Nanosized DNA Hydrogel Functionalized with a DNAzyme Tetrahedron for Highly Efficient Gene Silencing.

DNAzymes are DNA oligonucleotides that have catalytic activity without the assistance of protein enzymes. In particular, RNA-cleaving DNAzymes were considered as ideal candidates for gene therapy due to their unique characteristics. Nevertheless, efforts to use DNAzyme as a gene therapeutic agent are limited by issues such as their low physiological stability in serum and intracellular delivery efficiency. In this study, we developed a nanosized synthetic DNA hydrogel functionalized with a DNAzyme tetrahedron (TDz Dgel) to overcome these limitations. We observed remarkable improvement in the gene-silencing effect as well as intracellular uptake without the support of gene transfection reagents using TDz Dgel. The improved catalytic activity of the DNAzyme resulted from the combination of the cell-penetrating DNA tetrahedron structure and high stability of DNA hydrogel. We envision that this approach will become a convenient and efficient strategy for gene-silencing therapy using DNAzyme in the future.

Systematic Selection of High-Affinity ssDNA Sequences to Carbon Nanotubes.

Single-walled carbon nanotubes (SWCNTs) have gained significant interest for their potential in biomedicine and nanoelectronics. The functionalization of SWCNTs with single-stranded DNA (ssDNA) enables the precise control of SWCNT alignment and the development of optical and electronic biosensors. This study addresses the current gaps in the field by employing high-throughput systematic selection, enriching high-affinity ssDNA sequences from a vast random library. Specific base compositions and patterns are identified that govern the binding affinity between ssDNA and SWCNTs. Molecular dynamics simulations validate the stability of ssDNA conformations on SWCNTs and reveal the pivotal role of hydrogen bonds in this interaction. Additionally, it is demonstrated that machine learning could accurately distinguish high-affinity ssDNA sequences, providing an accessible model on a dedicated webpage (http://service.k-medai.com/ssdna4cnt). These findings open new avenues for high-affinity ssDNA-SWCNT constructs for stable and sensitive molecular detection across diverse scientific disciplines.

Recent Advances in Biological Applications of Aptamer-Based Fluorescent Biosensors.

Aptamers have been spotlighted as promising bio-recognition elements because they can be tailored to specific target molecules, bind to targets with a high affinity and specificity, and are easy to chemically synthesize and introduce functional groups to. In particular, fluorescent aptasensors are widely used in biological applications to diagnose diseases as well as prevent diseases by detecting cancer cells, viruses, and various biomarkers including nucleic acids and proteins as well as biotoxins and bacteria from food because they have the advantages of a high sensitivity, selectivity, rapidity, a simple detection process, and a low price. We introduce screening methods for isolating aptamers with q high specificity and summarize the sequences and affinities of the aptamers in a table. This review focuses on aptamer-based fluorescence detection sensors for biological applications, from fluorescent probes to mechanisms of action and signal amplification strategies.

Advances and Trends in miRNA Analysis Using DNAzyme-Based Biosensors.

miRNAs are endogenous small, non-coding RNA molecules that function in post-transcriptional regulation of gene expression. Because miRNA plays a pivotal role in maintaining the intracellular environment, and abnormal expression has been found in many cancer diseases, detection of miRNA as a biomarker is important for early diagnosis of disease and study of miRNA function. However, because miRNA is present in extremely low concentrations in cells and many types of miRNAs with similar sequences are mixed, traditional gene detection methods are not suitable for miRNA detection. Therefore, in order to overcome this limitation, a signal amplification process is essential for high sensitivity. In particular, enzyme-free signal amplification systems such as DNAzyme systems have been developed for miRNA analysis with high specificity. DNAzymes have the advantage of being more stable in the physiological environment than enzymes, easy to chemically synthesize, and biocompatible. In this review, we summarize and introduce the methods using DNAzyme-based biosensors, especially with regard to various signal amplification methods for high sensitivity and strategies for improving detection specificity. We also discuss the current challenges and trends of these DNAzyme-based biosensors.

