Nano-flares: probes for transfection and mRNA detection in living cells

Duplex-forming oligocarbamates with tunable nonbonding sites

In biopolymers such as proteins and nucleic acids, monomer sequence encodes for highly specific intra- and intermolecular interactions that direct self-assembly into complex architectures with high fidelity. This remarkable structural control translates into precise control over the properties of the biopolymer. Polymer scientists have sought to achieve similarly precise control over the structure and function of synthetic assemblies. A common strategy for achieving this goal has been to exploit existing biopolymers, known to associate with specific geometries and stoichiometries, for the assembly of synthetic building blocks. However, such systems are neither scalable nor amenable to the relatively harsh conditions required by various materials science applications, particularly those involving non-aqueous environments. To overcome these limitations, we have synthesized sequence-defined oligocarbamates (SeDOCs) that assemble into duplexes through complementary hydrogen bonds between thymine (T) and diaminotriazine (D) pendant groups. The SeDOC platform makes it simple to incorporate non-hydrogen-bonding sites into an oligomer's array of recognition motifs, thereby enabling an investigation into this unexplored handle for controlling the hybridization of complementary ligands. We successfully synthesized monovalent, divalent, and trivalent SeDOCs and characterized their self-assembly via diffusion ordered spectroscopy, 1H-NMR titration, and isothermal titration calorimetry. Our findings reveal that the binding strength of monovalent oligomers with complementary pendant groups is entropically driven and independent of monomer sequence. The results further show that the hybridization of multivalent oligomers is cooperative, that their binding enthalpy (ΔH) and entropy (TΔS) depend on monomer sequence, and that sequence-dependent changes in ΔH and TΔS occur in tandem to minimize the overall change in binding free energy.

Smart Stimuli-Responsive Spherical Nucleic Acids: Cutting-Edge Platforms for Biosensing, Bioimaging, and Therapeutics

Spherical nucleic acids (SNAs) with exceptional colloidal stability, multiple modularity, and programmability are excellent candidates to address common molecular delivery-related issues. Based on this, the higher targeting accuracy and enhanced controllability of stimuli-responsive SNAs render them precise nanoplatforms with inestimable prospects for diverse biomedical applications. Therefore, tailored diagnosis and treatment with stimuli-responsive SNAs may be a robust strategy to break through the bottlenecks associated with traditional nanocarriers. Various stimuli-responsive SNAs are engineered through the incorporation of multifunctional modifications to meet biomedical demands with the development of nucleic acid functionalization. This review provides a comprehensive overview of prominent research in this area and recent advancements in the utilization of stimuli-responsive SNAs in biosensing, bioimaging, and therapeutics. For each aspect, SNA nanoplatforms that exhibit responsive behavior to both internal stimuli (including sequence, enzyme, redox reactions, and pH) and external stimuli (such as light and temperature) are highlighted. This review is expected to offer inspiration and guidance strategies for the rational design and development of stimuli-responsive SNAs in the field of biomedicine.

Pt-Decorated Gold Nanoflares for High-Fidelity Phototheranostics: Reducing Side-Effects and Enhancing Cytotoxicity toward Target Cells

Functionalized with the Au-S bond, gold nanoflares have emerged as promising candidates for theranostics. However, the presence of intracellular abundantly biothiols compromises the conventional Au-S bond, leading to the unintended release of cargoes and associated side-effects on non-target cells. Additionally, the hypoxic microenvironment in diseased regions limits treatment efficacy, especially in photodynamic therapy. To address these challenges, high-fidelity photodynamic nanoflares constructed on Pt-coated gold nanoparticles (Au@Pt PDNF) were communicated to avoid false-positive therapeutic signals and side-effects caused by biothiol perturbation. Compared with conventional photodynamic gold nanoflares (AuNP PDNF), the Au@Pt PDNF were selectively activated by cancer biomarkers and exhibited high-fidelity phototheranostics while reducing side-effects. Furthermore, the ultrathin Pt-shell catalysis was confirmed to generate oxygen which alleviated hypoxia-related photodynamic resistance and enhanced the antitumor effect. This design might open a new venue to advance theranostics performance and is adaptable to other theranostic nanomaterials by simply adding a Pt shell.

Persistent Targeting DNA Nanocarrier Made of 3D Structural Unit Assembled from Only One Basic Multi-Palindromic Oligonucleotide for Precise Gene Cancer Therapy

Construction of a simple, reconfigurable, and stimuli-responsive DNA nanocarrier remains a technical challenge. In this contribution, by designing three palindromic fragments, a simplest four-sticky end-contained 3D structural unit (PS-unit) made of two same DNA components is proposed. Via regulating the rotation angle of central longitudinal axis of PS-unit, the oriented assembly of one-component spherical architecture is accomplished with high efficiency. Introduction of an aptamer and sticky tail warehouse into one component creates a size-change-reversible targeted siRNA delivery nanovehicle. Volume swelling of 20 nm allows one carrier to load 1987 siPLK1s. Once entering cancer cells and responding to glutathione (GSH) stimuli, siPLK1s are almost 100% released and original size of nanovehicle is restored, inhibiting the expression of PLK1 protein and substantially suppressing tumor growth (superior to commercial transfection agents) in tumor-bearing mice without systemic toxicity.

Dynamic Assembly of DNA Nanostructures in Cancer Cells Enables the Coupling of Autophagy Activating and Real-Time Tracking

Developing dynamic nanostructures for in situ regulation of biological processes inside living cells is of great importance in biomedical research. Herein we report the cascaded assembly of Y-shaped branched DNA nanostructure (YDN) during intracellular autophagy. YDN contains one arm with semi-i-motif sequence and Cy3-BHQ2, and another arm with an apurinic/apyrimidinic (AP) site and Cy5-BHQ3. Upon uptake by cancer cells, intermolecular i-motif structures are formed in response to lysosomal H+, causing the formation of YDN-dimer and the recovery of Cy3 fluorescence; when escapes occur from the lysosome to the cytoplasm, the YDN-dimer responds to the overexpressed APE1, leading to the assembly of YDN into the DNA network and the fluorescence recovery of Cy5. Simultaneously, the cascaded assembly activates autophagy, and thus the process of assembly of YDN and autophagy flux can be spatiotemporally coupled. This work illustrates the potential of DNA nanostructures for the in situ regulation of intracellular dynamic events with spatiotemporal control.

