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Chemistry, An Asian Journal Oct 2023Red fluorescent proteins (RFPs) represent an increasingly popular class of genetically encodable bioprobes and biomarkers that can advance next-generation breakthroughs... (Review)
Review
Red fluorescent proteins (RFPs) represent an increasingly popular class of genetically encodable bioprobes and biomarkers that can advance next-generation breakthroughs across the imaging and life sciences. Since the rational design of RFPs with improved functions or enhanced versatility requires a mechanistic understanding of their working mechanisms, while fluorescence is intrinsically an ultrafast event, a suitable toolset involving steady-state and time-resolved spectroscopic techniques has become powerful in delineating key structural features and dynamic steps which govern irreversible photoconverting or reversible photoswitching RFPs, and large Stokes shift (LSS)RFPs. The pertinent cis-trans isomerization and protonation state change of RFP chromophores in their local environments, involving key residues in protein matrices, lead to rich and complicated spectral features across multiple timescales. In particular, ultrafast excited-state proton transfer in various LSSRFPs showcases the resolving power of wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in mapping a photocycle with crucial knowledge about the red-emitting species. Moreover, recent progress in noncanonical RFPs with a site-specifically modified chromophore provides an appealing route for efficient engineering of redder and brighter RFPs, highly desirable for bioimaging. Such an effective feedback loop involving physical chemists, protein engineers, and biomedical microscopists will enable future successes to expand fundamental knowledge and improve human health.
Topics: Humans; Luminescent Proteins; Spectrum Analysis, Raman; Protons
PubMed: 37682793
DOI: 10.1002/asia.202300668 -
Molecules (Basel, Switzerland) Dec 2023In recent years, there has been renewed interest in the maintenance of food quality and food safety on the basis of metabolomic fingerprinting using vibrational... (Review)
Review
In recent years, there has been renewed interest in the maintenance of food quality and food safety on the basis of metabolomic fingerprinting using vibrational spectroscopy combined with multivariate chemometrics. Nontargeted spectroscopy techniques such as FTIR, NIR and Raman can provide fingerprint information for metabolomic constituents in agricultural products, natural products and foods in a high-throughput, cost-effective and rapid way. In the current review, we tried to explain the capabilities of FTIR, NIR and Raman spectroscopy techniques combined with multivariate analysis for metabolic fingerprinting and profiling. Previous contributions highlighted the considerable potential of these analytical techniques for the detection and quantification of key constituents, such as aromatic amino acids, peptides, aromatic acids, carotenoids, alcohols, terpenoids and flavonoids in the food matrices. Additionally, promising results were obtained for the identification and characterization of different microorganism species such as fungus, bacterial strains and yeasts using these techniques combined with supervised and unsupervised pattern recognition techniques. In conclusion, this review summarized the cutting-edge applications of FTIR, NIR and Raman spectroscopy techniques equipped with multivariate statistics for food analysis and foodomics in the context of metabolomic fingerprinting and profiling.
Topics: Spectrum Analysis, Raman; Spectroscopy, Fourier Transform Infrared; Food Analysis; Food Quality; Food Safety
PubMed: 38067662
DOI: 10.3390/molecules28237933 -
Radiology Sep 2023
Topics: Humans; Cystathionine; Spectrum Analysis
PubMed: 37668521
DOI: 10.1148/radiol.232100 -
Journal of Advanced Research Sep 2023The rapid and reliable detection of pathogenic bacteria at an early stage is a highly significant research field for public health. However, most traditional approaches... (Review)
Review
BACKGROUND
The rapid and reliable detection of pathogenic bacteria at an early stage is a highly significant research field for public health. However, most traditional approaches for pathogen identification are time-consuming and labour-intensive, which may cause physicians making inappropriate treatment decisions based on an incomplete diagnosis of patients with unknown infections, leading to increased morbidity and mortality. Therefore, novel methods are constantly required to face the emerging challenges of bacterial detection and identification. In particular, Raman spectroscopy (RS) is becoming an attractive method for rapid and accurate detection of bacterial pathogens in recent years, among which the newly developed surface-enhanced Raman spectroscopy (SERS) shows the most promising potential.
