Terahertz absorption of DNA decamer duplex

Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example

Water molecules were easy to combine with organic molecules and embed into the lattice of solid molecules to form a hydrate. Compared with anhydrous compounds, a hydrate has completely different physical and chemical properties. In this paper, terahertz (THz) spectra of five nucleosides in the solid and liquid phases were studied experimentally by Fourier-transform infrared spectroscopy (FTIR) in the frequency of 0.5-9 THz. In addition, the lattice energy, geometric structure, and vibration spectrum of the molecular crystal of the nucleosides were analyzed theoretically by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF). Furthermore, different nucleoside molecular morphology (monomer, polymer, and crystal), solvent (implicit and explicit water), and temperature/theoretical model effect on the THz spectra were mainly investigated. It was found that in the low-frequency band, the vibrational modes were generally originated from the collective vibration of all molecules involved (more than 99% of them were vibration; only less than 1% of them were rotation and translation), which can reflect the molecular structure and spatial distribution of different substances. The Gibbs free energy of thymidine monomer, dimer, tetramer, and crystal was studied. It was found that the cell-stacking energy had the greatest influence on the spectrum, indicating that only the crystal structure constrained by the periodic boundary conditions could well describe the experimental results. In addition, hydrophobic forces dominated the formation of new chemical bonds and strong inter-molecular interactions; the free water had little contribution to the THz spectrum of nucleosides, while crystalline water had a great influence on the spectrum.

Characterizing hydrogen bonds in crystalline form of guanidinium salicylate in the terahertz range

For pharmaceutical compounds with poor solubility, there is an effective method to address this dilemma without tampering their intrinsic chemical properties by forming weak hydrogen bonds. Guanidinium salicylate, which is a typical pharmaceutical salt with a complex crystal structure, was systematically investigated by terahertz time-domain spectroscopy combined with density functional theory in order to obtain the complete information of weak hydrogen bonds. As a result of the influence of weak hydrogen bonds, there are substantial differences between guanidinium salicylate and its parent molecule (salicylic acid) in the experimental fingerprint spectra in the range of 0.2-2.5 THz, such as the number, amplitude and frequency positions of absorption peaks. With the help of isolated molecule density functional theory calculations, the possible sites of weak hydrogen bonds were determined by natural bond orbital analysis. It can be concluded that there is an intricate hydrogen bond network due to the polar distribution of molecular electrostatic potential. Furthermore, all THz absorption peaks were assigned to their corresponding vibrational modes and the complete information of the related hydrogen bonds (including type, role, angle, and bond length) was determined by using dispersion-corrected density functional theory. The results laid a good foundation for further study on the enhancement of solubility of pharmaceutical salts by forming weak hydrogen bonds.

Sub-THz spectroscopic characterization identification for pine wood nematode ribosomal DNA

This paper, we introduced Sub-terahertz (Sub-THz) technology to identify nematode DNA sequence. First, data mining technology and restriction enzyme digestion were used to cut out two corresponding sequences, each containing about 100 base pairs that could represent the characteristic fragments of Bursaphelenchus xylophilus (Bx) and Bursaphelenchus mucronatus (Bm) rDNA in internal transcribed spacer 1 (ITS1) region. Then, vibration spectra of the two enzyme-cut sequences were measured by Fourier transform infrared spectroscopy (FTIR). Meanwhile, the spectrum was analyzed by molecular dynamics method. It was found that the calculated and experimental spectra of the two enzyme-cut sequences were consistent, although the differences of the sequences could not be well reflected in the spectra. The vibration modes corresponding to diverse absorption peaks in the spectra were quite different, which were closely related to the internal bases sequencing. This can be used as an indicator for identifying Bx and Bm DNA. Moreover, the normal mode analysis (NMA) method was first adopted for spectral attribution analysis of DNA long sequences. Finally, the vibration spectra of shorter sequences predicted by second-order Markov chains and Monte Carlo method were studied. To some extent, the predicted short sequences can represent the complete sequence as the initial calculation structure.

Molecular recognition and interaction between uracil and urea in solid-state studied by terahertz time-domain spectroscopy

Using terahertz time-domain spectroscopy characterization, we observe that urea is able to recognize and interact with uracil efficiently even in the solid phase without involving water or solvents. A cocrystal configuration linked by a pair of hydrogen bonds between uracil and urea was formed. The terahertz absorption spectrum of the cocrystal shows a distinct new absorption at 0.8 THz (26.7 cm(-1)), which originates from the intermolecular hydrogen bonding. Both mechanical milling and heating can accelerate the reaction efficiently. Density functional theory was adopted to simulate the vibrational modes of the cocrystal, and the results agree well with the experimental observation. Multiple techniques, including powder X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy, were performed to investigate the reaction process, and they presented supportive evidence. This work enables in-depth understanding of recognition and interaction of urea with nucleobases and comprehension of the denaturation related to RNA. We also demonstrate that terahertz spectroscopy is an effective and alternative tool for online measurement and quality control in pharmaceutical and chemical industries.

Terahertz-time domain spectroscopy for the detection of PCR amplified DNA in aqueous solution

In this work we present a label free quantitative detection method for DNA samples amplified by polymerase chain reaction (PCR) in aqueous medium using terahertz-time domain spectroscopy (THz-TDS) in the frequency range from 0.3 to 1.2 THz. The DNA samples of 133 and 697 base pairs were prepared using PCR. We measured the absorption coefficients of DNA solutions in the concentration range of 0-0.3 ng μl(-1). For both DNA types, the absorption coefficients decreased with increasing DNA concentrations. The average change in absorption coefficients compared to buffer within the frequency range of 0.8-1.0 THz showed a linear behavior. Our results demonstrate that THz-TDS can detect PCR amplified DNA in aqueous solution with a minimum concentration of 0.1 ng μl(-1) and a minimum sample volume of 10 μl.

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.