Characterisation of DNA methylation status using spectroscopy (mid‐IR versus Raman) with multivariate analysis

Methylation status plays important roles in the regulation of gene expression and significantly influences the dynamics, bending and flexibility of DNA. The aim of this study was to determine whether attenuated total reflection Fourier‐transform infrared (ATR‐FTIR) or Raman spectroscopy with subsequent multivariate analysis could determine methylation patterning in oligonucleotides variously containing 5‐methylcytosine, cytosine and guanine bases. Applied to Low‐E reflective glass slides, 10 independent spectral acquisitions were acquired per oligonucleotide sample. Resultant spectra were baseline‐corrected and vector normalised over the 1750 cm^–1–760 cm^–1 (for ATR‐FTIR spectroscopy) or the 1750 cm^–1–600 cm^–1 (for Raman spectroscopy) regions. Data were then analysed using principal component analysis (PCA) coupled with linear discriminant analysis (LDA). Exploiting this approach, biomolecular signatures enabling sensitive and specific discrimination of methylation patterning were derived. For DNA sequence and methylation analysis, this approach has the potential to be an important tool, especially when material is scarce. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Order and fluidity in the terminal methyl region of dipalmitoyl phosphatidylcholine multibilayers: A comparison of raman and H-NMR spectroscopy

Deuterium magnetic resonance (²H-NMR) and Raman spectroscopy are used to investigate order and fluidity at the terminal methyl position in 16-d₃, 16′-d₃ dipalmitoylphosphatidylcholine (16-d₆ DPPC) multibilayers. These methods reveal substantial motion and disorder in the gel phase, 5–10°C below the gel-liquid crystal phase transition temperature (T_m). The phase transition is sensed in the ²H-NMR spectrum as a reduction in the quadrupole splitting from 14 kHz to 3 kHz. In contrast, the Raman parameter used to characterize the CD₃ vibrations is quite insensitive to the melting process, although an analogous parameter does sense disordering at T_m at the 10 and 10′ position in 10-d₂, 10′-d₂ DPPC. The difference in the response of the NMR and Raman parameters may arise because the vibrational spectrum of the CD₃ group is inhomogenously broadened and is therefore quite sensitive to alterations in the local environment around the methyl group. In contrast, the NMR quadrupole splitting is sensitive to both local motion of the methyl group and, near Tm, to motions of the CD₂ group induced by transgauche isomerizations further up the chain. The difficulties that arise when results from different spectroscopic techniques are compared are demonstrated.     

Vibrational spectroscopy of fossils

Over the last two decades, there has an been increasing interest in applying vibrational spectroscopy in palaeontological research. For example, this chemical analytical technique has been used to elucidate the chemical composition of a wide variety of fossils, including Archaean putative microfossils, stromatolites, chitinozoans, acritarchs, fossil algae, fossil plant cuticles, putative fossil arthropods, conodonts, scolecodonts and dinosaur bones. The insights provided by these data have been equally far ranging: to taxonomically identify a fossil, to determine biogenicity of a putative fossil, to identify preserved biologically synthesized compounds and to elucidate the preservational mechanisms of fossil material. Vibrational spectroscopy has clearly been a useful tool for investigating various palaeontological problems. However, it is also a tool that has been misapplied and misinterpreted, and thus, this review is dedicated to providing a palaeontologist who is new to vibrational spectroscopy with a basic understanding of these techniques, and the types of chemical information that can be obtained. Two example applications of these techniques are discussed in detail, one looking into fossil palynomorph taxonomy and other into the enigmatic Burgess Shale‐type preservation.     

