Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy

Investigating antibody interactions with a polar liquid using terahertz pulsed spectroscopy

In this article, we use terahertz spectroscopy to study the dielectric properties of the peroxidase-conjugated affinity purified goat anti-cat immunoglobulin G and the fluorescein-conjugated affinity purified goat anti-cat immunoglobulin G when they interact with polar liquids. The influence of protein concentration, as well as presence of glycerol as a cosolvent, is determined by estimation of the effective hydration shell radius of the protein in solution. The dielectric spectra in this study are measured over the frequency range 0.1-1.3 THz and it is found that the dielectric properties are dependent on the type of the charges in the hydrogen-bonded antibodies' networks. Our results indicate that the terahertz dielectric properties of polar liquids are strongly affected by the presence of the antibody and suggest that the dielectric spectrum is particularly powerful in the study of structural and conformational properties of proteins. Therefore, terahertz spectroscopy is a very sensitive approach to investigate structural features of biological systems.

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

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

Improved detection sensitivity of D-mannitol crystalline phase content using differential spectral phase shift terahertz spectroscopy measurements

We report quantitative measurement of the relative proportion of δ- and β-D-mannitol crystalline phases inserted into polyethylene powder pellets, obtained by time-domain terahertz spectroscopy. Nine absorption bands have been identified from 0.2 THz to 2.2 THz. The best quantification of the δ-phase proportion is made using the 1.01 THz absorption band. Coherent detection allows using the spectral phase shift of the transmitted THz waveform to improve the detection sensitivity of the relative δ-phase proportion. We argue that differential phase shift measurements are less sensitive to samples' defects. Using a linear phase shift compensation for pellets of slightly different thicknesses, we were able to distinguish a 0.5% variation in δ-phase proportion.

Mammalian stem cells reprogramming in response to terahertz radiation

We report that extended exposure to broad-spectrum terahertz radiation results in specific changes in cellular functions that are closely related to DNA-directed gene transcription. Our gene chip survey of gene expression shows that whereas 89% of the protein coding genes in mouse stem cells do not respond to the applied terahertz radiation, certain genes are activated, while other are repressed. RT-PCR experiments with selected gene probes corresponding to transcripts in the three groups of genes detail the gene specific effect. The response was not only gene specific but also irradiation conditions dependent. Our findings suggest that the applied terahertz irradiation accelerates cell differentiation toward adipose phenotype by activating the transcription factor peroxisome proliferator-activated receptor gamma (PPARG). Finally, our molecular dynamics computer simulations indicate that the local breathing dynamics of the PPARG promoter DNA coincides with the gene specific response to the THz radiation. We propose that THz radiation is a potential tool for cellular reprogramming.

Application of terahertz time-domain spectroscopy in intracellular metabolite detection

Using terahertz time-domain spectroscopy (THz-TDS), we have investigated the THz spectra of astaxanthin and riboflavin and the spectra of two kinds of cell, haenatcoccus plusivalis and bacillus subtilis, which could produce astaxanthin and riboflavin, respectively, during their metabolite process. Riboflavin was found to be much more absorptive to THz radiation and have richer spectral characteristics than astaxanthin. As an intracellular metabolite, riboflavin could be distinguished from the cells by using THz-TDS. The technique has potential applications in high-throughput screening of industrial strains.

Dielectric properties of fully hydrated nucleotides in the terahertz frequency range

We use terahertz time domain spectroscopy (THz-TDS) to determine the complex frequency-dependent dielectric response of all four nucleotides at different dilute concentrations. In addition, the suspension model's ability to extract the dielectric response of just the nucleotide with the hydration shell epsilon(b) excluding the dielectric information relating to the bulk will be verified. The suspension model enables us to make the determination that the nucleotides have influences on the water molecules out to the fourth hydration shell. We use a two Debye relaxation fit model for water, all concentrations and all epsilon(b) values. We observed how the nucleotides affect the relaxation parameters in relation to that of pure bulk water. With this information, we notice a transition between purines and pyrimidines, where one is a hydrogen-bond network structure building type material with a low concentration increment and the other is a structure breaking type material with a low concentration decrement. Due to conductivity measurements, we determine that kinetic depolarization is a negligible affect compared to that of dielectric saturation, which we find to dominate where a decrement is found.

