Sub-terahertz vibrational spectroscopy of ovarian cancer and normal control tissue for molecular diagnostic technology.

We introduce here recently developed highly resolved Sub-Terahertz resonance spectroscopy of biological molecules and cells combined with molecular dynamics (MD) computational analysis as a new approach for optical visualization and quantification of the presence of microRNAs, particularly the mir-200 family, as potential biomarkers in samples from tissue of epithelial ovarian cancers for disease early detection, analysis, prognosis and treatment.METHOD: A set of samples for this study was prepared from anonymized archival formalin-fixed, paraffin-embedded ovarian epithelial tissue containing regions of invasive neoplastic cells from cases of high-histologic grade serous papillary ovarian carcinoma. Control samples were normal mucosa from fallopian tubes of patients with no known malignancy. Spectroscopic characterization of tissue samples in this study was performed using a continuous wave, frequency domain automated spectrometer operating at room temperature in the spectral region of 310-500 GHz. The spectral results were compared with molecular dynamics simulations and absorption coefficient calculations utilized to predict the absorption spectra.RESULTS: The characteristic spectroscopic features in absorption spectra, particularly the presence of absorption peaks near 13 cm-1 have been identified as cancer indicators. Tissue samples heterogeneity, reflected by diverse spectral signatures, provides additional, very specific information that may be used for identification of cancer subtypes, clinical behavior or sensitivity to specific therapies. Further work is warranted to determine if this signature can be detected in bio-fluids from ovarian cancer patients. If strongly correlated with cancer burden, it may then be investigated as a potential new biomarker for disease monitoring, and also perhaps as a biomarker for cancer screening.

Sub-THz specific relaxation times of hydrogen bond oscillations in E.coli thioredoxin. Molecular dynamics and statistical analysis.

Hydrogen bonds (H-bonds) in biological macromolecules are important for the molecular structure and functions. Since interactions via hydrogen bonds are weaker than covalent bonds, it can be expected that atomic movements involving H-bonds have low frequency vibrational modes. Sub-Terahertz (sub-THz) vibrational spectroscopy that combines measurements with molecular dynamics (MD) computational prediction has been demonstrated as a promising approach for biological molecule characterization. Multiple resonance absorption lines have been reported. The knowledge of relaxation times of atomic oscillations is critical for the successful application of THz spectroscopy for hydrogen bond characterization. The purpose of this work is to use atomic oscillations in the 0.35-0.7 THz range, found from molecular dynamic (MD) simulations of E.coli thioredoxin (2TRX), to study relaxation dynamics of two intra-molecular H-bonds, OH-N and OH-C. Two different complimentary techniques are used in this study, one is the analysis of the statistical distribution of relaxation time and dissipation factor values relevant to low frequency oscillations, and the second is the analysis of the autocorrelation function of low frequency quasi-periodic movements. By studying hydrogen bond atomic displacements, it was found that the atoms are involved in a number of collective oscillations, which are characterized by different relaxation time scales ranging from 2-3 ps to more than 150 ps. The existence of long lasting relaxation processes opens the possibility to directly observe and study H-bond vibrational modes in sub-THz absorption spectra of bio-molecules if measured with an appropriate spectral resolution. The results of measurements using a recently developed frequency domain spectroscopic sensor with a spectral resolution of 1 GHz confirm the MD analysis.

Molecular dynamics modeling of the sub-THz vibrational absorption of thioredoxin from E. coli.

Sub-terahertz (THz) vibrational modes of the protein thioredoxin in a water environment were simulated using molecular dynamics (MD) in order to find the conditions needed for simulation convergence, improve the correlation between experimental and simulated absorption frequencies, and ultimately enhance the predictive capabilities of computational modeling. Thioredoxin from E. coli was used as a model molecule for protocol development and to optimize the simulation parameters. The empirically parameterized software packages Amber 8 and 10 were used in this work. Using atomic trajectories from the constant energy and volume MD simulations, thioredoxin's sub-THz vibrational spectra and absorption coefficients were calculated in a quasi-harmonic approximation. An optimal production run length ~100 ps was found, in agreement with experimental data on thioredoxin relaxation dynamics. At the same time, a new procedure was developed for averaging correlation matrices of atomic coordinates in MD simulations. In particular, the open source package ptraj was edited to improve a matrix-analyzing function. Averaging only six matrices gave much more consistent results, with absorption peak intensities exceeding those from the individual spectra and a rather good correlation between simulated vibrational frequencies and experimental data.

The influence of environment on terahertz spectra of biological molecules.

The variability of molecular vibrations and low terahertz spectra of biological molecules depending on the three-dimensional structure of molecular clusters, chemical bonding, and molecular concentration in the surrounding media is studied using computer simulations. The resonant terahertz spectra of biological molecules and their associations are described within the framework of molecular mechanics using an all-atom molecular mechanical force field for proteins and nucleic acids. Both the absolute values of absorption coefficients and their spectral properties are considered for murein-lipoprotein and thioredoxin of E. coli and models of bacterial DNAs using energy minimization and molecular dynamics. The obtained results indicate that structural changes introduced by chemical reactions and molecule associations can strongly affect terahertz spectra, causing significant changes in absorption peak intensities and shifts in peak positions. Terahertz light absorption intensities of studied proteins are predicted to be strongly affected by solvents.

Terahertz absorption of DNA decamer duplex.

This work combines experimental and theoretical approaches to investigate terahertz absorption spectra of the DNA formed by the sequence oligomer 5'-CCGGCGCCGG-3'. The three-dimensional structure of this self-complimentary DNA decamer has been well-studied, permitting us to perform direct identification of the low-frequency phonon modes associated with specific conformation and to conduct comprehensive computer simulations. Two modeling techniques, normal-mode analysis and nanosecond molecular dynamics with explicit solvent molecules, were employed to extract the low-frequency vibrational modes based on which the absorption spectra were calculated. The absorption spectra of the DNA decamer in aqueous solution were measured in the frequency range 10-25 cm(-1) using the terahertz Fourier transform infrared spectroscopy. Multiple well-resolved and reproducible resonance modes were observed. When calculated and experimental spectra were compared, the spectrum based on molecular dynamics simulations showed a better correlation with the experimental spectra than the one based on normal-mode analysis. These results demonstrate that there exist a considerable number of active low-frequency phonon modes in this short DNA duplex.

Enhanced coupling of subterahertz radiation with semiconductor periodic slot arrays.

In this work, a theoretical study of the coupling of TM polarized subterahertz (THz) radiation with periodic semiconductor rectangular slot arrays was conducted, using InSb as an example. Simulation results showed that the structure with 4-12 microm thickness provides over a 20-30-fold increase in the electric field at slot edges in a nanosize region ( approximately 500 nm). The enhancement of the THz electromagnetic field extends across the slots and reaches peak values at the edges due to discontinuity effects. Because of the strong local electromagnetic field enhancement, the structure can potentially be used for the development of novel biophotonic sensors, leading to improved detection sensitivity.