Aptamer-based flares hybridized with single-stranded DNA-conjugated MoS2 nanosheets for ratiometric fluorescence sensing and imaging of potassium ions and adenosine triphosphate in human fluids and living cells

Addressing the limitations observed in previous studies, where the quantitative range of nanoprobes for detecting K+ and adenosine triphosphate (ATP) did not cover concentrations found within living cells, the present study aimed to develop ratiometric nanoprobes that can accurately sense changes in K+ and ATP levels in living cells and quantify them in human fluids. The proposed nanoprobes consisted of recognition flares modified with 6-carboxyfluorescein (FAM) and 5-carboxytetramethylrhodamine (TAMRA), along with thiolate single-stranded DNA (ssDNA) and molybdenum disulfide nanosheets (MoS2 NSs). The thiolate ssDNA acts as a linker between the flares and the MoS2 NSs, directly forming a functional nanostructure at room temperature. The direct conjugation of labeled flares to the MoS2 NSs simplifies the fabrication process. In the absence of K+ and ATP, the hybridization of flares and thiolate ssDNA caused FAM to move away from TAMRA, suppressing the fluorescence resonance energy transfer (FRET) process. However, upon the introduction of K+ and ATP, the flares undergo a structural transformation via the formation of G-quadruplex formation and the generation of hairpin-shaped structures, respectively. This structural change leads to the release of the flares from the ssDNA-conjugated nanosheet surface. The release of the flares brings FAM and TAMRA into close proximity, allowing FRET to occur, leading to FRET and static quenching. By monitoring the ratio between the fluorescence intensities of FAM and TAMRA, the concentration of K+ (5-100 mM) and ATP (0.3-5 mM) can be accurately determined by the proposed nanoprobes. The advantages of these nanoprobes lie in their ability to provide ratiometric measurements, which enhance the accuracy and reliability of the quantification process. The proposed nanoprobes offer potential applications as ratiometric imaging probes for monitoring K+ and ATP-related reactions in living cells, providing valuable insights into cellular processes. Additionally, they can be employed for determining the levels of K+ and ATP in human fluids, offering potential diagnostic applications in various clinical settings.

Accurate Quantification and Imaging of Cellular Uptake Using Single-Particle Surface-Enhanced Raman Scattering

Understanding the uptake, distribution, and stability of gold nanoparticles (NPs) in cells is of fundamental importance in nanoparticle sensors and therapeutic development. Single nanoparticle imaging with surface-enhanced Raman spectroscopy (SERS) measurements in cells is complicated by aggregation-dependent SERS signals, particle inhomogeneity, and limited single-particle brightness. In this work, we assess the single-particle SERS signals of various gold nanoparticle shapes and the role of silica encapsulation on SERS signals to develop a quantitative probe for single-particle level Raman imaging in living cells. We observe that silica-encapsulated gap-enhanced Raman tags (GERTs) provide an optimized probe that can be quantifiable per voxel in SERS maps of cells. This approach is validated by single-particle inductively coupled mass spectrometry (spICP-MS) measurements of NPs in cell lysate post-imaging. spICP-MS also provides a means of measuring the tag stability. This analytical approach can be used not only to quantitatively assess nanoparticle uptake on the cellular level (as in previous digital SERS methods) but also to reliably image the subcellular distribution and to assess the stability of NPs in cells.

All-in-one nanoflare biosensor combined with catalyzed hairpin assembly amplification for in situ and sensitive exosomal miRNA detection and cancer classification

Exosomal miRNAs can reflect tumor progression and metastasis, and are effective biomarkers for cancer diagnosis. However, the accuracy of exosomal miRNA-based cancer diagnosis is limited by the low sensitivity and complicated RNA extraction of traditional approaches. Herein, a novel biosensor is developed for in situ, extraction-free, and highly sensitive analysis of exosomal miRNAs via nanoflare combined with catalyzed hairpin assembly (CHA) amplification. Without cumbersome and costly miRNA extraction or transfection agents, nanoflare can directly enter the exosomes to bind target miRNAs and generate a fluorescence signal that can be amplified by the CHA reaction to achieve the in situ and highly sensitive detection of exosomal miRNAs. Under the optimal conditions, the detection limit of 5 aM is obtained for three exosomal miRNAs, which is an order of magnitude lower than quantitative real time polymerase chain reaction (qRT-PCR). In combination with the linear discriminant analysis algorithm, five exosomes are distinguished with 100% accuracy. Importantly, five cancers including breast, lung, liver, cervical, and colon cancer from 64 patients are distinguished with 99% accuracy by testing exosomal miRNAs in clinical plasma. This simple, accurate, and sensitive biosensor holds the potential to be expanded into clinical non-invasive cancer diagnostic tests.

Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids

Owing to the versatile photophysical and chemical properties, spherical nucleic acids (SNAs) have been widely used in biosensing. However, traditional SNAs are formed by self-assembly of thiolated DNA on the surface of a gold nanoparticle (AuNP), where it is challenging to precisely control the orientation and surface density of DNA. As a new SNA, a polyadenine (polyA)-mediated SNA using the high binding affinity of consecutive adenines to AuNPs shows controllable surface density and configuration of DNA, which can be used to improve the performance of a biosensor. Herein, we first introduce the properties of polyA-mediated SNAs and fundamental principles regarding the polyA-AuNP interaction. Then, we provide an overview of current representative synthesis methods of polyA-mediated SNAs and their advantages and disadvantages. After that, we summarize the application of polyA-mediated SNAs in biosensing based on fluorescence and colorimetric methods, followed by discussion and an outlook of future challenges in this field.

