed models for condensation and organization of double-stranded and single-stranded viral DNA.

Interactions of cyclic AMP and its dibutyryl analogue with model membrane: X-ray diffraction and Raman spectroscopic study using cubic liquid-crystalline phases of monoolein

Interactions of adenosine 3':5'-cyclic monophosphate (cAMP) and its dibutyryl analogue, N6,2'-O-dibutyryladenosine 3':5'-cyclic monophosphate (dbcAMP), with a lipid bilayer were studied by small-angle X-ray diffraction (SAXD) and Raman spectroscopy. The cubic Pn3m phase of monoolein (MO) served as a bilayer-based model system. SAXD measurements have indicated that incorporation of approximately 3 wt.% cAMP leaves the phase parameters practically unaltered, whereas the same content of dbcAMP induces the intercubic Pn3m-->Ia3d transition. By applying the concepts of lipid shape parameter and infinite periodic minimal surface to these MO phases, we have suggested that, as opposed to cAMP, dbcAMP associates with the MO bilayer. This conclusion has been supported by the different effects of phase matrix on the Raman shifts of the adenine and phosphate vibrational modes of these two nucleotides. Moreover, Raman spectra have indicated that dbcAMP inserts into the bilayer through the butyryladenine group, positioning dbcAMP preferentially at the polar/apolar interface.

Unexpected BII conformer substate population in unoriented hydrated films of the d(CGCGAATTCGCG)2 dodecamer and of native B-DNA from salmon testes

Conformational substates of B-DNA had been observed so far in synthetic oligonucleotides but not in naturally occurring highly polymeric B-DNA. Our low-temperature experiments show that native B-DNA from salmon testes and the d(CGCGAATTCGCG)2 dodecamer have the same BI and BII substates. Nonequilibrium distribution of conformer population was generated by quenching hydrated unoriented films to 200 K, and isothermal structural relaxation toward equilibrium by interconversion of substates was followed by Fourier transform infrared spectroscopy. BI interconverts into BII on isothermal relaxation at 200 K, whereas on slow cooling from ambient temperature, BII interconverts into BI. Our estimation of the dodecamer's BI-to-BII conformer substate population by curve resolution of the symmetrical stretching vibration of the ionic phosphate is 2.4 +/- 0.5 to 1 at 200 K, and it is 1.3 +/- 0.5 to 1 between 270 and 290 K. Pronounced spectral changes upon BI-to-BII interconversion are consistent with base destacking coupled with migration of water from ionic phosphate toward the phosphodiester and sugar moieties. Nonspecific interaction of proteins with the DNA backbone could become specific by induced-fit-type interactions with either BI or BII backbone conformations. This suggests that the BI-to-BII substate interconversion could be a major contributor to the protein recognition process.

Vibrational analysis of phosphorothioate DNA: II. The POS group in the model compound dimethyl phosphorothioate [(CH3O)2(POS)]-

The results of Raman and Infrared (IR) spectroscopic investigations on the vibrational modes of dimethyl phosphorothioate (DMPS) anion, [(CH3O)2(POS)]-, are reported. Ab initio calculations of the vibrational modes, the IR and Raman spectra and the interatomic force constants of DMPS were performed. A normal mode calculation was performed and the results were used to calculate the potential energy distribution for the vibrational modes. This analysis shows that in DMPS the P-S stretching mode has a frequency of about 630 cm-1 and an angle bending mode involving the sulfur atom has a frequency of about 440 cm-1. The proposed vibrational mode assignments will serve as marker bands in the conformational studies of phosphorothioate oligonucleotides which play a central role in the novel antisense therapeutic paradigm.

Stabilization of the B conformation in unoriented films of calf thymus DNA by NaCl: a Raman and IR study

Unoriented films of calf thymus NaDNA with either 3.0 or 5.0 NaCl per base pair were prepared by dehydrating unstressed gels. These films were studied by Raman and ir spectroscopy. The 5.0 samples showed very strong vibrational modes characteristic of the B conformation at relative humidities (RH) as low as 30%, indicating that those samples were entirely in the B conformation. The 3.0 samples showed weaker features: some of the DNA in these samples were in the B conformation at 80% RH while the DNA is essentially in a disordered phase at 30% RH.

Vibrational analysis of nucleic acids. IV. Normal modes of the DNA phosphodiester structure modeled by diethyl phosphate

Raman and ir spectra are reported for diethyl phosphate [(CH3CH2O)2PO2-] and diethyl phosphate isotopomers incorporating carbon-13 at methylene group sites [(CH313CH2O)2PO2-] and deuterium substituents on methyl and methylene carbons [(CH3CD2O)2PO2-, (CD3CH2O)2PO2-, (CD3CD2O)2PO2-]. The vibrational spectra are analyzed to develop a consistent set of assignments for the C-C-O-P(O2-)-O-C-C network, which serves as a model for the nucleic acid phosphodiester backbone. The present study resolves previously conflicting vibrational assignments for the phosphodiester skeleton and provides a firm empirical basis for interpreting conformationally sensitive modes of DNA and RNA. Ab initio vibrational analyses have also been conducted on the above isotopomers of diethyl phosphate in the trans-gauche-gauche-trans conformation, optimized using the 3-21+G* basis set at the restricted Hartree-Fock level. The ab initio calculations are in good agreement with the empirical results, thus strengthening the proposed assignment scheme for Raman and infrared spectra. The present study provides a basis for improvement of empirical force fields utilized in previous normal coordinate analyses of the nucleic acid phosphodiester group.

