Protein and RNA dynamical fingerprinting

A new horizon for neuroscience: terahertz biotechnology in brain research

Terahertz biotechnology has been increasingly applied in various biomedical fields and has especially shown great potential for application in brain sciences. In this article, we review the development of terahertz biotechnology and its applications in the field of neuropsychiatry. Available evidence indicates promising prospects for the use of terahertz spectroscopy and terahertz imaging techniques in the diagnosis of amyloid disease, cerebrovascular disease, glioma, psychiatric disease, traumatic brain injury, and myelin deficit. In vitro and animal experiments have also demonstrated the potential therapeutic value of terahertz technology in some neuropsychiatric diseases. Although the precise underlying mechanism of the interactions between terahertz electromagnetic waves and the biosystem is not yet fully understood, the research progress in this field shows great potential for biomedical noninvasive diagnostic and therapeutic applications. However, the biosafety of terahertz radiation requires further exploration regarding its two-sided efficacy in practical applications. This review demonstrates that terahertz biotechnology has the potential to be a promising method in the field of neuropsychiatry based on its unique advantages.

Tubulin Vibration Modes Are in the Subterahertz Range, and Their Electromagnetic Absorption Is Affected by Water

Many proteins are thought to coordinate distant sites in their structures through a concerted action of global structural vibrations. However, the direct experimental spectroscopic detection of these vibration modes is rather elusive. We used normal-mode analysis to explore the dominant vibration modes of an all-atom model of the tubulin protein and described their characteristics using a large ensemble of tubulin structures. We quantified the frequency range of the normal vibrational modes to be in the subterahertz band, specifically between ∼40 and ∼160 GHz. Adding water layers to the model increases the frequencies of the low-frequency modes and narrows the frequency variations of the modes among the protein ensemble. We also showed how the electromagnetic absorption of tubulin vibration modes is affected by vibrational damping. These results contribute to our understanding of tubulin's vibrational and electromagnetic properties and provide a foundation for future attempts to control protein behavior via external electromagnetic fields.

A handheld polarimetric imaging device and calibration technique for accurate mapping of terahertz Stokes vectors

In recent years, handheld and portable terahertz instruments have been in rapid development for various applications ranging from non-destructive testing to biomedical imaging and sensing. For instance, we have deployed our Portable Handheld Spectral Reflection (PHASR) Scanners for in vivo full-spectroscopic imaging of skin burns in large animal models in operating room settings. In this paper, we debut the polarimetric version of the PHASR Scanner, and describe a generalized calibration technique to map the spatial and spectral dependence of the Jones matrix of an imaging scanner across its field of view. Our design is based on placement of two orthogonal photoconductive antenna (PCA) detectors separated by a polarizing beam splitter in the PHASR Scanner housing. We show that as few as three independent measurements of a well-characterized polarimetric calibration target are sufficient to determine the polarization state of the incident beam at the sample location, as well as to extract the Jones propagation matrix from the sample location to the detectors. We have tested the accuracy of our scanner by validating polarimetric measurements obtained from a birefringent crystal rotated to various angles, as compared to the theoretically predicted response of the sample. This new version of our PHASR scanner can be used for high-speed imaging and investigation of heterogeneity of polarization-sensitive samples in the field.

Exploring the Application of Terahertz Metamaterials Based on Metallic Strip Structures in Detection of Reverse Micelles

Terahertz spectroscopy has unique advantages in the study of biological molecules in aqueous solutions. However, water has a strong absorption capability in the terahertz region. Reducing the amount of liquid could decrease interference with the terahertz wave, which may, however, affect the measurement accuracy. Therefore, it is particularly important to balance the amount and water content of liquid samples. In this work, a terahertz metamaterial sensor based on metallic strips is designed, fabricated, and used to detect reverse micelles. An aqueous confinement environment in reverse micelles can improve the signal-to-noise ratio of the terahertz response. Due to "water pool" trapped in reverse micelles, the DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) solution and DOPC emulsion can successfully be identified in intensity by terahertz spectroscopy. Combined with the metamaterial sensor, an obvious frequency shift of 30 GHz can be achieved to distinguish the DOPC emulsion (5%) from the DOPC solution. This approach may provide a potential way for improving the sensitivity of detecting trace elements in a buffer solution, thus offering a valuable toolkit toward bioanalytical applications.

