Tatiana Globus

THz-Spectroscopy of Biological Molecules.

The terahertz frequency absorption spectraof DNA molecules reflect low-frequencyinternal helical vibrations involvingrigidly bound subgroups that are connectedby the weakest bonds, including thehydrogen bonds of the DNA base pairs,and/or non-bonded interactions. Althoughnumerous difficulties make the directidentification of terahertz phonon modes inbiological materials very challenging, ourresearch has shown that such measurementsare both possible and fruitful. Spectra ofdifferent DNA samples reveal a large numberof modes and a reasonable level ofsequence-specific uniqueness. In an attemptto show that the long wavelength absorptionfeatures are intrinsic properties ofbiological materials determined by phononmodes, a normal mode analysis has been usedto predict the absorption spectra ofpolynucleotide RNA Poly[G]-Poly[C]. Directcomparison demonstrated a correlationbetween calculated and experimentallyobserved spectra of the RNA polymers, thusconfirming that the fundamental physicalnature of the observed resonance structureis caused by the internal vibration modesin the macromolecules.In this work we demonstrate results fromFourier-Transform Infrared (FTIR)spectroscopy of DNA macromolecules andrelated biological materials in theterahertz frequency range. Carefulattention was paid to the possibility ofinterference or etalon effects in thesamples, and phenomena were clearlydifferentiated from the actual phononmodes. In addition, we studied thedependence of transmission spectra ofaligned DNA and polynucleotide film sampleson molecule orientation relative to theelectromagnetic field, showing the expectedchange in mode strength as a function ofsample orientation. Further, the absorptioncharacteristics were extracted from thetransmission data using the interferencespectroscopy technique, and a stronganisotropy of terahertz characteristics wasdemonstrated.

Terahertz Fourier transform characterization of biological materials in a liquid phase

Significant progress has been achieved during the last several years relating to experimental and theoretical aspects of terahertz (or submillimetre wave) Fourier transform spectroscopy of biological macromolecules. However, previous research in this spectral range has been focused on bio-materials in solid state since it was common opinion that high water absorption will obscure the spectral signatures of the bio-molecules in solutions. At the same time, the biological functions of DNA and proteins take place in water solutions. In this work, the spectra of DNA samples have been measured in liquid phase (gel) over the spectral range 10–25 cm−1 and compared with spectra obtained from solid films. The results demonstrate that there is very little interference between the spectral features of the material under test and the water background except for the band around 18.6 cm−1. Multiple resonances due to low frequency vibrational modes within biological macromolecules in solutions are unambiguously demonstrated. Higher level of sensitivity and higher sharpness of vibrational modes are observed in the liquid environment in comparison with the solid phase, with the width of spectral lines 0.3–0.5 cm−1. Gel sample spectra are found to be polarization-dependent. The ability of THz spectroscopy to characterize samples in liquid phase could be very important since it permits examination of DNA interactions in real (wet) samples. One demonstrated example of practical importance is the ability to discriminate between spectral patterns for native and denaturated DNA.

Terahertz sources and detectors and their application to biological sensing

Terahertz spectroscopy has long been used as an important measurement tool in fields such as radio astronomy, physical chemistry, atmospheric studies and plasma research. More recently terahertz technology has been used to develop an exciting new technique to investigate the properties of a wide range of biological materials. Although much research remains before a full understanding of the interaction between biomaterials and terahertz radiation is developed, these initial studies have created a compelling case for further scientific study. Also, the potential development of practical tools to detect and identify biological materials such as biological–warfare agents and food contaminants, or of medical diagnostic tools, is driving the need for improved terahertz technology. In particular, improved terahertz sources and detectors that can be used in practical spectroscopy systems are needed. This paper overviews some of the recent measurements of the terahertz spectra of biomaterials and the ongoing efforts to create an all–solid–state technology suitable not only for improved scientific experiments but also for military and commercial applications.

