Engineering DNA on the Surface of Upconversion Nanoparticles for Bioanalysis and Therapeutics

Recent progress of UCNPs-MoS2 nanocomposites as a platform for biological applications

Composite materials can take advantages of the functional benefits of multiple pure nanomaterials to a greater degree than single nanomaterials alone. The UCNPs-MoS2 composite is a nano-application platform that combines upconversion luminescence and photothermal properties. Upconversion nanoparticles (UCNPs) are inorganic nanomaterials with long-wavelength excitation and short-wavelength tunable emission capabilities, and are able to effectively convert near-infrared (NIR) light into visible light for increased photostability. However, UCNPs have a low capacity for absorbing visible light, whereas MoS2 shows better absorption in the ultraviolet and visible regions. By integrating the benefits of UCNPs and MoS2, UCNPs-MoS2 nanocomposites can convert NIR light with a higher depth of detection into visible light for application with MoS2 through fluorescence resonance energy transfer (FRET), which compensates for the issues of MoS2's low tissue penetration light-absorbing wavelengths and expands its potential biological applications. Therefore, starting from the construction of UCNPs-MoS2 nanoplatforms, herein, we review the research progress in biological applications, including biosensing, phototherapy, bioimaging, and targeted drug delivery. Additionally, the current challenges and future development trends of UCNPs-MoS2 nanocomposites for biological applications are also discussed.

Near-Infrared Light-Controlled MicroRNA-21-Loaded Upconversion Nanoparticles to Promote Bone Formation in the Midpalatal Suture

Rapid maxillary expansion (RME) is a common therapy for maxillary transverse deficiency. However, relapses after RME usually occur because of insufficient bone formation. MicroRNA-21 (miR-21) was reported as an important post-transcriptional modulator for osteogenesis. Herein, a photocontrolled miR-21 (PC-miR-21)-loaded nanosystem using upconversion nanoparticles (UCNPs) modified with poly(ether imide) (PEI), i.e., UCNPs@PEI@PC-miR-21, was constructed to promote bone formation in the midpalatal suture. UCNPs@PEI was constructed as the light transducer and delivery carrier. The UCNPs@PEI@PC-miR-21 nanocomplexes have good aqueous dispersibility and biocompatibility. The in vitro cell experiment suggested that UCNPs@PEI could protect PC-miR-21 from biodegradation and release PC-miR-21 into the cytoplasm under near-infrared light (NIR) irradiation. Furthermore, UCNPs@PEI@PC-miR-21 upregulated the expression of the osteogenic key markers, ALP, RUNX2, and COL1A1, at the levels of both genes and proteins. Besides, the results of the in vivo RME mice models further corroborated that photocontrollable UCNPs@PEI@PC-miR-21 accelerated bone formation with upregulating osteogenic markers of ALP, RUNX2, and osteoprotegerin and inducing fewer osteoclasts formation. In conclusion, UCNPs@PEI@PC-miR-21 nanoparticles with a NIR light could facilitate the remote and precise delivery of exogenous miR-21 to the midpalatal suture to promote bone formation during RME. This work represents a cutting-edge approach of gene therapy to promote osteogenesis in the midpalatal suture during RME and provides a frontier scientific basis for later clinical treatment.

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.

Surface ligand-assisted synthesis and biomedical applications of metal-organic framework nanocomposites

Metal-organic framework (MOF) nanocomposites have recently gained intensive attention for biosensing and disease therapy applications owing to their outstanding physiochemical properties. However, the direct growth of MOF nanocomposites is usually hindered by the mismatched lattice in the interface between the MOF and other nanocomponents. Surface ligands, molecules with surfactant-like properties, are demonstrated to exhibit the robust capability to modify the interfacial properties of nanomaterials and can be utilized as a powerful strategy for the synthesis of MOF nanocomposites. Besides this, surface ligands also exhibit significant functions in the morphological control and functionalization of MOF nanocomposites, thus greatly enhancing their performance in biomedical applications. In this review, the surface ligand-assisted synthesis and biomedical applications of MOF nanocomposites are comprehensively reviewed. Firstly, the synthesis of MOF nanocomposites is discussed according to the diverse roles of surface ligands. Then, MOF nanocomposites with different properties are listed with their applications in biosensing and disease therapy. Finally, current challenges and further directions of MOF nanocomposites are presented to motivate the development of MOF nanocomposites with elaborate structures, enriched functions, and excellent application prospects.

