Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Design and evaluation of Raman reporters for the Raman-silent region.

ABSTRACT: Rationale: Surface enhanced Raman scattering (SERS) is proving to be a useful tool for biomedical imaging. However, this imaging technique can suffer from poor signal-to-noise ratio, as the complexity of biological tissues can lead to overlapping of Raman bands from tissues and the Raman reporter molecule utilized. Methods: Herein we describe the synthesis of triple bond containing Raman reporters that scatter light in the biological silent window, between 1750 cm^-1 and 2750 cm^-1. Results: Our SERS nanoprobes are comprised of uniquely designed Raman reporters containing either alkyne- or cyano-functional groups, enabling them to be readily distinguished from background biological tissue. Conclusion: We identify promising candidates that eventually can be moved forward as Raman reporters in SERS nanoparticles for highly specific contrast-enhanced Raman-based disease or analyte detection in biological applications.

SUBMITTER: Plakas K

PROVIDER: S-EPMC8671958 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Design and evaluation of Raman reporters for the Raman-silent region.

Plakas Konstantinos K Rosch Lauren E LE Clark Michael D MD Adbul-Rashed Shukree S Shaffer Travis M TM Harmsen Stefan S Gambhir Sanjiv S SS Detty Michael R MR

Nanotheranostics 20220101 1

Rationale: Surface enhanced Raman scattering (SERS) is proving to be a useful tool for biomedical imaging. However, this imaging technique can suffer from poor signal-to-noise ratio, as the complexity of biological tissues can lead to overlapping of Raman bands from tissues and the Raman reporter molecule utilized. Methods: Herein we describe the synthesis of triple bond containing Raman reporters that scatter light in the biological silent window, between 1750 cm-1 and ...[more]

PMID: 34976577

Similar Datasets

Design and Synthesis of Novel Raman Reporters for Bioorthogonal SERS Nanoprobes Engineering.

Project description:Surface-enhanced Raman spectroscopy (SERS) exploiting Raman reporter-labeled nanoparticles (RR@NPs) represents a powerful tool for the improvement of optical bio-assays due to RRs' narrow peaks, SERS high sensitivity, and potential for multiplexing. In the present work, starting from low-cost and highly available raw materials such as cysteamine and substituted benzoic acids, novel bioorthogonal RRs, characterized by strong signal (103 counts with FWHM < 15 cm-1) in the biological Raman-silent region (>2000 cm-1), RRs are synthesized by implementing a versatile, modular, and straightforward method with high yields and requiring three steps lasting 18 h, thus overcoming the limitations of current reported procedures. The resulting RRs' chemical structure has SH-pendant groups exploited for covalent conjugation to high anisotropic gold-NPs. RR@NPs constructs work as SERS nanoprobes demonstrating high colloidal stability while retaining NPs' physical and vibrational properties, with a limit of detection down to 60 pM. RR@NPs constructs expose carboxylic moieties for further self-assembling of biomolecules (such as antibodies), conferring tagging capabilities to the SERS nanoprobes even in heterogeneous samples, as demonstrated with in vitro experiments by transmembrane proteins tagging in cell cultures. Finally, thanks to their non-overlapping spectra, we envision and preliminary prove the possibility of exploiting RR@NPs constructs simultaneously, aiming at improving current SERS-based multiplexing bioassays.

| S-EPMC9144405 | biostudies-literature

Biomedical applications, perspectives and tag design concepts in the cell - silent Raman window.

Project description:Spectroscopic studies increasingly employ Raman tags exhibiting a signal in the cell - silent region of the Raman spectrum (1800-2800 cm-1), where bands arising from biological molecules are inherently absent. Raman tags bearing functional groups which contain a triple bond, such as alkyne and nitrile or a carbon-deuterium bond, have a distinct vibrational frequency in this region. Due to the lack of spectral background and cell-associated bands in the specific area, the implementation of those tags can help overcome the inherently poor signal-to-noise ratio and presence of overlapping Raman bands in measurements of biological samples. The cell - silent Raman tags allow for bioorthogonal imaging of biomolecules with improved chemical contrast and they have found application in analyte detection and monitoring, biomarker profiling and live cell imaging. This review focuses on the potential of the cell - silent Raman region, reporting on the tags employed for biomedical applications using variants of Raman spectroscopy.

| S-EPMC10989507 | biostudies-literature

Raman

Project description:Raman spectroscopy for pathogen detection and antibiotic resistance identification

| PRJEB59025 | ENA

Raman

Project description:Multi-excitation Raman Spectroscopy Complements Whole Genome Sequencing for Rapid Detection of Bacterial Infection and Resistance in WHO Priority Pathogens

| PRJEB59061 | ENA

Enzyme Sensing Using 2-Mercaptopyridine-Carbonitrile Reporters and Surface-Enhanced Raman Scattering.