Nonlinear optical spectroscopy of chiral molecules

We review nonlinear optical processes that are specific to chiral molecules in solution and on surfaces. In contrast to conventional natural optical activity phenomena, which depend linearly on the electric field strength of the optical field, we discuss how optical processes that are nonlinear (quadratic, cubic, and quartic) functions of the electromagnetic field strength may probe optically active centers and chiral vibrations. We show that nonlinear techniques open entirely new ways of exploring chirality in chemical and biological systems: The cubic processes give rise to nonlinear circular dichroism and nonlinear optical rotation and make it possible to observe dynamic chiral processes at ultrafast time scales. The quadratic second-harmonic and sum-frequency-generation phenomena and the quartic processes may arise entirely in the electric-dipole approximation and do not require the use of circularly polarized light to detect chirality. They provide surface selectivity and their observables can be relatively much larger than in linear optical activity. These processes also give rise to the generation of light at a new color, and in liquids this frequency conversion only occurs if the solution is optically active. We survey recent chiral nonlinear optical experiments and give examples of their application to problems of biophysical interest.     

Determination of the absolute configurations of synthetic daunorubicin analogues using vibrational circular dichroism spectroscopy and density functional theory

The absolute configurations of three synthesized anthracycline analogues have been determined using vibrational circular dichroism (VCD) spectroscopy and the density functional theory (DFT) calculations. The experimental VCD spectra of the three compounds have been measured for the first time in the film state, prepared from their CDCl₃ solutions. Conformational searches for the monomers and some dimers of the three compounds have been performed at the DFT level using the B3LYP functional and the 6‐311G** and 6‐311++G** basis sets. The corresponding vibrational absorption and VCD spectra have been calculated. The good agreement between the experimental and the calculated spectra allows one to assign the absolute configurations of the three compounds with high confidence. In addition, the dominant conformers of the three compounds have also been identified. Chirality, 2010. © 2010 Wiley‐Liss, Inc.     

Functional near infrared spectroscopy using spatially resolved data to account for tissue scattering: A numerical study and arm‐cuff experiment

Functional Near‐Infrared Spectroscopy (fNIRS) aims to recover changes in tissue optical parameters relating to tissue hemodynamics, to infer functional information in biological tissue. A widely‐used application of fNIRS relies on continuous wave (CW) methodology that utilizes multiple distance measurements on human head for study of brain health. The typical method used is spatially resolved spectroscopy (SRS), which is shown to recover tissue oxygenation index (TOI) based on gradient of light intensity measured between two detectors. However, this methodology does not account for tissue scattering which is often assumed. A new parameter recovery algorithm is developed, which directly recovers both the scattering parameter and scaled chromophore concentrations and hence TOI from the measured gradient of light‐attenuation at multiple wavelengths. It is shown through simulations that in comparison to conventional SRS which estimates cerebral TOI values with an error of ±12.3%, the proposed method provides more accurate estimate of TOI exhibiting an error of ±5.7% without any prior assumptions of tissue scatter, and can be easily implemented within CW fNIRS systems. Using an arm‐cuff experiment, the obtained TOI using the proposed method is shown to provide a higher and more realistic value as compared to utilizing any prior assumptions of tissue scatter.     

Characterisation of Ca- and Al-pectate gels by thermal analysis and FT-IR spectroscopy

Thermal analysis (TG-DTA) and FT-IR spectroscopy have been performed on calcium-pectate membranes to investigate their structure and the consequent variation caused by aluminium sorption. Calcium-polygalacturonate (Ca-PG) membranes, model systems of the soil-root interface, were exposed to aluminium solutions at different concentrations (25-800 microM). Three different pHs (3.50, 4.00 and 4.50) were chosen to study the influence of different aluminium species, such as [Al(H2O)6]3+, [Al(OH)(H2O)5]2+ and [Al(OH)2(H2O)(4)]+, on the structure of the Ca-PG membrane. The DTA profiles and FT-IR spectra showed how aluminium sorption induces structural modifications leading to a reorganisation of the chain aggregates and a weakening of the structure. Higher pH, that is, 4.00 and 4.50, and thus hydrolytic aluminium species and related higher calcium content maintain a more regular structure than at pH 3.50. At pH 3.50, both the effect of [Al(H2O)6]3+ and a major calcium release had a greater impact and thus induced a greater weakening of the structure.     