Nanoparticle Spikes Enhance Cellular Uptake via Regulating Myosin IIA Recruitment

Spike-like nanostructures are omnipresent in natural and artificial systems. Although biorecognition of nanostructures to cellular receptors has been indicated as the primary factor for virus infection pathways, how the spiky morphology of DNA-modified nanoparticles affects their cellular uptake and intracellular fate remains to be explored. Here, we design dually emissive gold nanoparticles with varied spikiness (from 0 to 2) to probe the interactions of spiky nanoparticles with cells. We discovered that nanospikes at the nanoparticle regulated myosin IIA recruitment at the cell membrane during cellular uptake, thereby enhancing cellular uptake efficiency, as revealed by dual-modality (plasmonic and fluorescence) imaging. Furthermore, the spiky nanoparticles also exhibited facilitated endocytosis dynamics, as revealed by real-time dark-field microscopy (DFM) imaging and colorimetry-based classification algorithms. These findings highlight the crucial role of the spiky morphology in regulating the intracellular fate of nanoparticles, which may shed light on engineering theranostic nanocarriers.

Erythrocyte membrane-camouflaged DNA-functionalized upconversion nanoparticles for tumor-targeted chemotherapy and immunotherapy

A synergistic combination of treatment with immunogenic cell death (ICD) inducers and immunoadjuvants may be a practical way to boost the anticancer response and successfully induce an immune response. The use of HR@UCNPs/CpG-Apt/DOX, new biomimetic drug delivery nanoparticles generated to combat breast cancer, is reported here as a unique strategy to produce immunogenicity and boost cancer immunotherapy. HR@UCNPs/CpG-Apt/DOX (HR-UCAD) consists of two parts. The core is composed of an immunoadjuvant CpG (a toll-like receptor 9 agonist) fused with a dendritic cell-specific aptamer sequence (CpG-Apt) to decorate upconversion nanoparticles (UCNPs) with the successful intercalation of doxorubicin (DOX) into the consecutive base pairs of Apt-CpG to construct an immune nanodrug UCNPs@CpG-Apt/DOX. The targeting molecule hyaluronic acid (HA) was inserted into a red blood cell membrane (RBCm) to form the shell (HR). HR-UCAD possessed a strong capacity to specifically induce ICD. Following DOX-induced ICD of cancer cells, sufficient exposure to tumor antigens and UCNPs@CpG-Apt (UCA) activated the tumor-specific immune response and reversed the immunosuppressive tumor microenvironment. In addition, HR-UCAD has good biocompatibility and increases the active tumor-targeting effect. Furthermore, HR-UCAD exhibits excellent near-infrared upconversion luminescence emission at 804 nm under irradiation with a 980 nm laser, which has great potential in biomedical imaging. Thus, the RBCm-camouflaged drug delivery system is a promising targeted chemotherapy and immunotherapy nanocomplex that could be used for effective targeted breast cancer treatment.