A magnetic control enrichment technique combined with terahertz metamaterial biosensor for detecting SARS-CoV-2 spike protein

The highly contagious SARS-CoV-2 virus, responsible for the COVID-19 pandemic continues to pose significant challenges to public health. Developing new methods for early detection and diagnosis is crucial in combatting the disease, mitigating its impact and be prepared for future challenges in pandemic diseases. In this study, we propose a terahertz (THz) biosensing technology that capitalizes on the properties of THz metamaterial in conjunction with magnetic nanoparticles. This approach can accurately identify the SARS-CoV-2 spike protein by pinpointing its location on the THz resonance sources grooved surface. The magnetic nanoparticles are employed to selectively bind with target molecules, and migrate towards the THz metamaterial unit cell when exposed to an applied magnetic field. The presence of target molecules in to the metamaterial variation in the frequency, amplitude, and phase of the resonance response, thus enabling swift, accurate and sensitive detection. To assess the effectiveness of the proposed technique, we have conducted a comparative analysis between real samples on platforms controlled by magnetic manipulation and those without the control. It was confirmed that the proposed THz sensing method demonstrated a linear detection range spanning from 0.005 ng mL-1 to 1000 ng mL-1 with a detection limit of 0.002 ng mL-1. Furthermore, it exhibited a frequency shift of 24 GHz and a stability index of 95%. The THz biosensing technique may pave a new avenue in identifying and preempting the spread of potential pandemic diseases.

High specificity THz metamaterial-based biosensor for label-free transcription factor detection in melanoma diagnostics

In this work, we present a promising diagnostic tool for melanoma diagnosis. With the proposed terahertz biosensor, it was possible to selectively and sensitively detect the early growth response protein 2, a transcription factor with an increased activity in melanoma cells, from a complex sample of cellular proteins. Fundamentally, the sensor belongs to the frequency selective surface type metamaterials and consists of a two-dimensional array of asymmetrically, doubly split ring resonator unit cells. The single elements are slits in a metallic layer and are complemented by an undercut etch. This allows a selective functionalization of the active area of the sensor and increases the sensitivity towards the target analyte. Hereby, specific detection of a defined transcription factor is feasible.

Nonthermal acceleration of protein hydration by sub-terahertz irradiation

The collective intermolecular dynamics of protein and water molecules, which overlap in the sub-terahertz (THz) frequency region, are relevant for expressing protein functions but remain largely unknown. This study used dielectric relaxation (DR) measurements to investigate how externally applied sub-THz electromagnetic fields perturb the rapid collective dynamics and influence the considerably slower chemical processes in protein-water systems. We analyzed an aqueous lysozyme solution, whose hydration is not thermally equilibrated. By detecting time-lapse differences in microwave DR, we demonstrated that sub-THz irradiation gradually decreases the dielectric permittivity of the lysozyme solution by reducing the orientational polarization of water molecules. Comprehensive analysis combining THz and nuclear magnetic resonance spectroscopies suggested that the gradual decrease in the dielectric permittivity is not induced by heating but is due to a slow shift toward the hydrophobic hydration structure in lysozyme. Our findings can be used to investigate hydration-mediated protein functions based on sub-THz irradiation.

Coulomb potential determining terahertz polarization in a two-color laser field

The orientation and ellipticity of terahertz (THz) polarization generated by a two-color strong field not only casts light on underlying mechanisms of laser-matter interaction, but also plays an important role for various applications. We develop the Coulomb-corrected classical trajectory Monte Carlo (CTMC) method to well reproduce the joint measurements, that the THz polarization generated by the linearly polarized 800 nm and circularly polarized 400 nm fields is independent on two-color phase delay. The trajectory analysis shows that the Coulomb potential twists the THz polarization by deflecting the orientation of asymptotic momentum of electron trajectories. Further, the CTMC calculations predict that, the two-color mid-infrared field can effectively accelerate the electron rapidly away from the parent core to relieve the disturbance of Coulomb potential, and simultaneously create large transverse acceleration of trajectories, leading to the circularly polarized THz radiation.