Submillimeter-wave Fourier transform spectroscopy of biological macromolecules

In this article we report experimental results on Fourier-transform infrared spectroscopy of deoxyribonucleic acid (DNA) macromolecules and related biological materials in the submillimeter range (i.e., ∼10–500 cm−1). Film samples made from commercial DNA fibers, polyadenylic acid potassium salt, and cellular agents such as the spore form of Bacillus subtillis have been prepared and measured. A broad series of measurements carried out in the low frequency region (10–50 cm−1) with a higher resolution of 0.2 cm−1 revealed fine features—multiple dielectric resonances in the submillimeter-wave spectra obtained from DNA samples. These long-wave absorption features are shown to be intrinsic properties of biological materials determined by phonon modes. The emphasis is on reproducibility of experimental spectra and on receiving reliable results. The effects of differences in sample preparation, including sample geometry, orientation, and aging are studied and separated from the phonon effects that determine the ...

Sub-millimetre wave absorption spectra of artificial RNA molecules

We demonstrate submillimetre-wave Fourier transform spectroscopy as a novel technique for biological molecule characterization. Transmission measurements are reported at frequencies 10–25 cm−1 for single- and double-stranded RNA molecules of known base-pair sequences: homopolymers poly[A], poly[U], poly[C] and poly[G], and double-stranded homopolymers poly[A]–poly[U] and poly[C]–poly[G]. Multiple resonances are observed (i.e. in the microwave through terahertz frequency regime). We also present a computational method to predict the low-frequency absorption spectra of short artificial DNA and RNA. Theoretical conformational analysis of molecules was utilized to derive the low-frequency vibrational modes. Oscillator strengths were calculated for all the vibrational modes in order to evaluate their weight in the absorption spectrum of a molecule. Normal modes and absorption spectra of the double-stranded RNA chain poly[C]–poly[G] were calculated. The absorption spectra extracted from the experiment were directly compared with the results of computer modelling thereby, confirming the fact that observed spectral features result from electromagnetic wave interactions with the DNA and RNA macromolecules. Correlation between experimental spectrum and modelling results demonstrates the ability of normal mode analysis to reproduce RNA vibrational spectra.

THZ-FREQUENCY SPECTROSCOPIC SENSING OF DNA AND RELATED BIOLOGICAL MATERIALS

The terahertz frequency absorption spectra of DNA molecules reflect low-frequency internal helical vibrations involving rigidly bound subgroups that are connected by the weakest bonds, including the hydrogen bonds of the DNA base pairs, and/or non-bonded interactions. Although numerous difficulties make the direct identification of terahertz phonon modes in biological materials very challenging, recent studies have shown that such measurements are both possible and useful. Spectra of different DNA samples reveal a large number of modes and a reasonable level of sequence-specific uniqueness. This chapter utilizes computational methods for normal mode analysis and theoretical spectroscopy to predict the low-frequency vibrational absorption spectra of short artificial DNA and RNA. Here the experimental technique is described in detail, including the procedure for sample preparation. Careful attention was paid to the possibility of interference or etalon effects in the samples, and phenomena were clearly differentiated from the actual phonon modes. The results from Fourier-transform infrared spectroscopy of DNA macromolecules and related biological materials in the terahertz frequency range are presented. In addition, a strong anisotropy of terahertz characteristics is demonstrated. Detailed tests of the ability of normal mode analysis to reproduce RNA vibrational spectra are also conducted. A direct comparison demonstrates a correlation between calculated and experimentally observed spectra of the RNA polymers, thus confirming that the fundamental physical nature of the observed resonance structure is caused by the internal vibration modes in the macromolecules. Application of artificial neural network analysis for recognition and discrimination between different DNA molecules is discussed.