Gold Nanoparticle-Carrying T Cells for the Combined Immuno-Photothermal Therapy.

Cancer immunotherapy is a promising therapy to treat cancer patients with minimal toxicity, but only a small fraction of patients responded to it as a monotherapy. In this study, a strategy to boost therapeutic efficacy by combining an immunotherapy based on ex vivo expanded tumor-reactive T cells is devised, or adoptive cell therapy (ACT), with photothermal therapy (PTT). Smart gold nanoparticles (sAuNPs), which aggregates to form gold nanoclusters in the cells, are loaded into T cells, and their photothermal effects within T cells are confirmed. When transferred into tumor-bearing mice, large number of sAuNP-carrying T cells successfully infiltrate into tumor tissues and exert anti-tumor activity to suspend tumor growth, but over time tumor cells evade and regrow. Of note, ≈20% of injected doses of sAuNPs are deposited in tumor tissues, suggesting T cells are an efficient nanoparticle tumor delivery vehicle. When T cells no longer control tumor growth, PTT is performed to further eliminate tumors. In this manner, ACT and PTT are temporally coupled, and the combined immuno-photothermal treatment demonstrated significantly greater therapeutic efficacy than the monotherapy.

Investigation of artificial intelligence integrated fluorescence endoscopy image analysis with indocyanine green for interpretation of precancerous lesions in colon cancer.

Indocyanine green (ICG) has been used in clinical practice for more than 40 years and its safety and preferential accumulation in tumors has been reported for various tumor types, including colon cancer. However, reports on clinical assessments of ICG-based molecular endoscopy imaging for precancerous lesions are scarce. We determined visualization ability of ICG fluorescence endoscopy in colitis-associated colon cancer using 30 lesions from an azoxymethane/dextran sulfate sodium (AOM/DSS) mouse model and 16 colon cancer patient tissue-samples. With a total of 60 images (optical, fluorescence) obtained during endoscopy observation of mouse colon cancer, we used deep learning network to predict four classes (Normal, Dysplasia, Adenoma, and Carcinoma) of colorectal cancer development. ICG could detect 100% of carcinoma, 90% of adenoma, and 57% of dysplasia, with little background signal at 30 min after injection via real-time fluorescence endoscopy. Correlation analysis with immunohistochemistry revealed a positive correlation of ICG with inducible nitric oxide synthase (iNOS; r > 0.5). Increased expression of iNOS resulted in increased levels of cellular nitric oxide in cancer cells compared to that in normal cells, which was related to the inhibition of drug efflux via the ABCB1 transporter down-regulation resulting in delayed retention of intracellular ICG. With artificial intelligence training, the accuracy of image classification into four classes using data sets, such as fluorescence, optical, and fluorescence/optical images was assessed. Fluorescence images obtained the highest accuracy (AUC of 0.8125) than optical and fluorescence/optical images (AUC of 0.75 and 0.6667, respectively). These findings highlight the clinical feasibility of ICG as a detector of precancerous lesions in real-time fluorescence endoscopy with artificial intelligence training and suggest that the mechanism of ICG retention in cancer cells is related to intracellular nitric oxide concentration.

Contrast Agents for Photoacoustic Imaging: A Review Focusing on the Wavelength Range.

Photoacoustic imaging using endogenous chromophores as a contrast has been widely applied in biomedical studies owing to its functional imaging capability at the molecular level. Various exogenous contrast agents have also been investigated for use in contrast-enhanced imaging and functional analyses. This review focuses on contrast agents, particularly in the wavelength range, for use in photoacoustic imaging. The basic principles of photoacoustic imaging regarding light absorption and acoustic release are introduced, and the optical characteristics of tissues are summarized according to the wavelength region. Various types of contrast agents, including organic dyes, semiconducting polymeric nanoparticles, gold nanoparticles, and other inorganic nanoparticles, are explored in terms of their light absorption range in the near-infrared region. An overview of the contrast-enhancing capacity and other functional characteristics of each agent is provided to help researchers gain insights into the development of contrast agents in photoacoustic imaging.