Semiconducting Polymer Nanospherical Nucleic Acid Probe for Transcriptomic Imaging of Cancer Chemo-Immunotherapy

Real-time in vivo imaging of RNA can enhance the understanding of physio-pathological processes. However, most nucleic acid-based sensors have poor resistance to nucleases and limited photophysical properties, making them suboptimal for this purpose. To address this, a semiconducting polymer nanospherical nucleic acid probe (SENSE) for transcriptomic imaging of cancer immunity in living mice is developed. SENSE comprises a semiconducting polymer (SP) backbone covalently linked with recognition DNA strands, which are complemented by dye-labeled signal DNA strands. Upon detection of targeted T lymphocyte transcript (Gzmb: granzyme B), the signal strands are released, leading to a fluorescence enhancement correlated to transcript levels with superb sensitivity. The always-on fluorescence of the SP core also serves as an internal reference for tracking SENSE uptake in tumors. Thus, SENSE has the dual-signal channel that enables ratiometric imaging of Gzmb transcripts in the tumor of living mice for evaluating chemo-immunotherapy; moreover, it has demonstrated sensitivity and specificity comparable to flow cytometry and quantitative polymerase chain reaction,  yet offering a faster and simpler means of T cell detection in resected tumors. Therefore, SENSE represents a promising tool for in vivo RNA imaging.

Spherical nucleic acids-based nanoplatforms for tumor precision medicine and immunotherapy

Precise diagnosis and treatment of tumors currently still face considerable challenges due to the development of highly degreed heterogeneity in the dynamic evolution of tumors. With the rapid development of genomics, personalized diagnosis and treatment using specific genes may be a robust strategy to break through the bottleneck of traditional tumor treatment. Nevertheless, efficient in vivo gene delivery has been frequently hampered by the inherent defects of vectors and various biological barriers. Encouragingly, spherical nucleic acids (SNAs) with good modularity and programmability are excellent candidates capable of addressing traditional gene transfer-associated issues, which enables SNAs a precision nanoplatform with great potential for diverse biomedical applications. In this regard, there have been detailed reviews of SNA in drug delivery, gene regulation, and dermatology treatment. Still, to the best of our knowledge, there is no published systematic review summarizing the use of SNAs in oncology precision medicine and immunotherapy, which are considered new guidelines for oncology treatment. To this end, we summarized the notable advances in SNAs-based precision therapy and immunotherapy for tumors following a classification standard of different types of precise spatiotemporal control on active species by SNAs. Specifically, we focus on the structural diversity and programmability of SNAs. Finally, the challenges and possible solutions were discussed in the concluding remarks. This review will promote the rational design and development of SNAs for tumor-precise medicine and immunotherapy.

Uncovering Molecular Quencher Effects on FRET Phenomena in Microsphere-Immobilized Probe Systems

Double-stranded (ds) oligonucleotide probes composed of quencher-dye sequence pairs outperform analogous single-stranded (ss) probes due to their superior target sequence specificity without any prerequisite target labeling. Optimizing sequence combinations for dsprobe design requires promoting a fast, accurate response to a specific target sequence while minimizing spontaneous dsprobe dissociation events. Here, flow cytometry is used to rapidly interrogate the stability and selective responsiveness of 20 candidate LNA and DNA dsprobes to a 24 base-long segment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and ∼243 degenerate RNA sequences serving as model variants. Importantly, in contrast to quantifying binding events of dye-labeled targets via flow cytometry, the current work employs the Förster resonance energy transfer (FRET)-based detection of unlabeled RNA targets. One DNA dsprobe with a 15-base-long hybridization partner containing a central abasic site emerged as very stable yet responsive only to the SARS-CoV-2 RNA segment. Separate displacement experiments, however, indicated that ∼12% of these quencher-capped hybridization partners remain bound, even in the presence of an excess SARS-CoV-2 RNA target. To examine their quenching range, additional titration studies varied the ratios and spatial placement of nonquencher and quencher-capped hybridization partners in the dsprobes. These titration studies indicate that these residual, bound quencher-capped partners, even at low percentages, act as nodes, enabling both static quenching effects within each residual dsprobe as well as longer-range quenching effects on neighboring FAM moieties. Overall, these studies provide insight into practical implications for rapid dsprobe screening and target detection by combining flow cytometry with FRET-based detection.

Unraveling the Possibilities: Recent Progress in DNA Biosensing

Due to the advantages of its numerous modification sites, predictable structure, high thermal stability, and excellent biocompatibility, DNA is the ideal choice as a key component of biosensors. DNA biosensors offer significant advantages over existing bioanalytical techniques, addressing limitations in sensitivity, selectivity, and limit of detection. Consequently, they have attracted significant attention from researchers worldwide. Here, we exemplify four foundational categories of functional nucleic acids: aptamers, DNAzymes, i-motifs, and G-quadruplexes, from the perspective of the structure-driven functionality in constructing DNA biosensors. Furthermore, we provide a concise overview of the design and detection mechanisms employed in these DNA biosensors. Noteworthy advantages of DNA as a sensor component, including its programmable structure, reaction predictility, exceptional specificity, excellent sensitivity, and thermal stability, are highlighted. These characteristics contribute to the efficacy and reliability of DNA biosensors. Despite their great potential, challenges remain for the successful application of DNA biosensors, spanning storage and detection conditions, as well as associated costs. To overcome these limitations, we propose potential strategies that can be implemented to solve these issues. By offering these insights, we aim to inspire subsequent researchers in related fields.

Inspired Beyond Nature: Three Decades of Spherical Nucleic Acids and Colloidal Crystal Engineering with DNA

The conception, synthesis, and invention of a nanostructure, now known as the spherical nucleic acid, or SNA, in 1996 marked the advent of a new field of chemistry. Over the past three decades, the SNA and its analogous anisotropic equivalents have provided an avenue for us to think about some of the most fundamental concepts in chemistry in new ways and led to technologies that are significantly impacting fields from medicine to materials science. A prime example is colloidal crystal engineering with DNA, the framework for using SNAs and related structures to synthesize programmable matter. Herein, we document the evolution of this framework, which was initially inspired by nature, and describe how it now allows researchers to chart paths to move beyond it, as programmable matter with real-world significance is envisioned and created.

Proximity-Driven DNA Nanosensors

In proximity-driven sensing, interactions between a probe and an analyte produce a detectable signal by causing a change in distance of two probe components or signaling moieties. By interfacing such systems with DNA-based nanostructures, platforms that are highly sensitive, specific, and programmable can be designed. In this Perspective, we delineate the advantages of using DNA building blocks in proximity-driven nanosensors and provide an overview of recent progress in the field, from sensors that rapidly detect pesticides in food to probes that identify rare cancer cells in blood. We also discuss current challenges and identify key areas that need further development.