Dielectric properties of biological molecules in the Terahertz gap

In this work, results from parallel measurements of reflection and transmission spectra of biological molecules were utilized to enable detailed and direct calculation of the refractive index and absorption coefficient spectra in the Terahertz gap. The DNA samples from herring and salmon, as well as the protein Ovalbumin sample, have been characterized. The modeling technique is described. The reflection spectra have resonance features similar to those demonstrated earlier for transmission, thereby reaffirming molecular vibrational modes in biological materials. The dispersion of refractive index and absorption coefficient is demonstrated within the Terahertz gap of 10cm−1to25cm−1. The data yielded higher refractive index and absorption coefficient for the single stranded salmon DNA than for the double stranded counterpart, with several different vibrational modes.

Optical characterization of hydrogenated silicon thin films using interference technique

This work introduces an application of an “interference spectroscopy technique” (IST) for determination of absorption coefficient and refractive index spectra of amorphous silicon (a-Si:H) and related thin film materials. The technique is based on computer analysis of measurements of optical transmission and specular reflection (T & R) of thin films (including the films on substrates) over a wide range of the incident photon energies (0.5–2.8 eV) using carefully controlled spectrometer conditions. IST is used to investigate the absorption spectrum in the sub-gap energy range (0.8–1.6 eV) of intrinsic and phosphorous-doped a-Si:H, “polymorphous-Si:H,” and microcrystalline silicon films. The enhanced sensitivity of the technique over conventional analysis of T & R data results from utilization of interference to obtain absorption coefficient values at the maxima of transmission. The factors limiting the accuracy of the calculated absorption coefficient are discussed in detail. Measurement on films of thickn...

Terahertz Fourier transform characterization of biological materials in solid and liquid phases

Significant progress has been achieved during the last several years relating to experimental and theoretical aspects of Terahertz (or Sub-millimeter wave) Fourier transform spectroscopy of biological macromolecules. Multiple resonance due to low frequency vibrational modes within biological macromolecules have been unambiguously demonstrated. However till now only solid films of bio-materials have been used for experimental characterization in this spectral range since it was common opinion that high water absorption will prevent from receiving the information on bio-molecules in a liquid phase. At the same time, all biological function of DNA and proteins take place in water solutions. In this work spectra of DNA samples and proteins have been measured in liquid phase (gel) in a spectral range 10-25 cm-1 and compared with spectra obtained from solid films. The results demonstrate that there is almost no interference between spectral features of material in test and water background except for the band around 18.6 cm-1. Much higher level of sensitivity and higher sharpness of vibrational modes in liquid environment in comparison with solid phase is observed with the width of spectral lines 0.3-0.5 cm-1. Gel samples demonstrate effects of polarization. The ability of THz spectroscopy to characterize samples in liquid phase could be very important since it permits to look at DNA interactions, protein-protein interactions in real (wet) samples. One demonstrated example of practical importance is the ability to discriminate between spectral patterns for native and denaturated DNA.

Highly Resolved Sub-Terahertz Vibrational Spectroscopy of Biological Macromolecules and Cells

Sub-terahertz (sub-THz) vibrational spectroscopy for biosensing is based on specific resonance features, vibrational modes or group of modes at close frequencies, in the absorption (transmission) spectra of large biological molecules and entire bacterial cells/spores. Further improvements in sensitivity, especially in the discriminative capability of sub-THz vibrational spectroscopy for detection, characterization, and identification of bacterial organisms, require spectral resolution adequate to the width of spectral features. Evidences exist for long-lasting relaxation processes for atomic dynamics (displacements) resulting in narrow spectral lines and justifying the development and application of highly resolved vibrational spectroscopy. Here we describe a new continuous-wave frequency-domain spectroscopic sensor with imaging capability operating at room temperature in the sub-THz spectral region between 315 and 480 GHz. We present experimental spectra from biological macromolecules and species obtained using this spectrometer and compare some spectra with simulation results using molecular dynamics. Observed multiple intense and specific resonances in transmission/absorption spectra from nano-gram samples with spectral line widths as small as 0.1 cm-1 provide conditions for reliable discriminative capability, potentially to the level of the strains of the same bacteria, and for monitoring interactions between biomaterials and reagents in near real-time.