AIM OF REVIEW
Recent advances in pathogen detection and diagnosis of bacterial infections were discussed with focuses on the development of the SERS approaches and its applications in complex clinical settings.
KEY SCIENTIFIC CONCEPTS OF REVIEW
The current review describes bacterial classification using surface enhanced Raman spectroscopy (SERS) for developing a rapid and more accurate method for the identification of bacterial pathogens in clinical diagnosis. The initial part of this review gives a brief overview of the mechanism of SERS technology and development of the SERS approach to detect bacterial pathogens in complex samples. The development of the label-based and label-free SERS strategies and several novel SERS-compatible technologies in clinical applications, as well as the analytical procedures and examples of chemometric methods for SERS, are introduced. The computational challenges of pre-processing spectra and the highlights of the limitations and perspectives of the SERS technique are also discussed.Taken together, this systematic review provides an overall summary of the SERS technique and its application potential for direct bacterial diagnosis in clinical samples such as blood, urine and sputum, etc.
Topics: Humans; Spectrum Analysis, Raman; Bacteria; Bacterial Infections
PubMed: 36549439
DOI: 10.1016/j.jare.2022.11.010 -
Methods (San Diego, Calif.) Aug 2023The implementation of early cancer detection benefits the treatment outcomes with remarkably improved survival rate through the detection of rare circulating biomarkers... (Review)
Review
The implementation of early cancer detection benefits the treatment outcomes with remarkably improved survival rate through the detection of rare circulating biomarkers in body fluids. Spectroscopic technologies play a crucial role in sensitive biomarker measurements by outputting extremely strong signals. In particular, the aggregation enhanced fluorescence and Raman technologies feature the detection of targets down to single-molecule level, thereby demonstrating the great promise of early cancer detection. In this review, we focus on the aggregation-induced emission (AIE) and aggregation-related surface-enhanced Raman scattering (SERS) spectroscopic strategies for detecting cancer biomarkers. We discuss the AIE and SERS based biomarker detection using target-driven aggregation as well as the aggregated nanoprobes. Furthermore, we deliberate on the progress of developing AIE and SERS integrated platforms. Ultimately, we put forth the potential challenges and perspectives on the way to use these two spectroscopic technologies in clinical settings. It is expected this review can inspire the design of AIE and SERS integrated platform for highly sensitive and accurate cancer detection.
Topics: Humans; Biomarkers, Tumor; Spectrum Analysis, Raman; Nanotechnology; Neoplasms; Metal Nanoparticles
PubMed: 37295579
DOI: 10.1016/j.ymeth.2023.06.001 -
Biophysical Journal Aug 2023Hybridization of short nucleic acid segments (<4 nt) to single-strand templates occurs as a critical intermediate in processes such as nonenzymatic nucleic acid...
Hybridization of short nucleic acid segments (<4 nt) to single-strand templates occurs as a critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood because of the experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential noncanonical base-pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2-40 μs depending on the template and temperature. Dinucleotide hybridization and dehybridization involve a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.
Topics: DNA; RNA; Nucleic Acid Hybridization; Thermodynamics; Kinetics; Spectrum Analysis; Molecular Dynamics Simulation
PubMed: 37469144
DOI: 10.1016/j.bpj.2023.07.009 -
International Journal of Molecular... Nov 2023Surface-enhanced Raman scattering (SERS) is of growing interest for a wide range of applications, especially for biomedical analysis, thanks to its sensitivity,... (Review)
Review
Surface-enhanced Raman scattering (SERS) is of growing interest for a wide range of applications, especially for biomedical analysis, thanks to its sensitivity, specificity, and multiplexing capabilities. A crucial role for successful applications of SERS is played by the development of reproducible, efficient, and facile procedures for the fabrication of metal nanostructures (SERS substrates). Even more challenging is to extend the fabrication techniques of plasmonic nano-textures to atomic force microscope (AFM) probes to carry out tip-enhanced Raman spectroscopy (TERS) experiments, in which spatial resolution below the diffraction limit is added to the peculiarities of SERS. In this short review, we describe recent studies performed by our group during the last ten years in which novel nanofabrication techniques have been successfully applied to SERS and TERS experiments for studying bio-systems and molecular species of environmental interest.
