Circular Intensity Differential Scattering for Label-Free Chromatin Characterization: A Review for Optical Microscopy

Chirality Quantification for High-Performance Nanophotonic Biosensors

Recent advancements in chiral metabolomics have facilitated the discovery of disease biomarkers through the enantioselective measurement of metabolites, offering new opportunities for diagnosis, prognosis, and personalized medicine. Although chiral photonic nanomaterials have emerged as promising platforms for chiral biosensing, enhancing sensitivity and enabling the detection of biomolecules at extremely low concentrations, a deeper understanding of the relationship between structural and optical chirality is crucial for optimizing these platforms. This perspective examines recent methods for quantifying chirality, including the Hausdorff Chirality Measure (HCM), Continuous Chirality Measure (CCM), Osipov-Pickup-Dunmur (OPD), and Graph-Theoretical Chirality (GTC) measure. These approaches have advanced the understanding of chirality in both materials and biomolecules, as well as its correlation with optical responses. This work emphasizes the role of chiral quantification in improving biosensor performance and explores the potential of near-field chiroptical studies to enhance sensor capabilities. Finally, this work addresses key challenges and outline future research directions for advancing chiral biosensors, with a focus on improving nano-bio interface interactions to drive the development of next-generation sensing technologies.

Resolving Artifacts and Improving the Detection Limit in Circular Differential Scattering Measurement of Chiral and Achiral Gold Nanorods

Circular differential scattering (CDS) spectroscopy has been developed as a powerful method for the characterization of the optical activity of individual plasmonic nanostructures and their complexes with chiral molecules. However, standard measurement setups often result in artifacts that have long raised concerns on the interpretation of spectral data. In fact, the detection limit of CDS setups is constrained by the high level of artifacts, to ±10%. We address this issue by means of a detailed theoretical description of changes in the polarization state when circularly polarized light is reflected at a dark-field condenser. As a result, we propose a modified CDS configuration based on sequentially placing the quarter-wave plate and linear polarizer within the detection optical path, to analyze the circular polarization state of the light scattered by individual particles. Extensive analysis demonstrates a detection limit of ±1.5% for the modified configuration, which is significantly lower than that for the conventional setup. As a standard system for CDS measurements, both achiral and chiral gold nanorods (AuNRs) were characterized using both setups. With achiral AuNRs, linear dichroism (LD) artifacts in the conventional setup are found to originate from LD present in the excitation light and are only present if anisotropic excitation is produced as a result of the misalignment of the excitation light to the condenser. With chiral AuNRs, CDS spectra recorded with the conventional setup depend on the orientation of the chiral AuNRs with respect to the x-axis of the microscope and are reversed compared to those on the colloid and measured in the modified configuration. The results are in good agreement with theoretical simulations for both configurations.

Orientation-independent-DIC imaging reveals that a transient rise in depletion attraction contributes to mitotic chromosome condensation

Genomic information must be faithfully transmitted into two daughter cells during mitosis. To ensure the transmission process, interphase chromatin is further condensed into mitotic chromosomes. Although protein factors like condensins and topoisomerase IIα are involved in the assembly of mitotic chromosomes, the physical bases of the condensation process remain unclear. Depletion attraction/macromolecular crowding, an effective attractive force that arises between large structures in crowded environments around chromosomes, may contribute to the condensation process. To approach this issue, we investigated the "chromosome milieu" during mitosis of living human cells using an orientation-independent-differential interference contrast module combined with a confocal laser scanning microscope, which is capable of precisely mapping optical path differences and estimating molecular densities. We found that the molecular density surrounding chromosomes increased with the progression from prophase to anaphase, concurring with chromosome condensation. However, the molecular density went down in telophase, when chromosome decondensation began. Changes in the molecular density around chromosomes by hypotonic or hypertonic treatment consistently altered the condensation levels of chromosomes. In vitro, native chromatin was converted into liquid droplets of chromatin in the presence of cations and a macromolecular crowder. Additional crowder made the chromatin droplets stiffer and more solid-like. These results suggest that a transient rise in depletion attraction, likely triggered by the relocation of macromolecules (proteins, RNAs, and others) via nuclear envelope breakdown and by a subsequent decrease in cell volumes, contributes to mitotic chromosome condensation, shedding light on a different aspect of the condensation mechanism in living human cells.

Theory of Rayleigh-Brillouin optical activity light scattering applicable to chiral liquids

It has long been understood that dilute samples of chiral molecules such as rarefied gases should exhibit Rayleigh optical activity. We extend the existing theory by accounting for molecular dynamics and correlations, thus obtaining a more general theory of Rayleigh-Brillouin optical activity applicable to dense samples such as neat liquids.

Multiparametric Remote Investigation in the near-IR through Optical Fiber for In Situ Measurements

Diffuse reflectance spectroscopy (DRS) has proven to be a powerful, reliable, and non-invasive optical method for characterizing a specimen. Nevertheless, these methods are based on a rudimentary interpretation of the spectral response and can be irrelevant to understanding 3D structures. In this work, we proposed adding optical modalities into a customized handheld probe head in order to increase the number of parameters in DRS acquired from the light/matter interaction. It consists of (1) placing the sample in a reflectance manual rotation stage to collect spectral backscattered angularly resolved light and (2) illuminating it with two sequential linear polarization orientations. We demonstrate that this innovative approach leads to a compact instrument, capable of performing fast polarization-resolved spectroscopic analysis. Due to the significant amount of data available with this technique in a short time, we observe sensitive quantitative discrimination between two types of biological tissue provided by a raw rabbit leg. We believe that this technique can pave the way for rapid meat quality check or biomedical diagnosis of pathological tissues in situ at an early stage.