Modeling terahertz heating effects on water

We apply Kirchhoff's heat equation to model the influence of a CW terahertz beam on a sample of water, which is assumed to be static. We develop a generalized model, which easily can be applied to other liquids and solids by changing the material constants. If the terahertz light source is focused down to a spot with a diameter of 0.5 mm, we find that the steady-state temperature increase per milliwatt of transmitted power is 1.8?C/mW. A quantum cascade laser can produce a CW beam in the order of several milliwatts and this motivates the need to estimate the effect of beam power on the sample temperature. For THz time domain systems, we indicate how to use our model as a worst-case approximation based on the beam average power. It turns out that THz pulses created from photoconductive antennas give a negligible increase in temperature. As biotissue contains a high water content, this leads to a discussion of worst-case predictions for THz heating of the human body in order to motivate future detailed study. An open source Matlab implementation of our model is freely available for use at www.eleceng.adelaide.edu.au/thz.

Terahertz pulsed spectroscopy and imaging in the pharmaceutical setting - a review

Terahertz pulsed spectroscopy (TPS) and terahertz pulsed imaging (TPI) are two novel techniques for the physical characterization of pharmaceutical drug materials and final solid dosage forms, utilizing spectral information in the far infrared region of the electromagnetic spectrum. This review focuses on the development and performance of pharmaceutical applications of terahertz technology compared with other tools for physical characterization. TPS can be used to characterize crystalline properties of drugs and excipients. Different polymorphic forms of a drug can be readily distinguished and quantified. Recent developments towards a better understanding of the fundamental theory behind spectroscopy in the far infrared have been discussed. Applications for TPI include the measurement of coating thickness and uniformity in coated pharmaceutical tablets, structural imaging and 3D chemical imaging of solid dosage forms.

DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation

We assess the role of DNA breathing dynamics as a determinant of promoter strength and transcription start site (TSS) location. We compare DNA Langevin dynamic profiles of representative gene promoters, calculated with the extended non-linear PBD model of DNA with experimental data on transcription factor binding and transcriptional activity. Our results demonstrate that DNA dynamic activity at the TSS can be suppressed by mutations that do not affect basal transcription factor binding–DNA contacts. We use this effect to establish the separate contributions of transcription factor binding and DNA dynamics to transcriptional activity. Our results argue against a purely ‘transcription factor-centric’ view of transcription initiation, suggesting that both DNA dynamics and transcription factor binding are necessary conditions for transcription initiation.

Accurate determination of optical coefficients from chemical samples using terahertz time-domain spectroscopy and effective medium theory

A technique for calculating the optical constants of powdered materials that have been pressed into pellets along with a diluent such as polyethylene, as is commonly used in the spectroscopy community, is introduced. The simple Beer-Lambert law typically used to calculate the optical constants has the inherent weakness that it treats the absorbing medium as a single nonporous solid, as opposed to a dielectric material embedded within a medium. This leads to a systematic underestimation of both the absorption coefficient and the refractive index, especially at low filling factors. Effective medium theory provides a way to calculate more accurate optical constants and produces similar optical constants across a wide range of filling factors, including crucially at the low filling factors commonly used experimentally. The technique can also be extended to estimate the porosity of the samples and provide a true, preparation-independent value for the optical properties of the sample material.

Terahertz time-domain spectroscopy as a tool to monitor the glass transition in polymers

We demonstrate the suitability of terahertz time-domain spectroscopy as a non-destructive, contact-free tool to monitor the glass transition in polymers--a core feature of the amorphous phase. Below the glass transition temperature T(g), segmental motions along the polymer chain are frozen due to the lack of free volume between neighboring macromolecules. We show that this transition also reflects in the temperature dependence of the refractive index at terahertz frequencies. Two domains can be identified, which differ in their sensitivity to temperature changes. To verify the proposed approach, we determine the glass transition temperature T(g) of semi-crystalline poly(oxymethylene) (POM) with terahertz time-domain spectroscopy and validate the results by destructive differential scanning calorimetry (DSC) measurements.