Topics: Spectrum Analysis, Raman; Nanostructures; Metals
PubMed: 38003354
DOI: 10.3390/ijms242216164 -
Journal of Biophotonics Oct 2023Estimating postmortem intervals (PMI) is crucial in forensic investigations, providing insights into criminal cases and determining the time of death. PMI estimation... (Review)
Review
Estimating postmortem intervals (PMI) is crucial in forensic investigations, providing insights into criminal cases and determining the time of death. PMI estimation relies on expert experience and a combination of thanatological data and environmental factors but is prone to errors. The lack of reliable methods for assessing PMI in bones and soft tissues necessitates a better understanding of bone decomposition. Several research groups have shown promise in PMI estimation in skeletal remains but lack valid data for forensic cases. Current methods are costly, time-consuming, and unreliable for PMIs over 5 years. Raman spectroscopy (RS) can potentially estimate PMI by studying chemical modifications in bones and teeth correlated with burial time. This review summarizes RS applications, highlighting its potential as an innovative, nondestructive, and fast technique for PMI estimation in forensic medicine.
Topics: Humans; Body Remains; Postmortem Changes; Spectrum Analysis, Raman; Bone and Bones; Burial
PubMed: 37494000
DOI: 10.1002/jbio.202300189 -
The Analyst May 2024To improve the laser utilization efficiency and avoid photodamage in surface-enhanced Raman spectroscopy (SERS), it is imperative to introduce photon technology into the...
To improve the laser utilization efficiency and avoid photodamage in surface-enhanced Raman spectroscopy (SERS), it is imperative to introduce photon technology into the field of SERS detection. A major challenge is the inefficient interaction between the substrate and the incident wavelength, resulting in limited Raman enhancement at a relatively low level. Here, we sputtered plasmonic Au nanoparticles (NPs) onto photonic TiO nanocavities, creating a novel hybrid photonic-plasmonic resonator that achieves a large degree of optical manipulation and long-term localization. By facilely controlling the size of Au NPs, the resonance wavelength of plasmonic Au NPs can be matched with the photonic nanocavity to maximize the light trapping intensity, which leads to a synergistic enhancement of SERS the electromagnetic and chemical mechanisms, resulting in a SERS enhancement up to 1.75 × 10 under non-resonant excitation. In particular, the substrate can achieve strong absorption and localization for long wavelengths, thus enabling a large SERS enhancement with a small light intensity, which can effectively avoid the photodamage that may occur in Raman testing. The substrate can detect various biomolecules, including biomarkers in serum, thus realizing the differentiation of different cancers. This study provides a powerful and sensitive platform for SERS, facilitating bioanalysis and disease diagnosis in complex systems.
Topics: Spectrum Analysis, Raman; Gold; Metal Nanoparticles; Humans; Photons; Titanium
PubMed: 38624145
DOI: 10.1039/d4an00384e -
Spectrochimica Acta. Part A, Molecular... Nov 2023Following its first observation 50 years ago Raman optical activity (ROA), which refers to a circular polarization dependence of Raman scattering from chiral molecules,... (Review)
Review
Following its first observation 50 years ago Raman optical activity (ROA), which refers to a circular polarization dependence of Raman scattering from chiral molecules, has evolved into a powerful chiroptical spectroscopy for studying a large range of biomolecules in aqueous solution. Among other things ROA provides information about motif and fold as well as secondary structure of proteins; structure of carbohydrates and nucleic acids; polypeptide and carbohydrate structure of intact glycoproteins; and protein and nucleic acid structure of intact viruses. Quantum chemical simulations of observed Raman optical activity spectra can provide complete three-dimensional structures of biomolecules, together with information about conformational dynamics. This article reviews how ROA has provided new insight into the structure of unfolded/disordered states and sequences, ranging from the complete disorder of the random coil to the more controlled type of disorder exemplified by poly L-proline II helix in proteins, high mannose glycan chains in glycoproteins and constrained dynamic states of nucleic acids. Possible roles for this 'careful disorderliness' in biomolecular function, misfunction and disease are discussed, especially amyloid fibril formation.
Topics: Optical Rotation; Peptides; Glycoproteins; Protein Structure, Secondary; Spectrum Analysis, Raman; Nucleic Acids
PubMed: 37269652
DOI: 10.1016/j.saa.2023.122959