Zwitterion-Coated Colloidal Magnetic Nanoparticle Clusters for Reduced Nonspecific Adsorption of Biomolecules.

This paper demonstrates fabrication of silica-shell-coated magnetic nanoparticle clusters (SMNCs) and subsequent surface engineering of SMNCs to produce surface-modified SMNCs that have zwitterionic and primary amine ligands (SMNC-ZW/Am). SMNC-ZW/Am was passivated by zwitterionic ligands for improved colloidal stability and reduced nonspecific adsorption and by primary amine ligands for facilitated conjugation with biomolecules. Hydrodynamic (HD) size and zeta potential of SMNC-ZW/Am could be flexibly tuned by controlling the relative amounts of zwitterionic and primary amine ligands. SMNC-ZW/Am had higher colloidal stability in high salt concentration and broad pH range than did bare SMNC. Nonspecific adsorption with biomolecules onto SMNC-ZW/Am surface was significantly suppressed by the zwitterionic ligands. The facile bioconjugation capability of SWNC-ZW/Am enabled conjugation of biotin and antibody to the SWNC-ZW/Am surface. Biomolecule-conjugated SMNC-ZW/Am showed specific binding affinity to streptavidin and Salmonella bacteria, with reduced nonspecific adsorption; therefore, SWMC-ZW/Am has potential use as an antifouling nanosubstrate for separation and bioanalysis.

Controlled Photoinduced Electron Transfer from InP/ZnS Quantum Dots through Cu Doping: A New Prototype for the Visible-Light Photocatalytic Hydrogen Evolution Reaction.

Photoexcited electron extraction from semiconductors can be useful for converting solar energy into useful forms of energy. Although InP quantum dots (QDs) are considered alternative materials for solar energy conversion, the inherent instability of bare InP QDs demands the use of passivation layers such as ZnS for practical applications, which impedes carrier extraction from the QDs. Here, we demonstrate that Cu-doped InP/ZnS (InP/Cu:ZnS) QDs improve the electron transfer ability due to hole capture by Cu dopants. Steady-state and time-resolved photoluminescence studies confirmed that electrons were effectively transferred from the InP/Cu:ZnS QDs to a benzoquinone acceptor by retarding the electron-hole recombination within the QD. We evaluated the photocatalytic H2 evolution performance of InP/Cu:ZnS QDs under visible light, which showed outstanding photocatalytic H2 evolution activity and stability under visible light illumination. The photocatalytic activity was preserved even in the absence of a cocatalyst.

Longitudinal shape evolution of Ag2S nanoparticles from nanospheres, rhombic dodecahedrons, nanorods, to nanocubes.

Longitudinal shape evolution of Ag2S nanoparticles is reported. Initially 9 nm nanospheres turn into faceted rhombic dodecahedrons and elongate to minimize surface energy. The elongated rhombic dodecahedrons show oriented attachments to 〈-104〉 directions sequentially yielding dimers, linear oligomers, and nanorods. Lateral sides of nanorods fuse to thermodynamically stable nanocubes upon ripening.

Evolution from unimolecular to colloidal-quantum-dot-like character in chlorine or zinc incorporated InP magic size clusters.

Magic-sized clusters (MSCs) can be isolated as intermediates in quantum dot (QD) synthesis, and they provide pivotal clues in understanding QD growth mechanisms. We report syntheses for two families of heterogeneous-atom-incorporated InP MSCs that have chlorine or zinc atoms. All the MSCs could be directly synthesized from conventional molecular precursors. Alternatively, each series of MSCs could be prepared by sequential conversions. 386-InP MSCs could be converted to F360-InP:Cl MSCs, then to F399-InP:Cl MSCs. Similarly, F360-InP:Zn MSCs could be converted to F408-InP:Zn MSCs, then to F393-InP:Zn MSCs. As the conversion proceeded, evolution from uni-molecule-like to QD-like characters was observed. Early stage MSCs showed active inter-state conversions in the excited states, which is characteristics of small molecules. Later stage MSCs exhibited narrow photoinduced absorptions at lower-energy region like QDs. The crystal structure also gradually evolved from polytwistane to more zinc-blende.