Low-frequency fourier transform infrared spectroscopy of the oxygen-evolving complex in Photosystem II*

In this communication, we report our progress on the development of low-frequency Fourier transform infrared (FTIR) spectroscopic techniques to study metal-substrate and metal-ligand vibrational modes in the Photosystem II/oxygen-evolving complex (PS II/OEC). This information will provide important structural and mechanistic insight into the OEC. Strong water absorption in the low-frequency region (below 1000 cm⁻¹), a lack of suitable materials, and temperature control problems have limited previous FTIR spectroscopic studies of the OEC to higher frequencies (>1000 cm⁻¹). We have overcome these technical difficulties that have blocked access to the low-frequency region and have developed successive instruments that allow us to move deeper into the low-frequency region (down to 350 cm⁻¹), while increasing both data accumulation efficiency and S/N ratio. We have detected several low-frequency modes in the S₂/S₁spectrum that are specifically associated with these two states. Our results demonstrate the utility of FTIR techniques in accessing low-frequency modes in Photosystem II and in proteins generally. This revised version was published online in June 2006 with corrections to the Cover Date.     

Differentiation of Pectobacterium and Dickeya spp. phytopathogens using infrared spectroscopy and machine learning analysis

Pectobacterium and Dickeya spp. are soft rot Pectobacteriaceae that cause aggressive diseases on agricultural crops leading to substantial economic losses. The accurate, rapid and low‐cost detection of these pathogenic bacteria are very important for controlling their spread, reducing the consequent financial loss and for producing uninfected potato seed tubers for future generations. Currently used methods for the identification of these bacterial pathogens at the strain level are based mainly on molecular techniques, which are expensive. We used an alternative method, infrared spectroscopy, to measure 24 strains of five species of Pectobacterium and Dickeya. Measurements were then analyzed using machine learning methods to differentiate among them at the genus, species and strain levels. Our results show that it is possible to differentiate among different bacterial pathogens with a success rate of ~99% at the genus and species levels and with a success rate of over 94% at the strain level.     

Linear and nonlinear optical effects in biophotonic structures using classical and nonclassical light

In this perspective article, we review the optical study of different biophotonic geometries and biological structures using classical light in linear and nonlinear regime, especially highlighting the link between these morphologies and modern biomedical research. Additionally, the importance of nonlinear optical study in biological research, beyond traditional cell imaging is also highlighted and described. Finally, we present a short introduction regarding nonclassical light and describe the new future perspective of quantum optical study in biology, revealing the link between quantum realm and biological research.      

Temperature-dependent downhill unfolding of ubiquitin. I. Nanosecond-to-millisecond resolved nonlinear infrared spectroscopy

Transient thermal unfolding of ubiquitin is investigated using nonlinear infrared spectroscopy after a nanosecond laser temperature jump (T-jump). The abrupt change in the unfolding free energy surface and the ns time resolution allow us to observe a fast response on ns to micros time-scales, which we attribute to downhill unfolding, before a cross-over to ms kinetics. The downhill unfolding by a sub-population of folded proteins is induced through a shift of the barrier toward the native state. By adjusting the T-jump width, the effect of the initial (T(i)) and final (T(f)) temperature on the unfolding dynamics can be separated. From the amplitude of the fast downhill unfolding, the fractional population prepared at the unfolding transition state is obtained. This population increases with both T(i) and with T(f). A two-state kinetic analysis of the ms refolding provides thermodynamic information about the barrier height. By a combination of the fast and slow unfolding and folding parameters, a quasi-two-state kinetic analysis is performed to calculate the time-dependent population changes of the folded state. This calculation coincides with the experimentally obtained population changes at low temperature but deviations are found in the T-jump from 67 to 78 degrees C. Using temperature-dependent barrier height changes, a temperature Phi value analysis is performed. The result shows a decreasing trend of Phi(T) with temperature, which indicates an increase of the heterogeneity of the transition state. We conclude that ubiquitin unfolds along a well-defined pathway at low temperature which expands with increasing temperature to include multiple routes.     