Methods to functionalize gold nanoparticles with tandem-phosphorothioate DNA: role of physicochemical properties of the phosphorothioate backbone in DNA adsorption to gold nanoparticles

Perception of the differences in the physicochemical properties of phosphorothioate DNA (PS-DNA) and phosphodiester DNA (PO-DNA) greatly aids in understanding the AuNP-DNA binding process. Replacing one non-bridging oxygen atom of the anionic phosphodiester backbone with a sulfur atom leads to a major change in the DNA adsorption mechanism of AuNPs. In this work, we investigated and compared salt-aging, low pH-assisted, and freeze-thaw methods for conjugating phosphorothioate-modified oligonucleotides to AuNPs. The results obtained clearly demonstrate that only the pH-assisted method can successfully bind tandem phosphorothioate DNA to gold nanoparticles and sufficiently maintain the colloidal stability of AuNPs. When a phosphate group is converted to a phosphorothioate group, the negative charge of the phosphate group is located on the sulfur atom. Due to the soft nature of sulfur (a very weak H-bond acceptor), the negative charge on the sulfur atom cannot be shielded even with the gradual addition of salt to increase the ionic strength, so, the pH-assisted based method is the best for the functionalization of AuNPs with tandem-PS DNA.

DNA Windmill Probe for Multiplexed mRNA Detection and Cell Type Discrimination

Accurate cancer diagnosis especially early diagnosis is of great importance for prompt therapy and elevated survival rate. mRNAs are widely used as biomarkers for cancer identification and treatment. mRNA expression levels are highly associated with cancer stage and malignant progression. Nevertheless, single type mRNA detection is insufficient and unreliable. Herein, we developed a DNA nano-windmill probe for in situ multiplexed mRNAs detection and imaging in this paper. The probe is designed to simultaneously target four types of mRNA through wind blades. Importantly, recognition of targets is independent from each other, which further facilitate cell type discrimination. The probe can specifically distinguish cancer cell lines from normal cells. In addition, it can identify changes in mRNA expression levels in living cells. The current strategy enriches the toolbox for improving the accuracy of cancer diagnosis and therapeutic solutions.

The role of protein corona on nanodrugs for organ-targeting and its prospects of application

Nowadays, nanodrugs become a hotspot in the high-end medical field. They have the ability to deliver drugs to reach their destination more effectively due to their unique properties and flexible functionalization. However, the fate of nanodrugs in vivo is not the same as those presented in vitro, which indeed influenced their therapeutic efficacy in vivo. When entering the biological organism, nanodrugs will first come into contact with biological fluids and then be covered by some biomacromolecules, especially proteins. The proteins adsorbed on the surface of nanodrugs are known as protein corona (PC), which causes the loss of prospective organ-targeting abilities. Fortunately, the reasonable utilization of PC may determine the organ-targeting efficiency of systemically administered nanodrugs based on the diverse expression of receptors on cells in different organs. In addition, the nanodrugs for local administration targeting diverse lesion sites will also form unique PC, which plays an important role in the therapeutic effect of nanodrugs. This article introduced the formation of PC on the surface of nanodrugs and summarized the recent studies about the roles of diversified proteins adsorbed on nanodrugs and relevant protein for organ-targeting receptor through different administration pathways, which may deepen our understanding of the role that PC played on organ-targeting and improve the therapeutic efficacy of nanodrugs to promote their clinical translation.

Oncogene-targeting nanoprobes for early imaging detection of tumor

Malignant tumors have been one of the major reasons for deaths worldwide. Timely and accurate diagnosis as well as effective intervention of tumors play an essential role in the survival of patients. Genomic instability is the important foundation and feature of cancer, hence, in vivo oncogene imaging based on novel probes provides a valuable tool for the diagnosis of cancer at early-stage. However, the in vivo oncogene imaging is confronted with great challenge, due to the extremely low copies of oncogene in tumor cells. By combining with various novel activatable probes, the molecular imaging technologies provide a feasible approach to visualize oncogene in situ, and realize accurate treatment of tumor. This review aims to declare the design of nanoprobes responded to tumor associated DNA or RNA, and summarize their applications in detection and bioimaging for tumors. The significant challenges and prospective of oncogene-targeting nanoprobes towards tumors diagnosis are revealed as well.

In Vivo Behavior of Ultrasmall Spherical Nucleic Acids

The biological properties of spherical nucleic acids (SNAs) are largely independent of nanoparticle core identity but significantly affected by oligonucleotide surface density. Additionally, the payload-to-carrier (i.e., DNA-to-nanoparticle) mass ratio of SNAs is inversely proportional to core size. While SNAs with many core types and sizes have been developed, all in vivo analyses of SNA behavior have been limited to cores >10 nm in diameter. However, "ultrasmall" nanoparticle constructs (<10 nm diameter) can exhibit increased payload-to-carrier ratios, reduced liver accumulation, renal clearance, and enhanced tumor infiltration. Therefore, we hypothesized that SNAs with ultrasmall cores exhibit SNA-like properties, but with in vivo behavior akin to traditional ultrasmall nanoparticles. To investigate, we compared the behavior of SNAs with 1.4-nm Au102 nanocluster cores (AuNC-SNAs) and SNAs with 10-nm gold nanoparticle cores (AuNP-SNAs). Significantly, AuNC-SNAs possess SNA-like properties (e.g., high cellular uptake, low cytotoxicity) but show distinct in vivo behavior. When intravenously injected in mice, AuNC-SNAs display prolonged blood circulation, lower liver accumulation, and higher tumor accumulation than AuNP-SNAs. Thus, SNA-like properties persist at the sub-10-nm length scale and oligonucleotide arrangement and surface density are responsible for the biological properties of SNAs. This work has implications for the design of new nanocarriers for therapeutic applications.

Challenges and opportunities for SERS in the infrared: materials and methods

In the wake of a global, heightened interest towards biomarker and disease detection prompted by the SARS-CoV-2 pandemic, surface enhanced Raman spectroscopy (SERS) positions itself again at the forefront of biosensing innovation. But is it ready to move from the laboratory to the clinic? This review presents the challenges associated with the application of SERS to the biomedical field, and thus, to the use of excitation sources in the near infrared, where biological windows allow for cell and through-tissue measurements. Two main tackling strategies will be discussed: (1) acting on the design of the enhancing substrate, which includes manipulation of nanoparticle shape, material, and supramolecular architecture, and (2) acting on the spectral collection set-up. A final perspective highlights the upcoming scientific and technological bets that need to be won in order for SERS to stably transition from benchtop to bedside.