Terahertz phase shift sensing and identification of a chiral amino acid based on a protein-modified metasurface through the isoelectric point and peptide bonding

The efficient sensing of amino acids, especially the distinction of their chiral enantiomers, is important for biological, chemical, and pharmaceutical research. In this work, a THz phase shift sensing method was performed for amino acid detection based on a polarization-dependent electromagnetically induced transparency (EIT) metasurface. More importantly, a method for binding the specific amino acids to the functional proteins modified on the metasurface was developed based on the isoelectric point theory so that the specific recognition for Arginine (Arg) was achieved among the four different amino acids. The results show that via high-Q phase shift, the detection precision for L-Arg is 2.5 × 10^-5g /ml, much higher than traditional sensing parameters. Due to the specific electrostatic adsorption by the functionalized metasurface to L-Arg, its detection sensitivity and precision are 22 times higher than the other amino acids. Furthermore, by comparing nonfunctionalized and functionalized metasurfaces, the D- and L-chiral enantiomers of Arg were distinguished due to their different binding abilities to the functionalized metasurface. Therefore, this EIT metasurface sensor and its specific binding method improve both detection precision and specificity in THz sensing for amino acids, and it will promote the development of THz highly sensitive detection of chiral enantiomers.

Terahertz all-dielectric metasurface sensor based on quasi-bound states in the continuum

We proposed a quasi-bound states in the continuum (QBICs) metasurface to realize sensing in the terahertz band. It consists of silicon split ellipse cylinders with different short-long axes and a quartz substrate. By introducing two asymmetric split ellipse cylinders unit cells, magnetic dipole and electric quadrupole resonances of the proposed structure are investigated by multiple Pole theory. This shows that the continuum bound states are transformed into quasi-BICs by tuning the length of the ellipse long axis, and so a high-quality factor can be obtained. The Q value of the proposed structure is 3205, and the figure of merit is 469.64. It has potential applications in gas, liquid, and biomaterial sensing.

Near-IR Light-Tunable Omnidirectional Broadband Terahertz Wave Antireflection Based on a PEDOT:PSS/Graphene Hybrid Coating

Omnidirectional broadband terahertz (THz) antireflection (AR) with an actively configurable coating promises the achievement of next-generation efficient and versatile THz components with high performance. We demonstrate a near-infrared (NIR) light-tunable and omnidirectional broadband THz AR coating based on an impedance matching method and composed of a poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS)/graphene composite film. The omnidirectional broadband properties of the active AR coating can be efficiently achieved by tunable NIR optical excitation of less than 0.27 W·cm^-2, which exhibits omnidirectional suppression of THz-wave reflection for incidence angles from 0 to 70°, concerning the broadband frequency range of 0.1-3.0 THz, with an ultrafast response time of ∼5 ps. Furthermore, we demonstrate that the active AR coating can improve the performance of a reflectance-tunable THz-wave polarization reflector by the elimination of Fabry-Pérot interference. The NIR irradiance-dependent active AR mechanism of the hybrid system is investigated, which demonstrates the essential role of the PEDOT:PSS/graphene layers in promoting the charge separation at the interface and therefore changing the photoconductivity of the composite film to achieve impedance matching under optical excitation. Several crucial advantages of the proposed and proven concept, including the wide-angle range, broad spectral range, flexible tunability, and easier fabrication, may revolutionize the AR strategy at THz frequencies for a wide range of THz applications.

Proteomic Applications in Aquatic Environment Studies

Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.

Tuning symmetry-protected quasi bound state in the continuum using terahertz meta-atoms of rotational and reflectional symmetry

Conventionally, a symmetry-protected quasi bound state of the continuum (BIC) becomes achievable by breaking the C₂ symmetry of meta-atoms. Our work exhibits a novel approach to achieving dual band quasi-BIC by breaking the C_2v symmetry into C_s symmetry. Also, we show that a single band quasi-BIC can be achieved by breaking the C_2v symmetry into C₂ symmetry. Our metasurface of C_2v symmetry is composed of double gaps split ring resonator (DSRR), and it degrades to C₂ symmetry when the double gaps are displaced in opposite directions. One band quasi-BIC can be observed occurring at around 0.36 and 0.61 THz respectively with the metasurface excited by x- and y-polarized terahertz radiation, respectively. A couple of dark dipole oscillator dominates the quasi-BIC at 0.36 THz, while a quadruple-like oscillator dominates the quasi-BIC at 0.61 THz. The damping ratio and coupling coefficients of the above single quasi-BIC are close to the orthogonal polarization of the incident terahertz wave. However, the metasurface of the DSRR array degrades down to C_s symmetry when the double gaps are displaced in the same directions. A dual band quasi-BIC (0.23 THz and 0.62 THz) is found to be sensitive to the y-polarized terahertz radiation. It is found that the inductive-capacitive (LC) resonance results in quasi-BIC at 0.23 THz, while a quadrupole-like oscillation results in quasi-BIC at 0.62 THz. The quasi-BIC at 0.62 THz has a higher coupling coefficient and lower damping ratio than quasi-BIC at 0.23 THz in a metasurface of C_s symmetry. The realization of the above locally symmetric breaking on the quasi-BIC of terahertz metasurfaces is helpful for the innovation of multi-band terahertz biosensors.