Applications of Mueller Matrix Polarimetry to Biological and Agricultural Diagnostics: A Review

The review contains a systematization of the main approaches to the practical implementation of Mueller matrix polarimetry and the prospects for its application in biology and agriculture. The most typical optical layouts for measuring the Mueller matrix of various objects, such as disperse systems, tissues and surface structures, are discussed. Mueller matrix measurements, being integrated into standard schemes of conventional optical methods, such as scatterometry, optical coherence tomography, fluorimetry, spectrophotometry and reflectometry, can significantly expand their capabilities in the characterization of biological systems and bioorganic materials. Additionally, microwave Mueller matrix polarimetry can be used for monitoring soil conditions and crop growth. The proposed systematization is aimed at outlining the conceptual directions for the development of non-invasive diagnostic tools based on measuring the Mueller matrix, primarily with a focus on biological research and agricultural practice.

Phasor map analysis to investigate Hutchinson-Gilford progeria cell under polarization-resolved optical scanning microscopy

Polarized light scanning microscopy is a non-invasive and contrast-enhancing technique to investigate anisotropic specimens and chiral organizations. However, such arrangements suffer from insensitivity to confined blend of structures at sub-diffraction level. Here for the first time, we present that the pixel-by-pixel polarization modulation converted to an image phasor approach issues an insightful view of cells to distinguish anomalous subcellular organizations. To this target, we propose an innovative robust way for identifying changes in the chromatin compaction and distortion of nucleus morphology induced by the activation of the lamin-A gene from Hutchinson–Gilford progeria syndrome that induces a strong polarization response. The phasor mapping is evaluated based on the modulation and phase image acquired from a scanning microscope compared to a confocal fluorescence modality of normal cell opposed to the progeria. The method is validated by characterizing polarization response of starch crystalline granules. Additionally, we show that the conversion of the polarization-resolved images into the phasor could further utilized for segmenting specific structures presenting various optical properties under the polarized light. In summary, image phasor analysis offers a distinctly sensitive fast and easy representation of the polarimetric contrast that can pave the way for remote diagnosis of pathological tissues in real-time.

Measurement of circular intensity differential scattering (CIDS) from single airborne aerosol particles for bioaerosol detection and identification

The circular intensity differential scattering (CIDS), i.e. the normalized Mueller matrix element -S₁₄/S₁₁, can be used to detect the helical structures of DNA molecules in biological systems, however, no CIDS measurement from single particles has been reported to date. We report an innovative method for measuring CIDS phase functions from single particles individually flowing through a scattering laser beam. CIDS signals were obtained from polystyrene latex (PSL) microspheres with or without coating of DNA molecules, tryptophan particles, and aggregates of B. subtilis spores, at the size of 3 μm in diameter. Preliminary results show that this method is able to measure CIDS phase function in tens of microseconds from single particles, and has the ability to identify particles containing biological molecules.

Computational Modeling of Chromatin Fiber to Characterize Its Organization Using Angle-Resolved Scattering of Circularly Polarized Light

Understanding the structural organization of chromatin is essential to comprehend the gene functions. The chromatin organization changes in the cell cycle, and it conforms to various compaction levels. We investigated a chromatin solenoid model with nucleosomes shaped as cylindrical units arranged in a helical array. The solenoid with spherical-shaped nucleosomes was also modeled. The changes in chiral structural parameters of solenoid induced different compaction levels of chromatin fiber. We calculated the angle-resolved scattering of circularly polarized light to probe the changes in the organization of chromatin fiber in response to the changes in its chiral parameters. The electromagnetic scattering calculations were performed using discrete dipole approximation (DDA). In the chromatin structure, nucleosomes have internal interactions that affect chromatin compaction. The merit of performing computations with DDA is that it takes into account the internal interactions. We demonstrated sensitivity of the scattering signal’s angular behavior to the changes in these chiral parameters: pitch, radius, the handedness of solenoid, number of solenoid turns, the orientation of solenoid, the orientation of nucleosomes, number of nucleosomes, and shape of nucleosomes. These scattering calculations can potentially benefit applying a label-free polarized-light-based approach to characterize chromatin DNA and chiral polymers at the nanoscale level.

Combined approach using circular intensity differential scattering microscopy under phasor map data analysis

Circular intensity differential scattering (CIDS) is based on the analysis of circular polarized light scattering and has been proven to be an interesting label-free microscopy technique sensitive to the chiral organization at the submicroscopic level. However, this approach averages the localized contrasts related to the sample polarimetric properties in the illumination volume. Additionally, the detection sensitivity suffers from the confinement of the mixture of structures, and it becomes an arduous task to discriminate the source of the signal. In this work, we show that a phasor map approach combined with CIDS microscopy has provided an intuitive view of the sample organization to recognize the presence of different molecular species in the illumination volume. The data represented in terms of polarization response mapped to a single point called a phasor also have the potential to pave the way for the analysis of large data sets. We validated this method by numerical simulations and compared the results with that of experimental data of optical devices of reference.

Review on Complete Mueller Matrix Optical Scanning Microscopy Imaging

Optical scanning microscopy techniques based on the polarization control of the light have the capability of providing non invasive label-free contrast. By comparing the polarization states of the excitation light with its transformation after interaction with the sample, the full optical properties can be summarized in a single 4×4 Mueller matrix. The main challenge of such a technique is to encode and decode the polarized light in an optimal way pixel-by-pixel and take into account the polarimetric artifacts from the optical devices composing the instrument in a rigorous calibration step. In this review, we describe the different approaches for implementing such a technique into an optical scanning microscope, that requires a high speed rate polarization control. Thus, we explore the recent advances in term of technology from the industrial to the medical applications.