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Journal of the American Chemical Society Mar 2021Post-translational modification of proteins with poly(ADP-ribose) (PAR) is an important component of the DNA damage response. Four PAR synthesis inhibitors have recently...
Post-translational modification of proteins with poly(ADP-ribose) (PAR) is an important component of the DNA damage response. Four PAR synthesis inhibitors have recently been approved for the treatment of breast, ovarian, and prostate cancers. Despite the clinical significance of PAR, a molecular understanding of its function, including its binding partners, remains incomplete. In this work, we synthesized a PAR photoaffinity probe that captures and isolates endogenous PAR binders. Our method identified dozens of known PAR-binding proteins and hundreds of novel candidates involved in DNA repair, RNA processing, and metabolism. PAR binding by eight candidates was confirmed using pull-down and/or electrophoretic mobility shift assays. Using PAR probes of defined lengths, we detected proteins that preferentially bind to 40-mer versus 8-mer PAR, indicating that polymer length may regulate the outcome and timing of PAR signaling pathways. This investigation produces the first census of PAR-binding proteins, provides a proteomics analysis of length-selective PAR binding, and associates PAR binding with RNA metabolism and the formation of biomolecular condensates.
Topics: Light; Molecular Probes; Poly-ADP-Ribose Binding Proteins; Proteomics; Signal Transduction
PubMed: 33596067
DOI: 10.1021/jacs.0c12246 -
Cell Chemical Biology Jun 2017Newly developed tissue clearing techniques can be used to render intact tissues transparent. When combined with fluorescent labeling technologies and optical sectioning... (Review)
Review
Newly developed tissue clearing techniques can be used to render intact tissues transparent. When combined with fluorescent labeling technologies and optical sectioning microscopy, this allows visualization of fine structure in three dimensions. Gene-transfection techniques have proved very useful in visualizing cellular structures in animal models, but they are not applicable to human brain tissue. Here, we discuss the characteristics of an ideal chemical fluorescent probe for use in brain and other cleared tissues, and offer a comprehensive overview of currently available chemical probes. We describe their working principles and compare their performance with the goal of simplifying probe selection for neuropathologists and stimulating probe development by chemists. We propose several approaches for the development of innovative chemical labeling methods which, when combined with tissue clearing, have the potential to revolutionize how we study the structure and function of the human brain.
Topics: Animals; Brain; Humans; Molecular Imaging; Molecular Probes
PubMed: 28644957
DOI: 10.1016/j.chembiol.2017.05.015 -
ACS Sensors Oct 2022Hydrogen peroxide (HO) is a type of reactive oxygen species that regulates essential biological processes. Despite the central role of HO in pathophysiological states,...
Hydrogen peroxide (HO) is a type of reactive oxygen species that regulates essential biological processes. Despite the central role of HO in pathophysiological states, available molecular probes for assessing HO are still limited. This work develops hyperpolarized N-boronobenzyl-4-cyanopyridinium (N-BBCP) as a rationally designed molecular probe for detecting HO. The N-BBCP demonstrated favorable physicochemical and biochemical properties for HO detection and dynamic nuclear polarization, allowing noninvasive detection of HO. In particular, N-BBCP and the products possessed long spin-lattice relaxation times and spectrally resolvable N chemical shift differences. The performance of hyperpolarized N-BBCP was demonstrated both and with time-resolved N-MRS. This study highlights a promising approach to designing a reaction-based N-labeled molecular imaging agent for detecting oxidative stress
Topics: Hydrogen Peroxide; Molecular Probes; Molecular Imaging; Reactive Oxygen Species; Oxidative Stress
PubMed: 36255172
DOI: 10.1021/acssensors.2c01720 -
Theranostics 2023Lipid droplets (LDs) are critical organelles associated with many physiological processes in eukaryotic cells. To visualize and study LDs, fluorescence imaging...