Cell Responsiveness to Physical Energies: Paving the Way to Decipher a Morphogenetic Code

We discuss emerging views on the complexity of signals controlling the onset of biological shapes and functions, from the nanoarchitectonics arising from supramolecular interactions, to the cellular/multicellular tissue level, and up to the unfolding of complex anatomy. We highlight the fundamental role of physical forces in cellular decisions, stressing the intriguing similarities in early morphogenesis, tissue regeneration, and oncogenic drift. Compelling evidence is presented, showing that biological patterns are strongly embedded in the vibrational nature of the physical energies that permeate the entire universe. We describe biological dynamics as informational processes at which physics and chemistry converge, with nanomechanical motions, and electromagnetic waves, including light, forming an ensemble of vibrations, acting as a sort of control software for molecular patterning. Biomolecular recognition is approached within the establishment of coherent synchronizations among signaling players, whose physical nature can be equated to oscillators tending to the coherent synchronization of their vibrational modes. Cytoskeletal elements are now emerging as senders and receivers of physical signals, "shaping" biological identity from the cellular to the tissue/organ levels. We finally discuss the perspective of exploiting the diffusive features of physical energies to afford in situ stem/somatic cell reprogramming, and tissue regeneration, without stem cell transplantation.

The origin and impact of bound water around intrinsically disordered proteins

Proteins and water couple dynamically over a wide range of time scales. Motivated by their central role in protein function, protein-water dynamics and thermodynamics have been extensively studied for structured proteins, where correspondence to structural features has been made. However, properties controlling intrinsically disordered protein (IDP)-water dynamics are not yet known. We report results of megahertz-to-terahertz dielectric spectroscopy and molecular dynamics simulations of a group of IDPs with varying charge content along with structured proteins of similar size. Hydration water around IDPs is found to exhibit more heterogeneous rotational and translational dynamics compared with water around structured proteins of similar size, yielding on average more restricted dynamics around individual residues of IDPs, charged or neutral, compared with structured proteins. The on-average slower water dynamics is found to arise from excess tightly bound water in the first hydration layer, which is related to greater exposure to charged groups. The more tightly bound water to IDPs correlates with the smaller hydration shell found experimentally, and affects entropy associated with protein-water interactions, the contribution of which we estimate based on the dielectric measurements and simulations. Water-IDP dynamic coupling at terahertz frequencies is characterized by the dielectric measurements and simulations.

Low-frequency collective motion of DNA-binding domain defines p53 function

Most mutations in the DNA-binding domain (DBD) of p53 inactivate or rescue the protein function interacting with the minor groove of DNA. However, how the conformation changes propagating from the mutation sites result in distinct molecular recognition is still not well understood. As the protein mobility is an intrinsic property encrypted in its primary structure, we examined if different structures of wild-type and mutant p53 core domains display any unique patterns of intrinsic mobility. Normal mode calculation was employed to characterize the collective dynamics of DBD in p53 monomer and tetramer as well as their mutants. Intriguingly, the low-frequency collective motions of DBD show similar patterns between the wild-type protein and the rescued mutants. The analysis on atomic backbone fluctuations and low-frequency vibration mode statistics does further support the correlation between the intrinsic collective motion of DBD and the p53 protein function. The mutations in the DBD influence the low-frequency vibration of the p53 tetramer via the change of the collective motions among its four monomers. These findings thus provide new insights for understanding the physical mechanism of p53 protein structure-function relationship and help find the small molecule drug to modulate protein dynamic for disease therapy.

Long-range DNA-water interactions

DNA functions only in aqueous environments and adopts different conformations depending on the hydration level. The dynamics of hydration water and hydrated DNA leads to rotating and oscillating dipoles that, in turn, give rise to a strong megahertz to terahertz absorption. Investigating the impact of hydration on DNA dynamics and the spectral features of water molecules influenced by DNA, however, is extremely challenging because of the strong absorption of water in the megahertz to terahertz frequency range. In response, we have employed a high-precision megahertz to terahertz dielectric spectrometer, assisted by molecular dynamics simulations, to investigate the dynamics of water molecules within the hydration shells of DNA as well as the collective vibrational motions of hydrated DNA, which are vital to DNA conformation and functionality. Our results reveal that the dynamics of water molecules in a DNA solution is heterogeneous, exhibiting a hierarchy of four distinct relaxation times ranging from ∼8 ps to 1 ns, and the hydration structure of a DNA chain can extend to as far as ∼18 Å from its surface. The low-frequency collective vibrational modes of hydrated DNA have been identified and found to be sensitive to environmental conditions including temperature and hydration level. The results reveal critical information on hydrated DNA dynamics and DNA-water interfaces, which impact the biochemical functions and reactivity of DNA.