Project description:The high sensitivity and functional group selectivity of surface-enhanced Raman scattering (SERS) make it an attractive method for enzyme sensing, but there is currently a severe lack of enzyme substrates that release SERS reporter molecules with favorable detection properties. We find that 2-mercaptopyridine-3-carbonitrile ( o-MPN) and 2-mercaptopyridine-5-carbonitrile ( p-MPN) are highly effective as SERS reporter molecules that can be captured by silver or gold nanoparticles to give intense SERS spectra, each with a distinctive nitrile peak at 2230 cm-1. p-MPN is a more sensitive reporter and can be detected at low nanomolar concentrations. An assay validation study synthesized two novel substrate molecules, Glc-o-MPN and Glc-p-MPN, and showed that they can be cleaved efficiently by β-glucosidase (K m = 228 and 162 μM, respectively), an enzyme with broad industrial and biomedical utility. Moreover, SERS detection of the released reporters ( o-MPN or p-MPN) enabled sensing of β-glucosidase activity and β-glucosidase inhibition. Comparative experiments using a crude almond flour extract showed that the presence of β-glucosidase activity could be confirmed by SERS detection in a much shorter time period (>10 time shorter) than by UV-vis absorption detection. It is likely that a wide range of enzyme assays and diagnostic tests can be developed using 2-mercaptopyridine-carbonitriles as SERS reporter molecules.

| S-EPMC8867545 | biostudies-literature

Intein-based Design Expands Diversity of Selenocysteine Reporters.

Project description:The presence of selenocysteine in a protein confers many unique properties that make the production of recombinant selenoproteins desirable. Targeted incorporation of Sec into a protein of choice is possible by exploiting elongation factor Tu-dependent reassignment of UAG codons, a strategy that has been continuously improved by a variety of means. Improving selenoprotein yield by directed evolution requires selection and screening markers that are titratable, have a high dynamic range, enable high-throughput screening, and can discriminate against nonspecific UAG decoding. Current screening techniques are limited to a handful of reporters where a cysteine (Cys) or Sec residue normally affords activity. Unfortunately, these existing Cys/Sec-dependent reporters lack the dynamic range of more ubiquitous reporters or suffer from other limitations. Here we present a versatile strategy to adapt established reporters for specific Sec incorporation. Inteins are intervening polypeptides that splice themselves from the precursor protein in an autocatalytic splicing reaction. Using an intein that relies exclusively on Sec for splicing, we show that this intein cassette can be placed in-frame within selection and screening markers, affording reporter activity only upon successful intein splicing. Furthermore, because functional splicing can only occur when a catalytic Sec is present, the amount of synthesized reporter directly measures UAG-directed Sec incorporation. Importantly, we show that results obtained with intein-containing reporters are comparable to the Sec incorporation levels determined by mass spectrometry of isolated recombinant selenoproteins. This result validates the use of these intein-containing reporters to screen for evolved components of a translation system yielding increased selenoprotein amounts.

| S-EPMC8847544 | biostudies-literature

Multiplexing potential of NIR resonant and non-resonant Raman reporters for bio-imaging applications.

Project description:Multiplexed imaging, which allows for the interrogation of multiple molecular features simultaneously, is vital for addressing numerous challenges across biomedicine. Optically unique surface-enhanced Raman scattering (SERS) nanoparticles (NPs) have the potential to serve as a vehicle to achieve highly multiplexed imaging in a single acquisition, which is non-destructive, quantitative, and simple to execute. When using laser excitation at 785 nm, which allows for a lower background from biological tissues, near infrared (NIR) dyes can be used as Raman reporters to provide high Raman signal intensity due to the resonance effect. This class of imaging agents are known as surface-enhanced resonance Raman scattering (SERRS) NPs. Investigators have predominantly utilized two classes of Raman reporters in their nanoparticle constructs for use in biomedical applications: NIR-resonant and non-resonant Raman reporters. Herein, we investigate the multiplexing potential of five non-resonant SERS: BPE, 44DP, PTT, PODT, and BMMBP, and five NIR resonant SERRS NP flavors with heptamethine cyanine dyes: DTTC, IR-770, IR-780, IR-792, and IR-797, which have been extensively used for biomedical imaging applications. Although SERRS NPs display high Raman intensities, due to their resonance properties, we observed that non-resonant SERS NP concentrations can be quantitated by the intensity of their unique emissions with higher accuracy. Spectral unmixing of five-plex mixtures revealed that the studied non-resonant SERS NPs maintain their detection limits more robustly as compared to the NIR resonant SERRS NP flavors when introducing more components into a mixture.

| S-EPMC10947999 | biostudies-literature

Design of the silent cerebral infarct transfusion (SIT) trial.