Spatiotemporal Monitoring of Subcellular mRNAs In Situ via Polyadenine-Mediated Dual-Color Sticky Flares

Spatiotemporal monitoring of multiple low-abundance messenger RNAs (mRNAs) is vitally important for the diagnosis and pathologic analysis of cancer. However, it remains a clinical challenge to monitor and track multiple mRNAs location simultaneously in situ at subcellular level with high efficiency. Herein, we proposed polyA-mediated dual-color sticky flares for simultaneous imaging of two kinds of intracellular mRNA biomarkers. Two kinds of fluorescent DNA specific for GalNac-T mRNA and c-Myc mRNA were functionalized onto gold nanoparticles (AuNPs) through efficient polyadenine (polyA) attachment. By tuning polyA length, the lateral spacing and densities of DNA on AuNPs could be precisely engineered. Compared to the traditional thio-DNA-modified nanoprobes, the uniformity, detection sensitivity, and response kinetics of sticky flares were greatly improved, which enables live-cell imaging of mRNAs with enhanced efficiency. With a sticky-end design, the fluorescent DNA could dynamically trace mRNAs after binding with target mRNAs, which realized spatiotemporal monitoring of subcellular mRNAs in situ. Compared to one target mRNA imaging mode, the multiple target imaging mode allows more accurate diagnosis of cancer. Furthermore, the proposed polyA-mediated dual-color sticky flares exhibit excellent cell entry efficiency and low cytotoxicity with a low-cost and simple assembling process, which provide a pivotal tool for multiple targets imaging in living cells.

Simultaneous Imaging and Visualizing the Association of Survivin mRNA and Telomerase in Living Cells by Using a Dual-Color Encoded DNA Nanomachine

Simultaneous imaging and especially visualizing the association of survivin mRNA and telomerase in living cells are of great value for the diagnosis and prognosis of cancer because their co-expression facilitates the development of cancer and identifies patients at high risk of tumor-related death. The challenge is to develop methods that enable visualizing the association of multiplex targets and avoid the distorted signals due to the different delivery efficiency of probes. Herein, we engineered a DNA triangular prism nanomachine (DTPN) for simultaneous multicolor imaging of survivin mRNA and telomerase and visualizing their association in living cells. Two recognizing probes targeted survivin mRNA and telomerase, and the reporter probe was assembled on the DTP in equal amounts, ensuring the same delivery efficiency of the probes to the living cells. The results showed that this DTPN could quantify intracellular survivin mRNA expression and telomerase activity. Moreover, it also enabled us to visualize the effect of the down-regulation of one target on the expression of another target under different drug stimulations. The results implied that our DTPN provided a promising platform for cancer diagnosis, prognosis, drug screening, and related biological research.

Single-cell RNA-sequence analysis of human bone marrow reveals new targets for isolation of skeletal stem cells using spherical nucleic acids

There is a wealth of data indicating human bone marrow contains skeletal stem cells (SSC) with the capacity for osteogenic, chondrogenic and adipogenic differentiation. However, current methods to isolate SSCs are restricted by the lack of a defined marker, limiting understanding of SSC fate, immunophenotype, function and clinical application. The current study applied single-cell RNA-sequencing to profile human adult bone marrow populations from 11 donors and identified novel targets for SSC enrichment. Spherical nucleic acids were used to detect these mRNA targets in SSCs. This methodology was able to rapidly isolate potential SSCs found at a frequency of <1 in 1,000,000 in human bone marrow, with the capacity for tri-lineage differentiation in vitro and ectopic bone formation in vivo. The current studies detail the development of a platform to advance SSC enrichment from human bone marrow, offering an invaluable resource for further SSC characterisation, with significant therapeutic impact therein.

Genetically encodable tagging and sensing systems for fluorescent RNA imaging

Live cell imaging of RNAs is crucial to interrogate their fundamental roles in various biological processes. The highly spatiotemporal dynamic nature of RNA abundance and localization has presented great challenges for RNA imaging. Genetically encodable tagging and sensing (GETS) systems that can be continuously produced in living systems have afforded promising tools for imaging and sensing RNA dynamics in live cells. Here we review the recent advances of GETS systems that have been developed for RNA tagging and sensing in live cells. We first describe the various GETS systems using MS2-bacteriophage-MS2 coat protein, pumilio homology domain and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9/13 for RNA labeling and tracking. The progresses of GETS systems for fluorogenic labeling and/or sensing RNAs by engineering light-up RNA aptamers, CRISPR-Cas9 systems and RNA aptamer stabilized fluorogenic proteins are then elaborated. The challenges and future perspectives in this field are finally discussed. With the continuing development, GETS systems will afford powerful tools to elucidate RNA biology in living systems.

Cruciate DNA probes for amplified multiplexed imaging of microRNAs in living cells

The real-time imaging of low-abundance tumor-related microRNAs (miRNAs) in living cells holds great potential for early clinical diagnosis of cancers. However, the relatively low detection sensitivity and possible false-positive signals of a probe in complex cellular matrices remain critical challenges for accurate RNA detection. Herein, we developed a novel aptamer-functionalized cruciate DNA probe that enabled amplified multiple miRNA imaging in living cells via catalytic hairpin assembly (CHA). The cross-shaped design of the cruciate DNA probe improved the stability against nucleases and acted as a modular scaffold for CHA circuits for efficient delivery into tumor cells. The cruciate DNA probe allowed self-assembly through thermal annealing and displayed excellent performance for sensitive miRNA detection in vitro. The cruciate DNA probe could be internalized into nucleolin-overexpressed cells specifically via cell-targeting of the AS1411 aptamer, achieving amplified fluorescence imaging and quantitative evaluation of the expression of miRNAs in living cells. Through the simultaneous detection of intracellular multiple miRNAs, the developed cruciate DNA probe could provide more accurate information and reduce the chances of false positive signals for cancer diagnosis. This approach offers a new opportunity for promoting the development of miRNA-related biomedical research and tumor diagnostic applications.