Functional-State Dependence of Picosecond Protein Dynamics

We examine temperature-dependent picosecond dynamics of two benchmarking proteins lysozyme and cytochrome c using temperature-dependent terahertz permittivity measurements. We find that a double Arrhenius temperature dependence with activation energies E₁ ∼ 0.1 kJ/mol and E₂ ∼ 10 kJ/mol fits the folded and ligand-free state response. The higher activation energy is consistent with the so-called protein dynamical transition associated with beta relaxations at the solvent-protein interface. The lower activation energy is consistent with correlated structural motions. When the structure is removed by denaturing, the lower-activation-energy process is no longer present. Additionally, the lower-activation-energy process is diminished with ligand binding but not for changes in the internal oxidation state. We suggest that the lower-energy activation process is associated with collective structural motions that are no longer accessible with denaturing or binding.

Terahertz pump-probe of liquid water at 12.3 THz

The dynamical complexity of the hydrogen-bonded water network can be investigated with intense Terahertz (THz) spectroscopy, which can drive the liquid into the nonlinear response regime and probe anharmonicity effects. Here we report single-color and polarization-dependent pump–probe experiments at 12.3 THz on liquid water, exciting the librational mode. By comparing results obtained on a static sample and a free-flowing water jet, we are able to disentangle the distinct contributions by thermal, acoustic, and nonlinear optical effects. We show that the transient transmission by the static water layer on a time scale of hundreds of microseconds can be described by thermal (slow) and acoustic (temperature-dependent) effects. In addition, during pump probe overlap we observe an anisotropic nonlinear optical response. This nonlinear signal is more prominent in the liquid jet than in the static cell, where temperature and density perturbations are more pronounced. Our measurements confirm that the THz excitation resonates with the rotationally-damped motion of water molecules, resulting in enhanced transient anisotropy. This model can be used to explain the non-linear response of water in the frequency range between about 1 and 20 THz.

The excitation on the librational band of liquid water at 12.3 THz resonates with the rotationally-damped motion of water molecules.

The necessity of periodic boundary conditions for the accurate calculation of crystalline terahertz spectra

Terahertz vibrational spectroscopy has emerged as a powerful spectroscopic technique, providing valuable information regarding long-range interactions - and associated collective dynamics - occurring in solids. However, the terahertz sciences are relatively nascent, and there have been significant advances over the last several decades that have profoundly influenced the interpretation and assignment of experimental terahertz spectra. Specifically, because there do not exist any functional group or material-specific terahertz transitions, it is not possible to interpret experimental spectra without additional analysis, specifically, computational simulations. Over the years simulations utilizing periodic boundary conditions have proven to be most successful for reproducing experimental terahertz dynamics, due to the ability of the calculations to accurately take long-range forces into account. On the other hand, there are numerous reports in the literature that utilize gas phase cluster geometries, to varying levels of apparent success. This perspective will provide a concise introduction into the terahertz sciences, specifically terahertz spectroscopy, followed by an evaluation of gas phase and periodic simulations for the assignment of crystalline terahertz spectra, highlighting potential pitfalls and good practice for future endeavors.

Metallodrug-protein interaction probed by synchrotron terahertz and neutron scattering spectroscopy

This experimental work applied coherent synchrotron-radiation terahertz spectroscopy and inelastic neutron scattering to address two processes directly associated with the mode of action of metal-based anticancer agents that can severely undermine chemotherapeutic treatment: drug binding to human serum albumin, occurring during intravenous drug transport, and intracellular coordination to thiol-containing biomolecules (such as metallothioneins) associated with acquired drug resistance. Cisplatin and two dinuclear platinum (Pt)- and palladium (Pd)-polyamine agents developed by this research group, which have yielded promising results toward some types of human cancers, were investigated. Complementary synchrotron-radiation-terahertz and inelastic neutron scattering data revealed protein metalation, through S- and N-donor ligands from cysteine, methionine, and histidine residues. A clear impact of the Pt and Pd agents was evidenced, drug binding to albumin and metallothionein having been responsible for significant changes in the overall protein conformation, as well as for an increased flexibility and possible aggregation.