Determination of absolute configuration using vibrational circular dichroism spectroscopy: the chiral sulfoxide 1-thiochromanone S-oxide

We reexamined the absolute configuration (AC) of the chiral sulfoxide 1-thiochromanone S-oxide (1) using vibrational circular dichroism (VCD) spectroscopy. The VCD spectrum of 1 was analyzed using density functional theory (DFT). DFT predicts two stable conformations of 1, separated by <1 kcal/mole. Their VCD spectra were calculated using the DFT/GIAO methodology. The VCD spectrum predicted for the equilibrium mixture of the two conformations of (S)-1 is in excellent agreement with the experimental spectrum of (+)-1. The AC of 1 is therefore definitively R(-)/S(+).     

Asymmetric lipid bilayer formation stabilized by DNA at the air/water interface

The lipid bis(guanidinium)-tren-cholesterol (BGTC) is a cationic cholesterol derivative bearing guanidinium polar headgroups used for gene transfection either alone or formulated as liposomes with the zwitterionic lipid 1,2-di-[cis-9-octadecenoyl]-sn-glycero-3-phosphoethanolamine (DOPE). Previous investigations have shown its ability to strongly interact with DNA and form asymmetric lipid bilayers at the air/water interface when mixed with DOPE. Here, with a view to further investigate its physicochemical behavior, we studied the interactions of mixtures of BGTC with another zwitterionic lipid, 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine, (DMPC), with DNA at the air/water interface by using the Langmuir monolayer technique coupled with Brewster Angle Microscopy (BAM) and Polarization Modulation Infra Red Reflexion Absorption (PMIRRAS) spectroscopy and we investigate DNA–BGTC/DMPC interactions. We demonstrate that when DNA is injected into the subphase in excess compared to the positive charges of BGTC, it adsorbs to BGTC/DMPC monolayers at 20 mN/m whatever the lipid monolayer composition (1/5, 2/3 or 3/2 BGTC/DMPC molar ratio) and forms an incomplete monolayer of either isotropic or anisotropic double strands depending on the BGTC content in the monolayer. Compression beyond the collapse of some mixed DNA–BGTC/DMPC (2/3 and 3/2 molar ratio) systems leads to the formation of DNA monolayers underneath asymmetric lipid bilayers characterized by a bottom layer of BGTC in contact with DNA and a top layer mainly constituted of DMPC.     

Age-grading the biting midge Culicoides sonorensis using near-infrared spectroscopy

Age-grading of insects is important in the control and monitoring of both insect populations and vector-borne diseases. Microscopy and morphological techniques exist to age-grade most blood-feeding flies, but these techniques are laborious, often destructive to the insects, and slow. Near-infrared spectroscopy (NIRS) can be automated and is a non-destructive technique for age-grading. We applied NIRS techniques to age-grade females of the biting midge, Culicoides sonorensis Wirth & Jones (Diptera: Ceratopogonidae), the vector of bluetongue and other arboviruses in North America. Female flies of five known age cohorts (1, 3, 6, 9 and 12 days post-emergence) from three laboratory colonies were used. The data indicate that NIRS can be used to differentiate age groups of C. sonorensis .     

DNA-probes for the highly sensitive identification of single nucleotide polymorphism using single-molecule spectroscopy

This article presents a new, highly sensitive method for the identification of single nucleotide polymorphisms (SNPs) in homogeneous solutions using fluorescently labeled hairpin-structured oligonucleotides (smart probes) and fluorescence single-molecule spectroscopy. While the hairpin probe is closed, fluorescence intensity is quenched due to close contact between the chromophore and several guanosine residues. Upon hybridization to the respective target SNP sequence, contact is lost and the fluorescence intensity increases significantly. High specificity is achieved by blocking sequences containing mismatch with unlabeled oligonucleotides. Time-resolved single-molecule fluorescence spectroscopy enables the detection of individual smart probes passing a small detection volume. This method leads to a subnanomolar sensitivity for this single nucleotide specific DNA assay technique.     