Project description:BackgroundSilent cerebral infarct (SCI) is the most common cause of serious neurological disease in sickle cell anemia (SCA), affecting approximately 22% of children. The goal of this trial is to determine whether blood transfusion therapy will reduce further neurological morbidity in children with SCI, and if so, the magnitude of this benefit.ProcedureThe Silent Cerebral Infarct Transfusion (SIT) Trial includes 29 clinical sites and 3 subsites, a Clinical Coordinating Center, and a Statistical and Data Coordinating Center, to test the following hypothesis: prophylactic blood transfusion therapy in children with SCI will result in at least an 86% reduction in the rate of subsequent overt strokes or new or progressive cerebral infarcts as defined by magnetic resonance imaging (MRI) of the brain. The intervention is blood transfusion versus observation. Two hundred and four participants (102 in each treatment assignment) will ensure 85% power to detect the effect necessary to recommend transfusion therapy (86% reduction), after accounting for 10% drop out and 19% crossover rates. MRI examination of the brain is done at screening, immediately before randomization and study exit. Each randomly assigned participant receives a cognitive test battery at study entry, 12-18 months later, and study exit and an annual neurological examination. Blood is obtained from all screened participants for a biologic repository containing serum and a renewable source of DNA.ConclusionThe SIT Trial could lead to a change in standard care practices for children affected with SCA and SCI, with a consequent reduction in neurological morbidity.

| S-EPMC5572477 | biostudies-literature

Isotopic graphene-isolated-Au-nanocrystals with cellular Raman-silent signals for cancer cell pattern recognition.

Project description:For cancer diagnosis, technologies must be capable of molecular recognition, and they must possess a built-in pattern recognition component for efficient imaging and discrimination of targeted cancer cells. Surface enhanced Raman scattering (SERS) tags based on plasmonically active nanoparticles hold promise for accurate and efficient cancer cell recognition, owing to ultra-narrow peak and sensitive optical properties. However, a complex fingerprint spectrum increases data analysis difficulty, making it necessary to develop multicolor SERS tags with a simple fingerprint spectrum. To address this, we herein fabricated SERS-encoded nanoparticles (NPs) with stable and simple fingerprint spectrum through synthesis of isotopic cellular Raman-silent graphene-isolated-Au-nanocrystals (GIANs) and conjugation with phospholipid-polyethylene glycol-linked aptamers to target proteins overexpressed on the cancer cell surface. GIANs, which possess the properties of graphitic nanomaterials, such as super-stable optical properties and high Raman cross-section, showed enhanced SERS signals. The 2D-band Raman shift of GIAN, which located in the cellular Raman-silent region, was easily regulated through fabrication of isotopic GIANs without changing their molecular structure. Such GIAN tags demonstrated multiplexed Raman imaging capability, both in vivo and in vitro, with low background interference. Moreover, cell membrane protein (nucleolin, mucin and epithelial cell adhesion molecule)-specific, aptamer-conjugated isotopic GIANs were fabricated and feasibly applied to built-in coding for rapid imaging and pattern recognition of targeted cancer cells. Such isotopic GIAN-aptamer-encoders show high potential for efficient cancer cell identification and diagnosis.

| S-EPMC5914539 | biostudies-literature

Design, synthesis, and electrophysiological evaluation of NS6740 derivatives: Exploration of the structure-activity relationship for alpha7 nicotinic acetylcholine receptor silent activation.

Project description:The α7 nicotinic acetylcholine receptor (nAChR) silent agonists, able to induce receptor desensitization and promote the α7 metabotropic function, are emerging as new promising therapeutic anti-inflammatory agents. Herein, we report the structure-activity relationship investigation of the archetypal silent agonist NS6740 (1,4-diazabicyclo[3.2.2]nonan-4-yl(5-(3-(trifluoromethyl)-phenyl)-furan-2-yl)methanone) (1) to elucidate the ligand-receptor interactions responsible for the α7 silent activation. In this study, NS6740 fragments 11-16 and analogs 17-32 were designed, synthesized, and assayed on human α7 nAChRs expressed in Xenopus laevis oocytes with two-electrode voltage clamping experiments. All together the structural portions of NS6740 were critical to engender its peculiar activity profile. The diazabicyclic nucleus was essential but not sufficient for inducing α7 silent activation. The central hydrogen-bond acceptor core and the aromatic moiety were crucial for promoting prolonged α7 receptor binding and sustained desensitization. Compounds 13 and 17 were efficacious partial agonists. Compounds 12, 21, 23-26, and 30 strongly desensitized α7 nAChR and therefore may be of interest for additional investigation of inflammation responses. We gained key structural information useful for further silent agonist development.

| S-EPMC7590973 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data