Terahertz dielectric spectroscopy and solid immersion microscopy of ex vivo glioma model 101.8: brain tissue heterogeneity

Terahertz (THz) technology holds strong potential for the intraoperative label-free diagnosis of brain gliomas, aimed at ensuring their gross-total resection. Nevertheless, it is still far from clinical applications due to the limited knowledge about the THz-wave-brain tissue interactions. In this work, rat glioma model 101.8 was studied ex vivo using both the THz pulsed spectroscopy and the 0.15λ-resolution THz solid immersion microscopy (λ is a free-space wavelength). The considered homograft model mimics glioblastoma, possesses heterogeneous character, unclear margins, and microvascularity. Using the THz spectroscopy, effective THz optical properties of brain tissues were studied, as averaged within the diffraction-limited beam spot. Thus measured THz optical properties revealed a persistent difference between intact tissues and a tumor, along with fluctuations of the tissue response over the rat brain. The observed THz microscopic images showed heterogeneous character of brain tissues at the scale posed by the THz wavelengths, which is due to the distinct response of white and gray matters, the presence of different neurovascular structures, as well as due to the necrotic debris and hemorrhage in a tumor. Such heterogeneities might significantly complicate delineation of tumor margins during the intraoperative THz neurodiagnosis. The presented results for the first time pose the problem of studying the inhomogeneity of brain tissues that causes scattering of THz waves, as well as the urgent need to use the radiation transfer theory for describing the THz-wave - tissue interactions.

Low-frequency vibrational modes in G-quadruplexes reveal the mechanical properties of nucleic acids

Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA–protein recognition. However, understanding the vibrational basis of these mechanisms relies on theoretical models due to the lack of experimental evidence. Here we present the low-frequency vibrational spectra of G-quadruplexes (structures formed by four strands of DNA) and B-DNA characterized using femtosecond optical Kerr-effect spectroscopy. Contrary to expectation, we found that G-quadruplexes show several strongly underdamped delocalized phonon-like modes that have the potential to contribute to the biology of the DNA at the atomic level. In addition, G-quadruplexes present modes at a higher frequency than B-DNA demonstrating that changes in the stiffness of the molecule alter its gigahertz to terahertz vibrational profile.

Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA–protein recognition.

Label-free terahertz microfluidic biosensor for sensitive DNA detection using graphene-metasurface hybrid structures

Metasurface assisted terahertz (THz) real-time and label-free biosensors have attracted intense attention. However, it is still challenging for specific detection of highly absorptive liquid samples with high sensitivity in the THz range. Here, we incorporated graphene with THz metasurface into a microfluidic cell for sensitive biosensing. The proposed THz graphene-metasurface microfluidic platform can effectively reduce the volume of the sample solution and boost the interaction between biomolecules and THz waves, thus enhancing the sensitivity. As a proof of concept, comparative experiments using other three kinds of microfluidic cells (pure microfluidic cell, metasurface-based microfluidic cell and graphene-based microfluidic cell) were conducted to explore and verify the sensing mechanism, which evidences the high sensitivity of delicate sensing based on the hybrid graphene-metasurface THz microfluidic device. Furthermore, to perform biosensing applications on that basis, specific aptamers were modified on the graphene-metasurface, enabling DNA sequences of foodborne pathogen Escherichia coli O157:H7 to be recognized. Based on the THz microfluidic biosensor, 100 nM DNA short sequences can be successfully detected. The sensing results of antibiotics and DNA based on the graphene-metasurface microfluidic biosensor confirm the superiority of the proposed design and considerable promise in THz biosensing. The novel sensing platform provides the merits of enabling highly sensitive, label-free, low-cost, easy to use, reusable, and real-time biosensing, which opens an exciting prospect for nanomaterial-metasurface hybrid structure assisted THz label-free biosensing in liquid environment.

Broadband terahertz signatures and vibrations of dopamine

Dopamine (DA) is an essential neurotransmitter and hormone of the nervous system, its structural and conformational properties play critical roles in biological functions and signal transmission processes. Although this neuroactive molecule has been studied extensively, the low-frequency vibration features that are closely related to the conformation and molecular interactions in the terahertz (THz) band still remain unclear. In this study, a broadband THz time-domain spectroscopy (THz-TDS) system in the frequency band of 0.5-18 THz was used to characterize the unique THz fingerprint of DA. In addition, density functional theory (DFT) calculations were performed to analyze the vibrational properties of DA. The results suggest that each THz resonant absorption peak of DA corresponds to specific vibrational modes, and the collective vibration also exists in the broadband THz range. Moreover, the interactions between the DA ligand and the D2 and D3 receptors were investigated by docking, and the simulated THz spectra were obtained. The results indicate the dominant role of hydrogen bonding interactions and the specificity of molecular conformation. This work may help to understand the resonance coupling between THz electromagnetic waves and neurotransmitters.

Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin

Water dynamics in the hydration layers of biomolecules play crucial roles in a wide range of biological functions. A hydrated protein contains multiple components of diffusional and vibrational dynamics of water and protein, which may be coupled at ∼0.1-THz frequency (10-ps timescale) at room temperature. However, the microscopic description of biomolecular functions based on various modes of protein-water-coupled motions remains elusive. A novel approach for perturbing the hydration dynamics in the subterahertz frequency range and probing them at the atomic level is therefore warranted. In this study, we investigated the effect of klystron-based, intense 0.1-THz excitation on the slow dynamics of ubiquitin using NMR-based measurements of hydrogen-deuterium exchange. We demonstrated that the subterahertz irradiation accelerated the hydrogen-deuterium exchange of the amides located in the interior of the protein and hydrophobic surfaces while decelerating this exchange in the amides located in the surface loop and short 3₁₀ helix regions. This subterahertz-radiation-induced effect was qualitatively contradictory to the increased-temperature-induced effect. Our results suggest that the heterogeneous water dynamics occurring at the protein-water interface include components that are nonthermally excited by the subterahertz radiation. Such subterahertz-excited components may be linked to the slow function-related dynamics of the protein.

Diffusivelike Motions in a Solvent-Free Protein-Polymer Hybrid

The interaction between proteins and hydration water stabilizes protein structure and promotes functional dynamics, with water translational motions enabling protein flexibility. Engineered solvent-free protein-polymer hybrids have been shown to preserve protein structure, function, and dynamics. Here, we used neutron scattering, protein and polymer perdeuteration, and molecular dynamics simulations to explore how a polymer dynamically replaces water. Even though relaxation rates and vibrational properties are strongly modified in polymer coated compared to hydrated proteins, liquidlike polymer dynamics appear to plasticize the conjugated protein in a qualitatively similar way as do hydration-water translational motions.

Ultra-broadband terahertz fingerprint spectrum of melatonin with vibrational mode analysis

Melatonin (MLT), as a neurotransmitter and an endogenous neurohormone, plays an important role in physiological functions through interactions with specific receptors. The conformations of MLT are closely related to its biological activities and functions. However, the internal relationship between the structure and interaction of MLT and its allosteric transition remains unclear. In this work, we obtain the broadband fingerprint terahertz (THz) spectrum of MLT in the range of 0.5-18 THz using the air-plasma terahertz time-domain spectroscopy (THz-TDS) system. DFT calculations are employed to analyze the vibration characteristics of MLT. The result shows that the low-frequency vibrations mainly come from the strong coupling between inter- and intramolecular vibrations, and the contribution of intramolecular vibrations gradually dominates with increasing frequency. Meanwhile, the local vibrations of the different functional groups distribute widely in the THz low-frequency band, relating to the diversity of conformational changes in the molecule. The intermolecular hydrogen bonds (HBs) have distinct resonant responses and play critical roles in the THz low-frequency vibrations. The study reveals the complex characteristics of the resonant coupling of MLT with THz electromagnetic waves. The results will help to understand the conformational preferences of MLT in neural signal transmission processes.

Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis

Proteins are allosteric machines that couple motions at distinct, often distant, sites to control biological function. Low-frequency structural vibrations are a mechanism of this long-distance connection and are often used computationally to predict correlations, but experimentally identifying the vibrations associated with specific motions has proved challenging. Spectroscopy is an ideal tool to explore these excitations, but measurements have been largely unable to identify important frequency bands. The result is at odds with some previous calculations and raises the question what methods could successfully characterize protein structural vibrations. Here we show the lack of spectral structure arises in part from the variations in protein structure as the protein samples the energy landscape. However, by averaging over the energy landscape as sampled using an aggregate 18.5 μs of all-atom molecular dynamics simulation of hen egg white lysozyme and normal-mode analyses, we find vibrations with large overlap with functional displacements are surprisingly concentrated in narrow frequency bands. These bands are not apparent in either the ensemble averaged vibrational density of states or isotropic absorption. However, in the case of the ensemble averaged anisotropic absorption, there is persistent spectral structure and overlap between this structure and the functional displacement frequency bands. We systematically lay out heuristics for calculating the spectra robustly, including the need for statistical sampling of the protein and inclusion of adequate water in the spectral calculation. The results show the congested spectrum of these complex molecules obscures important frequency bands associated with function and reveal a method to overcome this congestion by combining structurally sensitive spectroscopy with robust normal mode ensemble analysis.