Dielectric and dielectrophoretic properties of DNA

The physical properties of DNA are quite important for molecular genetics as well as for its nanotechnological applications. Studying the interactions of alternating current (AC) electric fields with deoxyribonucleic acid (DNA) allows one to draw conclusions about these properties. These interactions are usually investigated in two different ways. In dielectric spectroscopy, a DNA solution is placed in a homogeneous AC field and electronic parameters are measured over several frequency decades in the Hz to GHz range. These electronic data are then interpreted on the basis of physico-chemical models as a result of certain phenomena on the molecular level. In dielectrophoretic studies, a DNA solution is exposed to an inhomogeneous AC field and the spatial response of few or single molecules is monitored by optical or scanning force microscopy. This response can involve translation, elongation and orientation of the molecular strings. In this review, a survey is given of the literature dealing with the dielectric and dielectrophoretic properties of DNA as well as with applications of DNA dielectrophoresis.

Terahertz pulsed spectroscopy of freshly excised human breast cancer

The complex refractive indices of freshly excised healthy breast tissue and breast cancers collected from 20 patients were measured in the range of 0.15 - 2.0 THz using a portable terahertz pulsed transmission spectrometer. Histology was performed to classify the tissue samples as healthy adipose tissue, healthy fibrous breast tissue, or breast cancers. The average complex refractive index was determined for each group and it was found that samples containing cancer had a higher refractive index and absorption coefficient. The terahertz properties of the tissues were also used to simulate the impulse response functions expected when imaging breast tissue in a reflection geometry as in terahertz pulsed imaging (TPI). Our results indicate that both TPS and TPI can be used to distinguish between healthy adipose breast tissue, healthy fibrous breast tissue and breast cancer due to the differences in the fundamental optical properties.

Terahertz spectroscopic differentiation of microstructures in protein gels

We demonstrate that terahertz (THz) spectroscopy can be used to differentiate soft protein microstructures. Differentiation of soft microstructures in gels has to date been performed using optical imaging techniques (e.g. electron microscope), but a non-destructive differentiation tool is lacking. Particulate and fine-stranded (fibrillar) soft protein microstructures are of interest, particularly to medical researchers, because they form from naturally occurring proteins that are thought to be involved in several human diseases, such as Alzheimer's disease. In this study, globular beta-lactoglobulin structures with diameters of 2 microm, and fibrillar structures with diameters less than 0.03 microm are observed between 0.8 and 1.5 THz. Results show that the globular structures have a decline in THz transmission when compared to the fibrillar ones. The cause of this decline is possibly due to Rayleigh scattering from the globular microstructures.

Improved sample characterization in terahertz reflection imaging and spectroscopy

For imaging applications involving biological subjects, the strong attenuation of terahertz radiation by water means that terahertz pulsed imaging is most likely to be successfully implemented in a reflection geometry. Many terahertz reflection geometry systems have a window onto which the sample is placed - this window may introduce unwanted reflections which interfere with the reflection of interest from the sample. In this paper we derive a new approach to account for the effects of these reflections and illustrate its success with improved calculations of sample optical properties.

Continuous wave terahertz spectrometer as a noncontact thickness measuring device

We present a low cost terahertz (THz) spectrometer with coherent detection based on two simple and robust dipole antennas driven by two laser diodes. The spectrometer covers frequencies up to 1 THz, with a peak signal-to-noise ratio exceeding 40 dB for a lock-in integration time of 30 ms. We demonstrate that the thickness profile of a sample can be reconstructed from an acquired THz image.

Analytical terahertz spectroscopy

Recent progress in analytical terahertz (THz) spectroscopy is reviewed with illustrative examples showing that it is an effective method for detecting and identifying intermolecular interactions in chemical compounds, such as hydrogen bonds. The unique and characteristic properties of THz waves, their significance to both science and industry, and the bases of one of the successful fields of analytical THz spectroscopy, namely THz time-domain spectroscopy and THz imaging for chemical analysis, are described. Preliminary quantitative studies are presented to show the potential of THz spectroscopy for the detection and identification of intermolecular hydrogen bonds in unknown mixture samples. The selective detection of intramolecular hydrogen bonds and the detection of intramolecular interactions in ice are also introduced. Some brief remarks are provided on future developments, the main issues, and the prospects for analytical THz spectroscopy.