Colloidal Porous AuAg Alloyed Nanoparticles for Enhanced Photoacoustic Imaging.

Colloidal porous AuAg alloyed nanoparticles (pAuAgNPs) were synthesized by galvanic replacement reaction from Ag nanocubes. pAuAgNPs have a 50 nm exterior diameter and half of their inner space consists of voids that have a bimodal size distribution with peaks at 21 and 8.3 nm. pAuAgNPs showed a plasmonic peak at 750 nm, which was exploited for photoacoustic (PA) imaging. Gold nanorods (AuNRs) were prepared and used as the control; they have a strong plasmonic peak at 720 nm. In in vitro experiments at respective plasmonic peak excitations, pAuAgNPs gave stronger PA signals than AuNRs by 8.9 times per particle and 11.7 times per dosage by exogenous atom. The high surface area per volume as a result of the inner voids amplified the PA signals by efficient thermoacoustic conversion. In experiments of chicken-tissue phantoms, pAuAgNPs showed PA signals through 4.5 cm thick tissue, whereas AuNRs gave no detectable signal. In whole-body in vivo experiments, pAuAgNPs injected into the body showed 2.7 times stronger PA signals than AuNRs. Coating the pAuAgNPs with a silica layer additionally increased their PA signal by 1.8 times when compared to the uncoated ones.

Multiplex Protein Imaging with Secondary Ion Mass Spectrometry Using Metal Oxide Nanoparticle-Conjugated Antibodies.

In spite of recent developments in mass spectrometry imaging techniques, high-resolution multiplex protein bioimaging techniques are required to unveil the complex inter- and intracellular biomolecular interactions for accurate understanding of life phenomena and disease mechanisms. Herein, we report multiplex protein imaging with secondary ion mass spectrometry (SIMS) using metal oxide nanoparticle (MONP)-conjugated antibodies with <300 nm spatial resolution in the low ion dose without ion beam damage because of the high secondary ion yields of the MONPs, which can provide simultaneous imaging of several proteins, especially from cell membranes. We applied our new imaging technique for the study of hippocampal tissue samples from control and Alzheimer's disease (AD) model mice; the proximity of protein clusters in the hippocampus CA1 region showed intriguing dependence on aging and AD progress, suggesting that protein cluster proximity may be helpful for understanding pathological pathways in the microscopic cellular level.

Reversibly pH-responsive gold nanoparticles and their applications for photothermal cancer therapy.

Microenvironment responsive nanomaterials are attractive for therapeutic applications with regional specificity. Here we report pH responsive gold nanoparticles which are designed to aggregate in acidic condition similar to cancer environment and returned to its original disassembled states in a physiological pH. The pH responsive behavior of the particles is derived by change of electrostatic interaction among the particles where attraction and repulsion play a major role in low and high pH of the environment, respectively. Since different electrostatic interaction behavior of the particles in varied pH is induced not by irreversible chemical change but by simple protonation differences, the pH responsive process of assembly and disassembly is totally reversible. The low pH specific aggregation of gold nanoparticles resulted in red shift of plasmonic absorption peak and showed higher photothermal efficacy in acidic pH than in normal physiological pH. The low pH specific photothermal effect with long wave laser irradiation was directly applied to cancer specific photothermal therapy and resulted higher therapeutic effect for melanoma cancer cells than non-pH responsive gold nanoparticles.

Synthesis of far-red- and near-infrared-emitting Cu-doped InP/ZnS (core/shell) quantum dots with controlled doping steps and their surface functionalization for bioconjugation.