Lipid droplets (LDs) are critical organelles associated with many physiological processes in eukaryotic cells. To visualize and study LDs, fluorescence imaging techniques including the confocal imaging as well as the emerging super-resolution imaging of stimulated emission depletion (STED), have been regarded as the most useful methods. However, directly limited by the availability of advanced LDs fluorescent probes, the performances of LDs fluorescence imaging are increasingly unsatisfied with respect to the fast research progress of LDs. We herein newly developed a superior LDs fluorescent probe named as a powerful tool for LDs fluorescence imaging and biological study. Colocalization imaging of and LDs fluorescent probe Ph-Red was conducted in four cell lines. The LDs staining selectivity and the photostability of were also evaluated by comparing with the commercial LDs probe Nile Red. The in-situ fluorescence lifetime of in LDs was determined by time-gated detection. The cytotoxicity of was assessed by MTT assay. The STED saturation intensity as well as the power- and gate time-dependent resolution were tested by Leica SP8 STED super-resolution nanoscopy. The time-lapse 3D confocal imaging and time-lapse STED super-resolution imaging were then designed to study the complex physiological functions of LDs. Featuring with the advantages of the super-photostability, high LDs selectivity, long fluorescence lifetime and low STED saturation intensity, the fluorescent probe was capable of the long-term time-lapse three-dimensional (3D) confocal imaging to in-situ monitor LDs in 3D space and the time-lapse STED super-resolution imaging (up to 500 STED frames) to track the dynamics of LDs with nanoscale resolution (37 nm). Based on the state-of-the-art fluorescence imaging results, some new biological insights into LDs have been successfully provided. For instance, the long-term time-lapse 3D confocal imaging has surely answered an important and controversial question that the number of LDs would significantly decrease rather than increase upon starvation stimulation; the time-lapse STED super-resolution imaging with the highest resolution has impressively uncovered the fission process of nanoscale LDs for the first time; the starvation-induced change of LDs in size and in speed has been further revealed at nanoscale by the STED super-resolution imaging. All of these results not only highlight the utility of the newly developed fluorescent probe but also significantly promote the biological study of LDs.
Topics: Molecular Probes; Microscopy, Fluorescence; Fluorescent Dyes; Lipid Droplets; Optical Imaging
PubMed: 36593956
DOI: 10.7150/thno.79052 -
Contrast Media & Molecular Imaging 2014A new method for imaging the tumor human vascular endothelial growth factor 165 (VEGF 165) is presented. A magnetic resonance imaging (MRI) probe was prepared by...
A new method for imaging the tumor human vascular endothelial growth factor 165 (VEGF 165) is presented. A magnetic resonance imaging (MRI) probe was prepared by crosslinking ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles to the aptamer for tumor vascular endothelial growth factor 165 (VEGF165-aptamer). The molecular probe was evaluated for its in vitro and in vivo activities toward VEGF165. Enzyme-linked immunosorbent assay showed that the VEGF165-aptamer-USPIO nanoparticles conjugate specifically binds to VEGF165 in vitro. A cell proliferation test showed that VEGF165-aptamer-USPIO seems to block the proliferation of human umbilical vein endothelial cells induced by free VEGF165, suggesting that VEGF165 is an effective target of this molecular probe. In xenograft mice carrying liver cancer that expresses VEGF165, T2-weighted imaging of the tumor displayed marked negative enhancement 3 h after the intravenous administration of VEGF165-aptamer-USPIO. The enhancement disappeared 6 h after administration of the probe. These results suggest the targeted imaging effect of VEGF165-aptamer-USPIO probe in vivo for VEGF165-expressing tumors. This is the first report of a targeted MRI molecular probe based on USPIO and VEGF165-aptamer.
Topics: Animals; Aptamers, Nucleotide; Aptamers, Peptide; Cell Line, Tumor; Contrast Media; Dextrans; Human Umbilical Vein Endothelial Cells; Humans; Magnetic Resonance Imaging; Magnetite Nanoparticles; Mice; Molecular Probes; Vascular Endothelial Growth Factor A
PubMed: 24729581
DOI: 10.1002/cmmi.1584 -
Current Opinion in Chemical Biology Aug 2016The monoclonal antibody (mAb) has proven to be a good platform for designing specific molecular imaging probes due to its superior binding specificity. Several optical... (Review)
Review
The monoclonal antibody (mAb) has proven to be a good platform for designing specific molecular imaging probes due to its superior binding specificity. Several optical imaging probes have been developed for surgical navigation in patients and are in early phase clinical trials. However, an inherent limitation of using the mAb is its pharmacokinetics which result in a prolonged circulating half-life and slow clearance from the body. This results in undesirable target to background ratios during imaging. In this review, we first describe the mAb as a platform material for optical probe design and then discuss optimizing the design of monoclonal antibody-based optical molecular imaging probes by focusing on chemistry, biology and pharmacology.