Perspectives in the use of spectroscopy to characterise pharmaceutical solids

Knowledge of the solid-state properties is one of the key issues in understanding the performance of drugs. Recent developments in spectroscopic techniques have made them popular tools for solid phase analysis; they are fast, accurate and suitable for real-time measurements during processing, and further, they can be used to obtain structural understanding of solid forms, for example, by the use of multivariate analysis and computational chemistry. In this article emerging topics related to spectroscopic analysis of pharmaceutical solids are reviewed. The following areas are highlighted: (1) the importance of multivariate methods in the analysis of solid forms when using spectroscopic techniques, (2) spectroscopic analysis of processing-induced solid phase transformations in the manufacturing setting, (3) novel spectroscopic techniques and pharmaceutical examples of their use, and (4) the advantages and the use of computational simulation of vibrational spectra. The topics listed are thought to be of the foremost importance in improving the understanding of pharmaceutical materials, processes and formulations.

Applications of terahertz spectroscopy in biosystems

Terahertz (THz) spectroscopic investigations of condensed-phase biological samples are reviewed ranging from the simple crystalline forms of amino acids, carbohydrates and polypeptides to the more complex aqueous forms of small proteins, DNA and RNA. Vibrationally resolved studies of crystalline samples have revealed the exquisite sensitivity of THz modes to crystalline order, temperature, conformational form, peptide sequence and local solvate environment and have given unprecedented measures of the binding force constants and anharmonic character of the force fields, properties necessary to improve predictability but not readily obtainable using any other method. These studies have provided benchmark vibrational data on extended periodic structures for direct comparisons with classical (CHARMm) and quantum chemical (density functional theory) theories. For the larger amorphous and/or aqueous phase samples, the THz modes form a continuum-like absorption that arises because of the full accessibility to conformational space and/or the rapid time scale for inter-conversion in these environments. Despite severe absorption by liquid water, detailed investigations have uncovered the photo- and hydration-induced conformational flexibility of proteins, the solvent shell depth of the water/biomolecule boundary layers and the solvent reorientation dynamics occurring in these interfacial layers that occur on sub-picosecond time scales. As such, THz spectroscopy has enhanced and extended the accessibility to intermolecular forces, length- and timescales important in biological structure and activity.

High-resolution waveguide THz spectroscopy of biological molecules

Low-frequency vibrational modes of biological molecules consist of intramolecular modes, which are dependent on the molecule as a whole, as well as intermolecular modes, which arise from hydrogen-bonding interactions and van der Waals forces. Vibrational modes thus contain important information about conformation dynamics of biological molecules, and can also be used for identification purposes. However, conventional Fourier transform infrared spectroscopy and terahertz time-domain spectroscopy (THz-TDS) often result in broad, overlapping features that are difficult to distinguish. The technique of waveguide THz-TDS has been recently developed, resulting in sharper features. For this technique, an ordered polycrystalline film of the molecule is formed on a metal sample plate. This plate is incorporated into a metal parallel-plate waveguide and probed via waveguide THz-TDS. The planar order of the film reduces the inhomogeneous broadening, and cooling of the samples to 77K reduces the homogenous broadening. This combination results in the line-narrowing of THz vibrational modes, in some cases to an unprecedented degree. Here, this technique has been demonstrated with seven small biological molecules, thymine, deoxycytidine, adenosine, D-glucose, tryptophan, glycine, and L-alanine. The successful demonstration of this technique shows the possibilities and promise for future studies of internal vibrational modes of large biological molecules.