In this study, we designed and synthesized far-red- and near-infrared-emitting Cu-doped InP-based quantum dots (QDs), and we also demonstrated their highly specific and sensitive biological imaging ability. Cu-doped InP/ZnS (core/shell) QDs were prepared using the hot colloidal synthesis method in the organic phase. The ZnS shell passivates the surface and improves the photoluminescence (PL) intensity. However, the InP : Cu/ZnS (core : dopants/shell) QDs, which were obtained after the Cu dopant was incorporated into bare InP QDs, followed by ZnS shell coating, had relatively low PL intensities (maximum PL quantum yield (QY) was only ∼16%) presumably due to the formation of defect sites in the InP-core QDs caused by dopant migration from the InP core to the ZnS shell. We prepared high-quality InP/ZnS : Cu/ZnS (core/shell : dopant/outer-shell) QDs, where thin ZnS shell layers were grown on bare InP QDs prior to Cu ion doping to prevent dopant migration and obtained PL QYs as high as 40%. The native hydrophobic ligands of the as-synthesized Cu-doped QDs were replaced with hydrophilic ligands including dihydrolipoic acid and a zwitterionic ligand, which rendered the QDs water-soluble. These QDs exhibited remarkable colloidal stabilities over a wide pH range, with hydrodynamic diameters less than 10 nm. Modified QD surfaces can also be used in conjugation with other functional moieties to apply highly specific and sensitive imaging probes with very low background levels. As a proof-of-concept study, we successfully demonstrated the selective imaging of streptavidin beads with biotin-conjugated QDs. These decorated Cu-doped InP/ZnS (core/shell) QDs are promising biological-probe candidates for imaging and assaying with reduced concerns regarding toxicity.

Tumor-Associated Macrophages Enhance Tumor Hypoxia and Aerobic Glycolysis.

Tumor hypoxia and aerobic glycolysis are well-known resistance factors for anticancer therapies. Here, we demonstrate that tumor-associated macrophages (TAM) enhance tumor hypoxia and aerobic glycolysis in mice subcutaneous tumors and in patients with non-small cell lung cancer (NSCLC). We found a strong correlation between CD68 TAM immunostaining and PET 18fluoro-deoxyglucose (FDG) uptake in 98 matched tumors of patients with NSCLC. We also observed a significant correlation between CD68 and glycolytic gene signatures in 513 patients with NSCLC from The Cancer Genome Atlas database. TAM secreted TNFα to promote tumor cell glycolysis, whereas increased AMP-activated protein kinase and peroxisome proliferator-activated receptor gamma coactivator 1-alpha in TAM facilitated tumor hypoxia. Depletion of TAM by clodronate was sufficient to abrogate aerobic glycolysis and tumor hypoxia, thereby improving tumor response to anticancer therapies. TAM depletion led to a significant increase in programmed death-ligand 1 (PD-L1) expression in aerobic cancer cells as well as T-cell infiltration in tumors, resulting in antitumor efficacy by PD-L1 antibodies, which were otherwise completely ineffective. These data suggest that TAM can significantly alter tumor metabolism, further complicating tumor response to anticancer therapies, including immunotherapy. SIGNIFICANCE: These findings show that tumor-associated macrophages can significantly modulate tumor metabolism, hindering the efficacy of anticancer therapies, including anti-PD-L1 immunotherapy.

Multi-Spectral Fluorescence Imaging of Colon Dysplasia InVivo Using a Multi-Spectral Endoscopy System.