DNA-enabled fluorescent-based nanosensors monitoring tumor-related RNA toward advanced cancer diagnosis: A review

As a burgeoning non-invasive indicator for reproducible cancer diagnosis, tumor-related biomarkers have a wide range of applications in early cancer screening, efficacy monitoring, and prognosis predicting. Accurate and efficient biomarker determination, therefore, is of great importance to prevent cancer progression at an early stage, thus reducing the disease burden on the entire population, and facilitating advanced therapies for cancer. During the last few years, various DNA structure-based fluorescent probes have established a versatile platform for biological measurements, due to their inherent biocompatibility, excellent capacity to recognize nucleic and non-nucleic acid targets, obvious accessibility to synthesis as well as chemical modification, and the ease of interfacing with signal amplification protocols. After decades of research, DNA fluorescent probe technology for detecting tumor-related mRNAs has gradually grown to maturity, especially the advent of fluorescent nanoprobes has taken the process to a new level. Here, a systematic introduction to recent trends and advances focusing on various nanomaterials-related DNA fluorescent probes and the physicochemical properties of various involved nanomaterials (such as AuNP, GO, MnO2, SiO2, AuNR, etc.) are also presented in detail. Further, the strengths and weaknesses of existing probes were described and their progress in the detection of tumor-related mRNAs was illustrated. Also, the salient challenges were discussed later, with a few potential solutions.

Biomolecule conjugated inorganic nanoparticles for biomedical applications: A review

Last decade has witnessed impressive progress in the fields of medicine and bioengineering with the aid of nanomaterials. Nanomaterials are favoured for their improved bio-chemical as well as mechanical properties with tremendous applications in biomedical domains such as disease diagnosis, targeted drug delivery, medical imaging, in vitro diagnostics, designing innovatory cross-functional implants and regenerative tissue engineering. The current situation insists upon crafting nanotools that are capable of catering to biological needs and construct more efficient biomedical strategies. In the recent years, surface functionalization and capping with biomolecules has initiated substantial interest towards research. In this regard, search of suitable biofunctionalized nanoparticles seem to be like finding pearls from ocean. Conjugating biological molecules with inorganic materials has paved the way for unravelling innovative functional materials with dramatically improved properties and a wide range of uses. Inorganic nanoparticles such as metals, metal oxides, as well as quantum dots have been hybridised or conjugated with biomolecules such as proteins, peptides, carbohydrates, and nucleic acids. The present review reports on various biomolecule functionalized inorganic nanomaterials highlighting the biomolecule-inorganic nanoparticle interaction studies, the mechanism of functionalization, antimicrobial efficacy of the functionalised nanoconjugates and its use in various biomedical applications.

CRISPR/Cas9-based coronal nanostructures for targeted mitochondria single molecule imaging

The biological state at the subcellular level is highly relevant to many diseases, and the monitoring of organelles such as mitochondria is crucial based on this. However, most DNA and protein based nanoprobes used for the detection of mitochondrial RNAs (mitomiRs) lack spatial selectivity, which leads to inefficiencies in probe delivery and signal turn-on. Herein, we constructed a novel DNA nanoprobe named protein delivery nano-corona (PDNC) to improve the delivery efficiency of Cas protein, for spatially selective imaging of mitomiRs in living cells switched on by a CRISPR/Cas system. Combined with a single-molecule counting method, this strategy enables highly sensitive detection of low-abundance mitomiR. Therefore, the strategy in this work opens up new opportunities for cell identification, early clinical diagnosis, and research in biological behaviour at the subcellular level.

Engineering nanosystems to overcome barriers to cancer diagnosis and treatment

Over the past two decades, multidisciplinary investigations into the development of nanoparticles for medical applications have continually increased. However, nanoparticles are still subject to biological barriers and biodistribution challenges, which limit their overall clinical potential. This has motivated the implementation of innovational modifications to a range of nanoparticle formulations designed for cancer imaging and/or cancer treatment to overcome specific barriers and shift the accumulation of payloads toward the diseased tissues. In recent years, novel technological and chemical approaches have been employed to modify or functionalize the surface of nanoparticles or manipulate the characteristics of nanoparticles. Combining these approaches with the identification of critical biomarkers provides new strategies for enhancing nanoparticle specificity for both cancer diagnostic and therapeutic applications. This review discusses the most recent advances in the design and engineering of nanoparticles as well as future directions for developing the next generation of nanomedicines.

DNA Strand Displacement Driven by Host-Guest Interactions

Base-pair-driven toehold-mediated strand displacement (BP-TMSD) is a fundamental concept employed for constructing DNA machines and networks with a gamut of applications─from theranostics to computational devices. To broaden the toolbox of dynamic DNA chemistry, herein, we introduce a synthetic surrogate termed host-guest-driven toehold-mediated strand displacement (HG-TMSD) that utilizes bioorthogonal, cucurbit[7]uril (CB[7]) interactions with guest-linked input sequences. Since control of the strand-displacement process is salient, we demonstrate how HG-TMSD can be finely modulated via changes to the structure of the input sequence (including synthetic guest head-group and/or linker length). Further, for a given input sequence, competing small-molecule guests can serve as effective regulators (with fine and coarse control) of HG-TMSD. To show integration into functional devices, we have incorporated HG-TMSD into machines that control enzyme activity and layered reactions that detect specific microRNA.

Quantification of mRNA in Single Cells Based on Dimerization-Induced Photoluminescence Nonblinking of Quantum Dots

Photoluminescence (PL) intermittency (or "blinking") is a unique characteristic of single quantum dot (QD) emission. Here, we report a novel single-molecule detection strategy for the intracellular mRNA of interest using the mRNA-induced nonblinking QD dimers as probes. The working principle of the method is that the DNA hybrid of the target DNA (or mRNA) with a biotin-modified ssDNA probe can induce two blinking streptavidin-modified QDs (SAV-QDs) conjugated. The formed QD dimer as a bright spot showed a nonblinking emission property, observed with total inner reflection fluorescence microscopy (TIRFM). In theory, one nonblinking spot indicated a target DNA (or mRNA). The experimental results from single-spot fluorescence trajectory analysis and single-particle brightness analysis based on TIRFM and fluorescence correlation spectroscopy (FCS) techniques verified this dimerization process of QDs or its induced nonblinking emission. Employing a target DNA with the same base sequences to Survivin mRNA as a model, the detection strategy was used to detect the target DNA concentration based on the linear relationship between the percentage of the nonblinking spots and the target DNA concentration. This single-molecule detection strategy was also successfully used for determining Survivin mRNA in a single HeLa cell. The method can simplify the hybridization steps, eliminate self-quenching and photobleaching of fluorophores, and reduce the influence of unspecific binding on the detection.