Terahertz time-domain spectra of aromatic carboxylic acids incorporated in nano-sized pores of mesoporous silicate

Terahertz time-domain spectroscopy (THz-TDS) is used to study the intra- and intermolecular vibrational modes of aromatic carboxylic acids, for example, o-phthalic acid, benzoic acid, and salicylic acid, which form either intra- or intermolecular hydrogen bond(s) in different ways. Incorporating the target molecules in nano-sized spaces in mesoporous silicate (SBA-16) is found to be effective for the separate detection of intramolecular hydrogen bonding modes and intermolecular modes. The results are supported by an analysis of the differences in the peak shifts, which depend on temperature, caused by the different nature of the THz absorption. Raman spectra revealed that incorporating the molecules in the nano-sized pores of SBA-16 slightly changes the molecular structures. In the future, THz-TDS using nanoporous materials will be used to analyze the intra- and intermolecular vibrational modes of molecules with larger hydrogen bonding networks such as proteins or DNA.

The guanidine hydrochloride-induced denaturation of CP43 and CP47 studied by terahertz time-domain spectroscopy

Terahertz time-domain spectroscopy (THz-TDS) is a new technique in studying the conformational state of a molecule in recent years. In this work, we reported the first use of THz-TDS to examine the denaturation of two photosynthesis membrane proteins: CP43 and CP47. THz-TDS was proven to be useful in discriminating the different conformational states of given proteins with similar structure and in monitoring the denaturation process of proteins. Upon treatment with guanidine hydrochloride (GuHCl), a 1.8 THz peak appeared for CP47 and free chlorophyll a (Chl a). This peak was deemed to originate from the interaction between Chl a and GuHCl molecules. The Chl a molecules in CP47 interacted with GuHCl more easily than those in CP43.

Sensing minute changes in biological cell monolayers with THz differential time-domain spectroscopy

We used terahertz differential time-domain spectroscopy (THz-DTDS) to measure minute changes of bovine lung microvessel endothelial cells (BLMVEC) in response to vascular endothelial growth factor (VEGF). These changes were reflected by alterations in THz wave attenuations and THz dielectric properties of the treated cells. The VEGF-induced THz attenuations of cell monolayers correlated well with changes in transendothelial resistance, as measured using electric cell-substrate impedance sensing (ECIS). However, the morphological differences that gave rise to these changes were not observed with standard optical phase contrast microscopy. We conclude that THz-DTDS is a highly sensitive, non-invasive, powerful new tool to measure minute changes in the morphology of live, cultured cell monolayers. This method enables spectroscopic investigations of cells in the THz band, providing information unavailable through other conventional methods such as optical phase contrast microscopy and ECIS.

Analysis of the inter-molecular interactions between amino acids and acetone by THz spectroscopy

The THz spectra of amino acids after application of spots of acetone were measured. The 0.6 THz band was commonly observed in many amino acids that formed the intra-molecular salt structure. The band can be attributed to the interaction vibration from the common structural configuration of amino acids and acetone molecules. The evidence suggests that the vibration between the amino acids with intra-molecular salt structure and acetone has a peak at 0.6 THz. A model of the interaction vibration of acetone and the functional groups of amino acids is proposed.

Terahertz time-domain spectroscopy of four hydroxycinnamic acid derivatives

The well-resolved absorption spectra of the hydroxycinnamic acid (HCA) derivatives, caffeic acid, ferulic acid, sinapic acid and chlorogenic acid, were measured over the frequency region from 0.3 to 2.0 THz at 294 K with terahertz time-domain spectroscopy (THz-TDS). Theoretical calculation was applied to assist the analysis and assignment of the individual THz absorption spectra of the HCA derivatives with density functional theory (DFT). The distinctive spectral features were originated from the collective motion of molecules held together by hydrogen bonds. The real and imaginary parts of dielectric function of the four HCA derivatives were also obtained.