BACKGROUND AND STUDY AIM: To develop a molecular imaging endoscopic system that eliminates tissue autofluorescence and distinguishes multiple fluorescent markers specifically on the cancerous lesions. METHODS: Newly developed multi-spectral fluorescence endoscope device has the potential to eliminate signal interference due to autofluorescence and multiplex fluorophores in fluorescent probes. The multiplexing capability of the multi-spectral endoscope device was demonstrated in the phantom studies and multi-spectral imaging with endoscopy and macroscopy was performed to analyze fluorescence signals after administration of fluorescent probe that targets cancer in the colon. Because of the limitations in the clinical application using rigid-type small animal endoscope, we developed a flexible channel insert-type fluorescence endoscope, which was validated on the colonoscopy of dummy and porcine model. RESULTS: We measured multiple fluorescent signals simultaneously, and the fluorescence spectra were unmixed to separate the fluorescent signals of each probe, in which multiple fluorescent probes clearly revealed spectral deconvolution at the specific targeting area in the mouse colon. The positive area of fluorescence signal for each probe over the whole polyp was segmented with analyzing software, and showed distinctive patterns and significantly distinguishable values: 0.46 ±â€¯0.04, 0.39 ±â€¯0.08 and 0.73 ±â€¯0.12 for HMRG, CET-553 and TRA-675 probes, respectively. The spectral unmixing was finally demonstrated in the dummy and porcine model, corroborating the targeted multi-spectral fluorescence imaging of colon dysplasia. CONCLUSION: The multi-spectral endoscopy system may allow endoscopists to clearly identify cancerous lesion that has different patterns of various target expression using multiple fluorescent probes.

Synthesis of Ag/Mn Co-Doped CdS/ZnS (Core/Shell) Nanocrystals with Controlled Dopant Concentration and Spatial Distribution and the Dynamics of Excitons and Energy Transfer between Co-Dopants.

We report lightly Ag/Mn co-doped CdS/ZnS (core/shell) nanocrystals (NCs) as a model system for studying interactions between co-dopants and between NCs and dopants. The co-doped NCs were prepared with a varying average number of Ag dopant atoms per CdS core of the NC from zero to eight; at the same time, the depth profile of the Mn dopants in the ZnS shells was controlled to be either close to or far from the Ag dopants. The incorporation of an average of one to two Ag dopant atoms per NC increased the band-edge photoluminescence (PL); however, it was quenched at higher doping concentration. This alternation is attributed to change of the Ag ion occupancy from PL-enhancing interstitial sites to PL-quenching substitutional sites. Mn PL increased as the number of Ag atoms per NC increased up to approximately seven and then decreased. For NCs doped only with Ag ions, the Ag dopants in substitutional sites acted as PL-quenching hole traps. In Ag/Mn co-doped NCs, the Ag dopants acted as Dexter-type relay sites that enhanced the energy transfer from NC to Mn ions; this effect increased as the distance between Ag and Mn dopants decreased. This model study demonstrates that the simultaneous control of dopant concentrations and spatial distributions in co-doped semiconductor NCs enables sophisticated control of their optical properties.

Multiplexed In Vivo Imaging Using Size-Controlled Quantum Dots in the Second Near-Infrared Window.

PbS/CdS core/shell quantum dots (QDs) that emit at the second near-infrared (NIR-II, 1000-1700 nm) window are synthesized. The PbS seed size and CdS shell thicknesses are carefully controlled to produce bright and narrow fluorescence that are suitable for multiplexing. A polymer encapsulation yields polymer-encapsulated NIR-II QDs (PQDs), which provides the QDs with long-term fluorescence stability over a week in biological media. Exploiting the simple bioconjugation capability of PQDs, folic acids are conjugated to PQDs that can efficiently label folate receptor overexpressing cell lines. The PQDs afford multiplexed and nearly real-time longitudinal whole-body in vivo imaging. Two NIR-II QD probes are prepared: folic acid-conjugated PQDs (FA-PQDs) emitting at 1280 nm and unconjugated PQDs emitting at 1080 nm. The two PQDs are engineered to have compact and similar hydrodynamic sizes. A mixture of the folic acid-conjugated PQD and unconjugated PQDs is injected intravenously into a tumor-xenografted mouse, and the signals from them are monitored. This NIR-II whole-body imaging with the two PQDs provides precise evaluation of the active ligand-assisted tumor-targeting capability of the FA-PQD probe because the hydrodynamic size control of the two PQDs effectively eliminates effects from the size-dependent accumulations by permeations and retentions in tumors.