Detection of phenolic compounds using impedance spectroscopy measurements

Langmuir-Blodgett (LB) and layer-by-layer films (LbL) of a PPV (p-phenylenevinylene) derivative, an azo compound and tetrasulfonated phthalocyanines were successfully employed as transducers in an “electronic tongue” system for detecting trace levels of phenolic compounds in water. The choice of the materials was based on their distinct electrical natures, which enabled the array to establish a fingerprint of very similar liquids. Impedance spectroscopy measurements were taken in the frequency range from 10 Hz to 1 MHz, with the data analysed with principal component analysis (PCA). The sensing units were obtained from five-layer LB films of (poly[(2-methoxy-5-n-hexyloxy)-p-phenylenevinylene]), OC₁OC₁₈-PPV (poly(2-methoxy,5-(n-octadecyl)-p-phenylenevinylene)), DR (HEMA-co-DR13MA (poly-(hydroxyethylmethacrylate-co-[4′-[[2-(methacryloyloxy)-ethyl]ethylamino]-2-chloro-4-nitroazobenzene]))) and five-bilayer LbL films of tetrasulfonated metallic phthalocyanines deposited onto gold interdigitated electrodes. The sensors were immersed into phenol, 2-chloro-4-methoxyphenol, 2-chlorophenol and 3-chlorophenol (isomers) solutions at 1 × 10⁻⁹ mol L⁻¹, with control experiments carried out in ultra pure water. Samples could be distinguished if the principal component analysis (PCA) plots were made with capacitance values taken at 10³ Hz, which is promising for detection of trace amounts of phenolic pollutants in natural water.     

FTIR spectroscopy of primary donor photooxidation in Photosystem I, Heliobacillus mobilis, and Chlorobium limicola. Comparison with purple bacteria

The photooxidation of the primary electron donor in several Photosystem I-related organisms (Synechocystis sp. PCC 6803, Heliobacillus mobilis, and Chlorobium limicola f. sp. thiosulphatophilum) has been studied by light-induced FTIR difference spectroscopy at 100 K in the 4000 to 1200 cm^–1 spectral range. The data are compared to the well-characterized FTIR difference spectra of the photooxidation of the primary donor P in Rhodobacter sphaeroides (both wild type and the heterodimer mutant HL M202) in order to get information on the charge localization and the extent of coupling within the (bacterio)chlorophylls constituting the oxidized primary donors. In Rb. sphaeroides RC, four marker bands mostly related to the dimeric nature of the oxidized primary donor have been previously observed at 2600, 1550, 1480, and 1295 cm^–1. The high-frequency band has been shown to correspond to an electronic transition (Breton et al. (1992) Biochemistry 31: 7503–7510) while the three other marker bands have been described as phase-phonon bands (Reimers and Hush (1995) Chem Phys 197: 323–332). The absence of these bands in PS I as well as in the heterodimer HL M202 demonstrates that in P700⁺ the charge is essentially localized on a single chlorophyll molecule. For both H. mobilis and C. limicola, the presence of a high-frequency band at 2050 and 2450 cm^–1, respectively, and of phase-phonon bands (at 1535 and 1300 cm^–1 in H. mobilis, at 1465 and 1280 cm^-1 in C. limicola) indicate that the positive charge in the photooxidized primary donor is shared between two coupled BChls. The structure of P840⁺ in C. limicola, in terms of the resonance interactions between the two BChl a molecules constituting the oxidized primary donor, is close to that of P⁺ in purple bacteria reaction centers while for H. mobilis the FTIR data are interpreted in terms of a weaker coupling of the two bacteriochlorophylls.Abbreviations (B)Chl (bacterio)chlorophyll - BPhe bacteriopheophytin - C. Chlorobium - FTIR Fourier transform infrared - H. Heliobacillus - PS I, PS II Photosystem I, Photosystem II - P primary electron donor - RC reaction center - Rb. Rhodobacter - Rp. Rhodopseudomonas - Q_A primary quinone acceptor - Wt wild type