Collective Dynamics of Lysozyme in Water: Terahertz Absorption Spectroscopy and Comparison with Theory

To directly measure the low-frequency vibrational modes of proteins in biologically relevant water environment rather than previously explored dry or slightly hydrated phase, we have developed a broadband terahertz spectrometer suitable for strongly attenuating protein solutions. Radiation is provided by harmonic multipliers (up to 0.21 THz), a Gunn oscillator (at 0.139 THz), and the UCSB free-electron lasers (up to 4.8 THz). Our spectrometer combines these intense sources with a sensitive cryogenic detector and a variable path length sample cell to detect radiation after it is attenuated by more than 7 orders of magnitudes by the aqueous sample. Using this spectrometer, we have measured the molar extinction of solvated lysozyme between 0.075 and 3.72 THz (2.5-124 cm(-1)), and we made direct comparison to several published theoretical models based on molecular dynamics simulations and normal-mode analysis. We confirm the existence of dense, overlapping normal modes in the terahertz frequency range. Our observed spectrum, while in rough qualitative agreement with these models, differs in detail. Further, we observe a low-frequency cutoff in terahertz dynamics between 0.2 and 0.3 THz, and we see no evidence of a predicted normal mode at approximately 0.09 THz for the protein.

Terahertz pulsed spectroscopy of human Basal cell carcinoma

Good contrast is seen between normal tissue and regions of tumor in terahertz pulsed imaging of basal cell carcinoma (BCC). To date, the source of contrast at terahertz frequencies is not well understood. In this paper we present results of a spectroscopy study comparing the terahertz properties (absorption coefficient and refractive index) of excised normal human skin and BCC. Both the absorption coefficient and refractive index were higher for skin that contained BCC. The difference was statistically significant over the range 0.2 to 2.0 THz (6.6 cm(-1) to 66.6 cm(-1)) for absorption coefficient and 0.25 to 0.90 THz (8.3 cm(-1) to 30 cm(-1)) for refractive index. The maximum difference for absorption was at 0.5 THz(16.7 cm(-1)). These changes are consistent with higher water content. These results account for the contrast seen in terahertz images of BCC and explain why parameters relating to the reflected terahertz pulse provide information about the lateral spread of the tumor. Knowing the properties of the tissue over the terahertz frequency range will enable the use of mathematical models to improve understanding of the terahertz response of normal and diseased tissue.

Angle-Dependent Terahertz Time-Domain Spectroscopy of Amino Acid Single Crystals

The measurement of absorption spectra using angle-dependent terahertz (THz) time-domain spectroscopy for amino acid single crystals of l-cysteine and l-histidine is reported for the first time. Linearly polarized THz radiation enables us to observe angle-dependent far-infrared absorption spectra of amino acid single crystals and determine the direction of the oscillating dipole of the molecules in the 20-100 cm(-1) range. By comparing the THz spectra of a single crystal and powder, we found that there was a clear hydrogen-bond peak in the crystal spectrum as a result of the larger hydrogen-bond network. The low-temperature THz spectra of amino acid microcrystals showed more intermolecular vibrational modes than those measured at room temperature. An ab initio frequency calculation of a single amino acid molecule was used to predict the intramolecular vibrational modes. The validity of the calculation models was confirmed by comparing the results with experimentally obtained data in the Raman spectral region.

Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy

Biological polymers are expected to exhibit functionally relevant, global, and subglobal collective modes in the terahertz (THz) frequency range (i.e., picosecond timescale). In an effort to monitor these collective motions, we have experimentally determined the absorption spectrum of solvated bovine serum albumin (BSA) from 0.3 to 3.72 THz (10-124 cm(-1)). We successfully extract the terahertz molar absorption of the solvated BSA from the much stronger attenuation of water and observe in the solvated protein a dense, overlapping spectrum of vibrational modes that increases monotonically with increasing frequency. We see no evidence of distinct, strong, spectral features, suggesting that no specific collective vibrations dominate the protein's spectrum of motions, consistent with the predictions of molecular dynamics simulations and normal mode analyses of a range of small proteins. The shape of the observed spectrum resembles the ideal quadratic spectral density expected for a disordered ionic solid, indicating that the terahertz normal mode density of the solvated BSA may be modeled, to first order, as that of a three-dimensional elastic nanoparticle with an aperiodic charge distribution. Nevertheless, there are important detailed departures from that of a disordered inorganic solid or the normal mode densities predicted for several smaller proteins. These departures are presumably the spectral features arising from the unique molecular details of the solvated BSA. The techniques used here and measurements have the potential to experimentally confront theoretical calculations on a frequency scale that is important for macromolecular motions in a biologically relevant water environment.