A terahertz metamaterial biosensor for sensitive detection of microRNAs based on gold-nanoparticles and strand displacement amplification

Terahertz (THz) spectroscopy has drawn great interest for the functional and conformational investigations of nucleic acids, but its intrinsic sensitivity hinders potential bio-sensing applications. Here, a novel THz biosensor was developed for detecting microRNA (miRNA) samples based on metamaterials coupled with nanoparticles and strand displacement amplification (SDA). In this method, the SDA reaction amplifies the target miRNA and generates copious yields of secondary DNA molecules (Trigger DNA), which are subsequently conjugated to metallic nanoparticles that form nanoparticle-Trigger DNA complexes. These complexes produce remarkable frequency shifts of metamaterials when linked to a large refractive index metallic nanoparticle like Au. The dependence of the metamaterial resonance on the nanoparticle diameter and metal type was investigated experimentally and theoretically. Under optimal conditions, the THz metamaterial biosensor presents good detection sensitivity with a limit of detection of 14.54 aM and exhibits a linear response for miRNA-21 at a concentration range from 1 fM to 10 pM. By measuring the miRNA-21 in spiked clinical serum samples, the sample recoveries were determined to be in the range between 90.92% and 107.01%. These findings demonstrate that the novel THz biosensor offers the capability for highly sensitive miRNA detection, with noteworthy potential applications in nucleic acid analysis and cancer diagnosis.

Terahertz time-domain polarimetry (THz-TDP) based on the spinning E-O sampling technique: determination of precision and calibration

We have developed a terahertz time-domain polarimetry (THz-TDP) system by applying frequency modulation to electro-optic sampling detection in a nonlinear crystal. We characterized the precision of this system in determining the polarization angles to be 1.3° for fixed time delay, and 0.5° for complete time-domain waveform. Furthermore, we calculated the Jones matrix of the optical components used for beam propagation to calibrate the induced systematic error. The advantages of employing this calibration approach are demonstrated on a sapphire crystal investigated at different sample test positions in transmission configuration, and using high resistivity Si, AlN and quartz in reflection geometry. The new THz-TDP technique has the advantage of not using any external polarizers, and therefore is not constrained by their optical performance limitations, such as restricted bandwidths and frequency-dependent extinction ratio. Finally, the THz-TDP technique can be easily implemented on existing time-domain spectroscopy (TDS) systems.

Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties

Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.

Tunable and Polarization-Independent Plasmon-Induced Transparency in a Fourfold Symmetric Metal-Graphene Terahertz Metamaterial

The introduction of graphene into metamaterials allows for more flexible and convenient control of electromagnetic waves. In this paper, one simple plasmon-induced transparency (PIT) structure with tunability and polarization independence is investigated in the terahertz (THz) regime. The simulation results indicate that the transparent window can be manipulated in a wide range and even switched off by merely changing the Fermi energy of graphene. By continuously altering the resonance intensity of the dark resonator using the graphene, the PIT resonance can be actively manipulated. The behavior can be elucidated by the classical coupled two-particle model, which corresponds well to the simulation results. Owing to the fourfold symmetric structure, the proposed PIT device exhibits polarization-independent characteristics. This work provides design guidance for metal-graphene THz modulators.

Near-field THz micropolarimetry

We introduce a method for rapid determination of anisotropic terahertz absorption with sub micron resolution and high spectral integrity in the terahertz range. The method is ideal for microscopic and environmentally sensitive materials such as 2-D materials and protein crystals where the anisotropic absorption is critical to understanding underlying physics. We introduce the idea of using an iso-response relationship between the THz polarization and electro optic probe polarization to enable stationary sample polarization measurements covering a full 2π polarization dependence measurement.

Tunable compact narrow band THz sources for frequency domain THz anisotropic spectroscopy

We demonstrate frequency domain THz anisotropy signature detection for protein crystal models using newly developed compact tunable narrow band THz sources based on Orientation Patterned Gallium Phosphide for turn-key spectroscopic systems.