The construction of CRISPR/Cas9-mediated FRET 16S rDNA sensor for detection of Mycobacterium tuberculosis

The simple and efficient detection of nucleic acids is important in the diagnosis of tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tuberculosis). However, base mismatch will lead to false positive and false negative nucleic acid test, which seriously interferes with the accuracy of the final results. Herein, we demonstrated a CRISPR/Cas-9-mediated fluorescent strategy utilizing fluorescence resonance energy transfer (FRET) for the detection of bacteria. High-variable region of M. tuberculosis 16S rDNA fragment was used as the target, and CRISPR/Cas9 was used as the recognition element. The binding of the P1 probe of upconversion nanoparticles (UCNPs) @SiO₂-P1 and the P2 probe of Fe₃O₄@Au-P2 caused the fluorescence quenching of UCNPs. In the presence of the target, the P2 probe hybridized with the target to form double-stranded DNA (dsDNA), which was recognized and cleaved by CRISPR/Cas9, resulting in the breaking of the P1-P2 duplex linkage. UCNPs moved away from Fe₃O₄@Au under a magnetic field, and the fluorescence signal was restored; bacteria were detected under the excitation of a 980 nm laser source. Using the CRISPR/Cas-9-mediated system, the sensor could distinguish single-base mismatches in 10 bases from the protospacer adjacent motif (PAM) region. The limit of detection (LOD) was 20 CFU mL^-1 and the detection time was 2 h. It developed a new way of accurate nucleic acid detection for disease diagnosis.

Understanding FRET in Upconversion Nanoparticle Nucleic Acid Biosensors

Upconversion nanoparticles (UCNPs) have been frequently applied in Förster resonance energy transfer (FRET) bioanalysis. However, the understanding of how surface coatings, bioconjugation, and dye-surface distance influence FRET biosensing performance has not significantly advanced. Here, we investigated UCNP-to-dye FRET DNA-hybridization assays in H₂O and D₂O using ∼24 nm large NaYF₄:Yb³⁺,Er³⁺ UCNPs coated with thin layers of silica (SiO₂) or poly(acrylic acid) (PAA). FRET resulted in strong distance-dependent PL intensity changes. However, the PL decay times were not significantly altered because of continuous Yb³⁺-to-Er³⁺ energy migration during Er³⁺-to-dye FRET. Direct bioconjugation of DNA to the thin PAA coating combined with the closest possible dye-surface distance resulted in optimal FRET performance with minor influence from competitive quenching by H₂O. The better comprehension of UCNP-to-dye FRET was successfully translated into a microRNA (miR-20a) FRET assay with a limit of detection of 100 fmol in a 80 μL sample volume.

Optimizing Upconversion Nanoparticles for FRET Biosensing

Upconversion nanoparticles (UCNPs) are some of the most promising nanomaterials for bioanalytical and biomedical applications. One important challenge to be still solved is how UCNPs can be optimally implemented into Förster resonance energy transfer (FRET) biosensing and bioimaging for highly sensitive, wash-free, multiplexed, accurate, and precise quantitative analysis of biomolecules and biomolecular interactions. The many possible UCNP architectures composed of a core and multiple shells doped with different lanthanoid ions at different ratios, the interaction with FRET acceptors at different possible distances and orientations via biomolecular interaction, and the many and long-lasting energy transfer pathways from the initial UCNP excitation to the final FRET process and acceptor emission make the experimental determination of the ideal UCNP-FRET configuration for optimal analytical performance a real challenge. To overcome this issue, we have developed a fully analytical model that requires only a few experimental configurations to determine the ideal UCNP-FRET system within a few minutes. We verified our model via experiments using nine different Nd-, Yb-, and Er-doped core-shell-shell UCNP architectures within a prototypical DNA hybridization assay using Cy3.5 as an acceptor dye. Using the selected experimental input, the model determined the optimal UCNP out of all theoretically possible combinatorial configurations. An extreme economy of time, effort, and material was accompanied by a significant sensitivity increase, which demonstrated the powerful feat of combining a few selected experiments with sophisticated but rapid modeling to accomplish an ideal FRET biosensor.