Vibrational analysis of nucleic acids. V. Force field and conformation-dependent modes of the phosphodiester backbone modeled by diethyl phosphate

A generalized valence force field is derived for the diethyl phosphate anion [(CH3CH2O)2PO2-] and its deuterium [(CH3CD2O)2PO2-, (CD3CH2O)2PO2- and (CD3CD2O)2PO2-] and carbon-13 [(CH3 13CH2O)2PO2-] derivatives in the stable trans-gauche-gauche-trans conformation. Normal coordinate analysis of the trans-gauche-gauche-trans conformer, which serves as a structural analog of the nucleic acid phosphodiester group, is based on comprehensive infrared and Raman spectroscopic data and vibrational assignments obtained for the diethyl phosphate anion. The generalized valence force field is in good agreement with the scaled ab initio force field of diethyl phosphate and represents significant improvement over earlier modeling of the phosphodiester moiety with dimethyl phosphate. The conformational dependence of skeletal C-C-O-P(O2-)-O-C-C stretching vibrations is also explored. Starting with the trans-gauche-gauche-trans conformation, the frequency dependence of skeletal stretching modes has been obtained by stepwise rotation of the torsion angles of the P-O and C-O bonds corresponding to nucleic acid torsions alpha (P-O5'), beta (O5'-C5'), epsilon (C3'-O3'), and zeta (O3'-P). Both symmetric and antisymmetric phosphoester stretching modes are highly sensitive to P-O and C-O torsions, whereas symmetric and antisymmetric phosphodioxy (PO2-) stretching modes are less sensitive. The present results provide an improved structural basis for understanding previously developed empirical correlations between vibrational marker bands and nucleic acid backbone conformation.

Cardiac sarcoplasmic reticulum phosphorylation increases Ca2+ release induced by flash photolysis of nitr-5

Effects on Ca(2+)-induced Ca2+ release due to phosphorylation of sarcoplasmic reticulum (SR) proteins were investigated in isoproterenol-treated saponin-permeabilized trabeculae from rat ventricles. In these experiments, Ca2+ release from the SR was induced by a rapid change in concentration of free Ca2+ (ie, trigger Ca2+) achieved by flash photolysis of nitr-5, and the amount of Ca2+ released was assessed by measuring isometric tension. Ca2+ uptake by the SR was more rapid, and the amount of Ca2+ released by a given concentration of trigger Ca2+ was greater in isoproterenol-treated trabeculae compared with control trabeculae. However, under the same conditions of Ca2+ loading, the amplitudes of caffeine-elicited tension transients in control trabeculae were similar to those in isoproterenol-treated trabeculae, suggesting that the Ca2+ available for release was similar in the two cases. Control experiments showed that there were no significant differences in Ca2+ sensitivity of tension between isoproterenol-treated and control trabeculae. Also, application of alkaline phosphatase to trabeculae that had previously been treated with isoproterenol returned SR Ca2+ release to control levels. We conclude that the greater release of Ca2+ in isoproterenol-treated trabeculae in response to a given concentration of trigger Ca2+ is due to phosphorylation of SR proteins, most likely the Ca2+ release channel.

Normal mode calculation of a netropsin-DNA complex: effect of structural deformation on vibrational spectrum

Calculations of the normal mode spectrum of a netropsin-DNA complex, an isolated DNA helix of the same sequence, and a free netropsin molecule were carried out and compared with observations. We find that the frequency of modes of the complex that are primarily vibrations localized to the helix are relatively unchanged from the frequencies found for similar modes of the isolated helix. On the other hand, the frequencies of thosemodes of the complex that are found to be primarily in the netropsin are found to change significantly in the complex from that of the free netropsin. Further analysis indicates that the changes in the "netropsin modes" are primarily due to the conformational deformation induced in the netropsin by formation of the complex. All the frequencies and shifts in frequency are in good agreement with recent Raman measurements.

Polarized Raman spectra of oriented fibers of A DNA and B DNA: anisotropic and isotropic local Raman tensors of base and backbone vibrations

Polarized Raman spectra of oriented fibers of calf thymus DNA in the A and B conformations have been obtained by use of a Raman microscope operating in the 180 degrees back-scattering geometry. The following polarized Raman intensities in the spectral interval 200-1800 cm-1 were measured with both 514.5 and 488.0 nm laser excitations: (1) Icc, in which the incident and scattered light are polarized parallel to the DNA helical axis (c axis); (2) Ibb, in which the incident and scattered light are polarized perpendicular to c; and (3) Ibc and Icb, in which the incident and scattered light are polarized in mutually perpendicular directions. High degrees of structural homogeneity and unidirectional orientation were confirmed for both the A and B form fibers, as judged by comparison of the observed Raman markers and intensity anisotropies with measurements reported previously for oligonucleotide single crystals of known three-dimensional structures. The fiber Raman anisotropies have been combined with solution Raman depolarization ratios to evaluate the local tensors corresponding to key conformation-sensitive Raman bands of the DNA bases and sugar-phosphate backbone. The present study yields novel vibrational assignments for both A DNA and BDNA conformers and also confirms many previously proposed Raman vibrational assignments. Among the significant new findings are the demonstration of complex patterns of A form and B form indicator bands in the spectral intervals 750-900 and 1050-1100 cm-1, the identification of highly anisotropic tensors corresponding to vibrations of base, deoxyribose, and phosphate moieties, and the determination of relatively isotropic Raman tensors for the symmetrical stretching mode of phosphodioxy groups in A and B DNA. The present fiber results provide a basis for exploitation of polarized Raman spectroscopy to determine DNA helix orientation as well as to probe specific nucleotide residue orientations in nucleoproteins, viruses, and other complex biological assemblies.