Nanoflare Couple: Multiplexed mRNA Imaging and Logic-Controlled Combinational Therapy

Theranostics, which combines both diagnostic and therapeutic capabilities in one dose, has always been an intractable challenge in personalized cancer treatment. Herein, a versatile nanotheranostic platform "nanoflare couple (NC)" has been developed for in situ multiplex cancer-related mRNA imaging and subsequent logic-controlled aggregation of gold nanoparticles, leading to gene therapy and photothermal therapy upon irradiation with infrared light. As a proof of concept, TK1 and survivin mRNAs that are highly expressed in most tumor tissues are selected as endogenous cancer indicators and therapy triggers to design the NC. Mice bearing breast cancer cells MCF-7 are prepared as a model to test its efficacy. The in vitro and in vivo assays validate that the NC show the capability for multiplexed mRNA imaging and high efficiency for logic-controlled combinational therapy of breast cancer.

Polymer–Metal Composite Healthcare Materials: From Nano to Device Scale

Metals have been investigated as biomaterials for a wide range of medical applications. At nanoscale, some metals, such as gold nanoparticles, exhibit plasmonics, which have motivated researchers’ focus on biosensor development. At the device level, some metals, such as titanium, exhibit good physical properties, which could allow them to act as biomedical implants for physical support. Despite these attractive features, the non-specific delivery of metallic nanoparticles and poor tissue–device compatibility have greatly limited their performance. This review aims to illustrate the interplay between polymers and metals, and to highlight the pivotal role of polymer–metal composite/nanocomposite healthcare materials in different biomedical applications. Here, we revisit the recent plasmonic engineered platforms for biomolecules detection in cell-free samples and highlight updated nanocomposite design for (1) intracellular RNA detection, (2) photothermal therapy, and (3) nanomedicine for neurodegenerative diseases, as selected significant live cell–interactive biomedical applications. At the device scale, the rational design of polymer–metallic medical devices is of importance for dental and cardiovascular implantation to overcome the poor physical load transfer between tissues and devices, as well as implant compatibility under a dynamic fluidic environment, respectively. Finally, we conclude the treatment of these innovative polymer–metal biomedical composite designs and provide a future perspective on the aforementioned research areas.

DNA Supramolecular Assembly on Micro/Nanointerfaces for Bioanalysis

ConspectusFacing increasing demand for precision medicine, materials chemistry systems for bioanalysis with accurate molecular design, controllable structure, and adjustable biological activity are required. As a genetic biomacromolecule, deoxyribonucleic acid (DNA) is created via precise, efficient, and mild processes in life systems and can in turn precisely regulate life activities. From the perspective of materials chemistry, DNA possesses the characteristics of sequence programmability and can be endowed with customized functions by the rational design of sequences. In recent years, DNA has been considered to be a potential biomaterial for analysis and has been applied in the fields of bioseparation, biosensing, and detection imaging. To further improve the precision of bioanalysis, the supramolecular assembly of DNA on micro/nanointerfaces is an effective strategy to concentrate functional DNA modules, and thus the functions of DNA molecules for bioanalysis can be enriched and enhanced. Moreover, the new modes of DNA supramolecular assembly on micro/nanointerfaces enable the integration of DNA with the introduced components, breaking the restriction of limited functions of DNA materials and achieving more precise regulation and manipulation in bioanalysis. In this Account, we summarize our recent work on DNA supramolecular assembly on micro/nanointerfaces for bioanalysis from two main aspects. In the first part, we describe DNA supramolecular assembly on the interfaces of microscale living cells. The synthesis strategy of DNA is based on rolling-circle amplification (RCA), which generates ultralong DNA strands according to circular DNA templates. The templates can be designed with complementary sequences of functional modules such as aptamers, which allow DNA to specifically bind with cellular interfaces and achieve efficient cell separation. In the second part, we describe DNA supramolecular assembly on the interfaces of nanoscale particles. DNA sequences are designed with functional modules such as targeting, drug loading, and gene expression and then are assembled on interfaces of particles including upconversion nanoparticles (UCNPs), gold nanoparticles (AuNPs), and magnetic nanoparticle (MNPs). The integration of DNA with these functional particles achieves cell manipulation, targeted tumor imaging, and cellular regulation. The processes of interfacial assembly are well controlled, and the functions of the obtained bioanalytical materials can be flexibly regulated. We envision that the work on DNA supramolecular assembly on micro/nanointerfaces will be a typical paradigm for the construction of more bioanalytical materials, which we hope will facilitate the development of precision medicine.

DNA-gold nanoprobe-based integrated biosensing technology for non-invasive liquid biopsy of serum miRNA: A new frontier in prostate cancer diagnosis

The low specificity of prostate-specific antigen contributes to overdiagnosis and ov ertreatment of prostate cancer (PCa) patients. Hence, there is an urgent need for inclusive diagnostic platforms that could improve the diagnostic accuracy of PCa. Dysregulated miRNAs are closely associated with the progression and recurrence and have emerged as promising diagnostic and prognostic biomarkers for PCa. Nevertheless, simple, rapid, and ultrasensitive quantification of serum miRNAs is highly challenging. This study designed, synthesized, and demonstrated the practicability of DNA-linked gold nanoprobes (DNA-AuNPs) for the single-step quantification of miR-21/miR-141/miR-375. In preclinical study, the assay differented PCa Pten conditional knockout (Pten^cKO) mice compared to their age-matched Pten wild-type (Pten^WT) control mice. In human sera, receiver operating characteristic (ROC) curve-based correlation analyses revealed clear discrimination between PCa patients from normal healthy controls using training and validation sets. Overall, we established integrated nano-biosensing technology for the PCR-free, non-invasive liquid biopsies of multiple miRNAs for PCa diagnosis.