Topics: Antibodies, Monoclonal; Fluorescent Dyes; Molecular Imaging; Molecular Probes
PubMed: 27281509
DOI: 10.1016/j.cbpa.2016.05.015 -
Theranostics 2017The precision oncology significantly relies on the development of multifunctional agents to integrate tumor targeting, imaging and therapeutics. In this study, a first...
The precision oncology significantly relies on the development of multifunctional agents to integrate tumor targeting, imaging and therapeutics. In this study, a first small-molecule theranostic probe, RhoSSCy is constructed by conjugating 5'-carboxyrhodamines (Rho) and heptamethine cyanine IR765 (Cy) using a reducible disulfide linker and pH tunable amino-group to realize thiols/pH dual sensing. experiments verify that RhoSSCy is highly sensitive for quantitative analysis and imaging intracellular pH gradient and biothiols. Furthermore, RhoSSCy shows superb tumor targeted dual-modal imaging via near-infrared fluorescence (NIRF) and photoacoustic (PA). Importantly, RhoSSCy also induces strongly reactive oxygen species for tumor photodynamic therapy (PDT) with robust antitumor activity both and . Such versatile small-molecule theranostic probe may be promising for tumor targeted imaging and precision therapy.
Topics: Adenocarcinoma; Animals; Disease Models, Animal; Humans; MCF-7 Cells; Mice, Inbred BALB C; Molecular Probes; Photochemotherapy; Photosensitizing Agents; Treatment Outcome
PubMed: 28638467
DOI: 10.7150/thno.18437 -
Molecular Imaging 2019Nonalcoholic fatty liver disease (NAFLD) is a significant public health challenge afflicting approximately 1 billion individuals both in the Western world and in the... (Review)
Review
Nonalcoholic fatty liver disease (NAFLD) is a significant public health challenge afflicting approximately 1 billion individuals both in the Western world and in the East world. While liver biopsy is considered as gold standard in the diagnosis and staging of liver fibrosis, noninvasive imaging technologies, including ultrasonography, computed tomography, single-photon emission computed tomography (SPECT), magnetic resonance imaging, and positron emission tomography (PET) could offer more sensitive, comprehensive, and quantitative measurement for NAFLD. In this review, we focus on recent development and applications of PET/SPECT molecular probes that enable multispatial/temporal visualization and quantification of physiopathological progress at the molecular level in the NAFLD. We shall also discuss the limitations of current radioligands and future direction for PET/SPECT probe development.
Topics: Biomarkers; Hematology; Humans; Molecular Probes; Non-alcoholic Fatty Liver Disease; Positron-Emission Tomography; Tomography, Emission-Computed, Single-Photon
PubMed: 31478458
DOI: 10.1177/1536012119871455 -
Molecular Imaging Dec 2011Molecular imaging allows clinicians to visualize disease-specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With... (Review)
Review
Molecular imaging allows clinicians to visualize disease-specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology--all essential to progress in molecular imaging probe development. In this review, we discuss target selection, screening techniques, and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents.
Topics: Animals; Antibodies; DNA; Humans; Molecular Imaging; Molecular Probe Techniques; Molecular Probes; Peptides; RNA
PubMed: 22201532
DOI: No ID Found -
Molecules (Basel, Switzerland) Mar 2022Biomolecules participate in various physiological and pathological processes through intermolecular interactions generally driven by non-covalent forces. In the present... (Review)
Review
Biomolecules participate in various physiological and pathological processes through intermolecular interactions generally driven by non-covalent forces. In the present review, the force-induced remnant magnetization spectroscopy (FIRMS) is described and illustrated as a novel method to measure non-covalent forces. During the FIRMS measurement, the molecular magnetic probes are magnetized to produce an overall magnetization signal. The dissociation under the interference of external force yields a decrease in the magnetic signal, which is recorded and collected by atomic magnetometer in a spectrum to study the biological interactions. Furthermore, the recent FIRMS development with various external mechanical forces and magnetic probes is summarized.
Topics: Magnetics; Mechanical Phenomena; Microscopy, Atomic Force; Molecular Probes; Spectrum Analysis
PubMed: 35408471
DOI: 10.3390/molecules27072072