Engineered upconversion nanocarriers for synergistic breast cancer imaging and therapy: Current state of art

Breast cancer is the most common type of cancer in women and is the second leading cause of cancer-related deaths worldwide. Early diagnosis and effective therapeutic interventions are critical determinants that can improve survival and quality of life in breast cancer patients. Nanotheranostics are emerging interventions that offer the dual benefit of in vivo diagnosis and therapeutics through a single nano-sized carrier. Rare earth metal-doped upconversion nanoparticles (UCNPs) with their ability to convert near-infrared light to visible light or UV light in vivo settings have gained special attraction due to their unique luminescence and tumor-targeting properties. In this review, we have discussed applications of UCNPs in drug and gene delivery, photothermal therapy (PTT), photodynamic therapy (PDT) and tumor targeting in breast cancer. Further, present challenges and future opportunities for UCNPs in breast cancer treatment have also been mentioned.

Facile Synthesis of Black Phosphorus Nanosheet@NaReF4 Nanocomposites for Potential Bioimaging

Black phosphorus nanomaterials (BPN) have been well developed in tumor therapy. However, lack of diagnostic function limits the development of BPN in biomedicine. Lanthanide-doped nanoparticles are considered as versatile materials for fluorescence or magnetic resonance imaging. Integration of BPN with lanthanide-doped nanoparticles was rarely reported owing to the complex synthesis processes and poor modification effect. Herein, we report a simple and general method for synthesizing BPN@NaReF₄ (Re: Gd or Y, Yb, Er) nanocomposite. TEM and XRD characterization confirm efficient combination of BPN and NaGdF₄ or NaYF₄:Yb,Er (18.2 mol %) after one-step mixing. The FTIR and XPS spectra were used to prove the generation of PO₄^3--Gd and P-Gd coordination bonds and clarify ligand exchange mechanism. The anchored nanoparticles on BPN were stable and become hydrophilic. The prepared BPN@NaGdF₄ exhibit the signals of photoacoustic and magnetic resonance imaging. The obtained BPN@NaYF₄:Yb,Er (18.2 mol %) have the potential in fluorescence bioimaging. We believe that this work will expand the applications of BPN in diagnosis and therapy together.

Bridge DNA guided assembly of nanoparticles to program chemical reaction networks

Bridge DNA is an essential structure for programming chemical reaction networks. In this work, a bridge DNA guided assembly of nanoparticles has been constructed to program one-step and multi-step reactions via toehold-mediated strand displacement reaction for higher structural complexity and dynamic regulation behaviors. The structures of the bridge DNA linker and the length of the toeholds have an essential effect on successful construction of a molecular machine and achievement of multi-step reactions. A six-base toehold is enough to achieve the toehold-mediated strand displacement reaction in bridge DNA. When the difference between toehold length-2 and toehold length-1 is equal to or larger than one, the multi-step reaction can be triggered and performed by the driving of bridge DNA. For application, both simultaneous detection of two target DNA strands as well as the construction of logic gates can be achieved by changing the four single-stranded tails on the bridge DNA. In principle, this approach of the bridge DNA guiding the assembly of AuNPs can implement any behavior that can be expressed mathematically.

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.

Recent progress in upconversion nanomaterials for emerging optical biological applications

The recent advances of upconversion nanoparticles (UCNPs) have made them the ideal "partner" for a variety of biological applications. In this review, we describe the emerging biological optical applications of UCNPs, focus on their potential therapeutic advantages. Firstly, we briefly review the development and mechanisms of upconversion luminescence, including organic and inorganic UCNPs. Next, in the section on UCNPs for imaging and detection, we list the development of UCNPs in visualization, temperature sensing, and detection. In the section on therapy, recent results are described concerning optogenetics and neurotherapy. Tumor therapy is another major part of this section, including the synergistic application of phototherapy such as photoimmunotherapy. In a special section, we briefly cover the integration of UCNPs in therapeutics. Finally, we present our understanding of the limitations and prospects of applications of UCNPs in biological fields, hoping to provide a more comprehensive understanding of UCNPs and attract more attention.