Smart Programmable Scalable Dual-Mode Diagnostic Logic Nanoflare Strategy for Dual-Tumor Marker Detection

Compared with the single-marker detection scheme, the detection of multiple targets in the complex cell and biological environment can obtain more reliable detection results. Herein, we detected miRNA-21 and APE1 in two modes, AND and OR, respectively, based on gold nanoflares and simple logic components. In both modes, DNAzyme and APE1 can get rich fluorescence recovery results by breaking the DNA strands from the gold nanorods (AuNRs) and unquenching under different conditions. In vivo and in vitro experiments suggest that both nanoflares exhibit excellent biocompatibility and make efficient and sensitive judgments on the two targets. This strategy emphasizes the reuse nature of enzymes, and a small amount of target can generate a large amount of fluorescent signal in the logic device, which greatly reduces the detection limit when monitoring low-abundance targets. Since the short-stranded DNA component of the detection device is simple in composition and easy to program its probe sequence, it can be expanded into a detection system for the detection of other sets of related markers, which increases its potential for clinical application.

A novel binding-induced DNAzyme motor triggered by survivin mRNA

The accurate and sensitive detection of survivin mRNA is of great significance for cancer diagnosis and treatment. However, limited by the low-abundance mRNA in live cells, most strategies of survivin mRNA detection that were one-to-one signal-triggered model (one target triggered one signal) were inapplicable in practice. Here, we reported a binding-induced DNAzyme motor triggered by the survivin mRNA, which was a one-to-more signal-triggered model (one target triggered more signals), amplifying the detection signal and enhancing the sensitivity. The nanomotor is constructed by assembling several DNAzyme motor strands silenced by the blocker strands, and dozens of FAM-labeled substrate strands on a single gold nanoparticle (AuNP), forming three-dimensional DNA tracks. Through building the survivin mRNA bridge between the blocker and the DNAzyme motor strand, the binding-induced DNA nanomotor could be triggered by survivin mRNA. The operation of the DNAzyme motor was self-powered. And each walking step of the DNAzyme motor was fueled by DNAzyme-catalyzed substrate cleavage, along with the cleavage of the fluorescent molecule, resulting in autonomous and progressive walking along the AuNP-based tracks, and the fluorescence increase. The DNAzyme motor exhibited excellent sensitivity and remarkable specificity for survivin mRNA, providing the potential for cell image.

Enzymatically Controlled Nanoflares for Specific Molecular Recognition and Biosensing

In situ sensing of physiological and pathological species in cancer cells is of great importance to unravel their molecular and cellular processes. However, the biosensing with conventional probes is often limited by the undesired on-target off-tumor interference. Here, we report a novel strategy to design enzymatically controlled nanoflares for sensing and imaging molecular targets in tumor cells. The triggerable nanoflare was designed via rational engineering of structure-switching aptamers with the incorporation of an enzyme-activatable site and further conjugation on gold nanoparticles. The nanoflare sensors did not respond to target molecules in normal cells, but they could be catalytically activated by specific enzymes in cancer cells, thereby enabling cancer-specific sensing and imaging in vitro and in vivo with improved tumor specificity. Considering that diverse aptamers were selected, we expect that this strategy would facilitate the precise detection of a broad range of targets in tumors and may promote the development of smart probes for cancer diagnosis.

Nanoswimmers Based on Capped Janus Nanospheres

Nanoswimmers are synthetic nanoscale objects that convert the available surrounding free energy to a directed motion. For example, bacteria with various flagella types serve as textbook examples of the minuscule swimmers found in nature. Along these lines, a plethora of artificial hybrid and non-hybrid nanoswimmers have been introduced, and they could find many uses, e.g., for targeted drug delivery systems (TDDSs) and controlled drug treatments. Here, we discuss a certain class of nanoparticles, i.e., functional, capped Janus nanospheres that can be employed as nanoswimmers, their subclasses and properties, as well as their various implementations. A brief outlook is given on different fabrication and synthesis methods, as well as on the diverse compositions used to prepare nanoswimmers, with a focus on the particle types and materials suitable for biomedical applications. Several recent studies have shown remarkable success in achieving temporally and spatially controlled drug delivery in vitro using Janus-particle-based TDDSs. We believe that this review will serve as a concise introductory synopsis for the interested readers. Therefore, we hope that it will deepen the general understanding of nanoparticle behavior in biological matrices.

Signal Transduction Strategies for Analyte Detection Using DNA-Based Nanostructures

The use of DNA-based nanostructures as probes has led to significant advances in chemical and biological sensing, allowing the detection of analytes in complex media, the understanding of fundamental biological processes, and the ability to diagnose diseases based on molecular signatures. The utility of these structures arises both from DNA's inherent ability to selectively recognize and bind a variety of chemical species and from the unique properties observed when DNA is restructured at the nanoscale. In this Minireview, we chronicle the most commonly used signal transduction strategies that have been interfaced with various DNA-based nanostructures. We discuss the types of analytes and the detection scenarios that are sought after, delineate the advantages and disadvantages of each signaling strategy, and outline the key considerations that guide the selection of each signaling method.

The Progress and Promise of RNA Medicine─An Arsenal of Targeted Treatments

In the past decade, there has been a shift in research, clinical development, and commercial activity to exploit the many physiological roles of RNA for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA has catapulted to the forefront of drug research. With diverse functions beyond the role of mRNA in producing antigens or therapeutic proteins, many classes of RNA serve regulatory roles in cells and tissues. These RNAs have potential as new therapeutics, with RNA itself serving as either a drug or a target. Here, based on the CAS Content Collection, we provide a landscape view of the current state and outline trends in RNA research in medicine across time, geography, therapeutic pipelines, chemical modifications, and delivery mechanisms.

Superwettable Biosensor for Disease Biomarker Detection

Bioinspired superwettable materials have aroused wide interests in recent years for their promising application fields from service life to industry. As one kind of emerging application, the superwettable surfaces used to fabricate biosensors for the detection of disease biomarkers, especially tumor biomarkers, have been extensively studied. In this mini review, we briefly summarized the sensing strategy for disease biomarker detection based on superwettable biosensors, including fluorescence, electrochemistry, surface-enhanced Raman scattering, and visual assays. Finally, the challenges and direction for future development of superwettable biosensors are also discussed.