Nondestructive Analysis of Tumor-Associated Membrane Protein Integrating Imaging and Amplified Detection in situ Based on Dual-Labeled DNAzyme

Recent advances in DNAzymes for bioimaging, biosensing and cancer therapy

DNAzymes, a class of single-stranded catalytic DNA with good stability, high catalytic activity, and easy synthesis, functionalization and modification properties, have garnered significant interest in the realm of biosensing and bioimaging. Their integration with fluorescent dyes or chemiluminescent moieties has led to remarkable bioimaging outcomes, while DNAzyme-based biosensors have demonstrated robust sensitivity and selectivity in detecting metal ions, nucleic acids, proteins, enzyme activities, exosomes, bacteria and microorganisms. In addition, by delivering DNAzymes into tumor cells, the mRNA therein can be cleaved to regulate the expression of corresponding proteins, which has further propelled the application of DNAzymes in cancer gene therapy and synergistic therapy. This paper reviews the strategies for screening attractive DNAzymes such as SELEX and high-throughput sequencing, and briefly describes the amplification strategies of DNAzymes, which mainly include catalytic hairpin assembly (CHA), DNA walker, hybridization chain reaction (HCR), DNA origami, CRISPR-Cas12a, rolling circle amplification (RCA), and aptamers. In addition, applications of DNAzymes in bioimaging, biosensing, and cancer therapy are also highlighted. Subsequently, the possible challenges of these DNAzymes in practical applications are further pointed out, and future research directions are suggested.

A magnetic DNAzyme walker for both in-situ imaging and sensitive detection of MUC1 on living cells

Mucin 1 (MUC1) is a transmembrane glycoprotein commonly expressed in epithelial cells with stable levels and polarized distribution. Their expression levels and spatial distribution abnormally altered during oncogenesis and play tumor-promoting roles synergistically. We herein propose a magnetic DNAzyme walker (MDW) for both in-situ imaging and sensitive detection of MUC1. This MDW was constructed by modifying specially designed track strands (TSs) and walking strands (WSs) on a streptavidin magnetic bead (SA-MB). The TSs contained cleavage sites for DNAzymes and were labeled with Cy3 at free ends. The WSs contained DNAzyme sequences and were firstly blocked by hybridizing with Cy5-labeled aptamers of MUC1. The DNAzymes were unlocked upon aptamers binding to MUC1 on cells. MDWs were then transferred to a buffer suitable for DNAzyme action, where the unlocked DNAzymes cleaved multiple TSs, releasing amplified Cy3-fragments, which were separated from the uncleaved ones by magnetic separation. In-situ imaging of MUC1 were achieved by the fluorescence of Cy5 on aptamers bound to MUC1. Sensitive detection of MUC1 were achieved by the amplified fluorescence of released Cy3. In-situ imaging and walker operation for detection were triggered by the same targets at the same time, ensuring the signals are real-time correlative. Moreover, MDWs' operation was separated from cells, reducing interference between imaging and detection. The proposed MDW offers a potential approach for comprehensive analysis of MUC1 in early diagnosis and progression assessment of tumor.

Computer-Aided Design of DNA Self-Limited Assembly for Relative Quantification of Membrane Proteins

Immunofluorescence imaging of cells plays a vital role in biomedical research and clinical diagnosis. However, when it is applied to relative quantification of proteins, it suffers from insufficient fluorescence intensity or partial overexposure, resulting in inaccurate relative quantification. Herein, we report a computer-aided design of DNA self-limited assembly (CAD-SLA) technology and apply it for relative quantification of membrane proteins, a concept proposed for the first time. CAD-SLA can achieve exponential cascade signal amplification in one pot and terminate at any desired level. By conjugating CAD-SLA with immunofluorescence, in situ imaging of cell membrane proteins is achieved with a controllable amplification level. Besides, comprehensive fluorescence intensity information from fluorescent images can be obtained, accurately showing relative quantitative information. Slight protein expression differences previously indistinguishable by immunofluorescence or Western blotting can now be discriminated, making fluorescence imaging-based relative quantification a promising tool for membrane protein analysis. From the perspectives of both DNA self-assembly technology and immunofluorescence technology, this work has solved difficult problems and provided important reference for future development.

A functional DNA-modified dual-response gold nanoprobe for simultaneously imaging the acidic microenvironment and membrane proteins of tumor cells

Tumor progression is a complicated process influenced by multiple factors, in which the acidic tumor microenvironment (TME) and altered tumor-associated membrane proteins (TA-MPs) are closely involved. Monitoring the status of these factors is of significance for tumor progression research. Here, we develop a novel probe for simultaneously imaging the acidic TME and TA-MPs in situ. In this probe, i-motif-forming sequences (strand I) are conjugated to a gold nanoparticle (AuNP) via gold-sulfur bonds for acid-response. Extended aptamers (strand A) for protein recognition are labeled with Cy3 and Cy5 respectively at two ends. The extended part of strand A hybridizes with strand I to quench Cy3 by the proximal AuNP, and the protein recognition part hybridizes with a strand labeled with BHQ2 (strand Q) to quench Cy5. When the integrated probe encounters an acidic TME, the strand I fold into i-motif quadruplexes and release the AQ duplexes from the AuNP, enabling Cy3 to be lit to indicate the acidic TME. The aptamers in AQ duplexes bind to target proteins, removing the hybridization between strand A and Q thus leading to the fluorescence recovery of Cy5 for in-situ imaging of the proteins. Fluorescence measurement and confocal microscopy imaging showed that the probe could sensitively respond to the alteration in acidity from pH 7.4 into pH 6.5, which is coincide with the acidity gap of extracellular microenvironment between normal and tumor cells. Besides, it enabled the in-situ imaging of MUC1 proteins on living cell surface, revealing their expression level and distribution. This probe demonstrates a new approach for simultaneously imaging the acidic TME and TA-MPs, providing a useful tool for multifactor research of tumor progression.

A DNA logic gate with dual-anchored proximity aptamers for the accurate identification of circulating tumor cells

We have designed a DNA logic gate that can integrate the recognition of multiple biomarkers with signal amplification to perform the accurate and sensitive analysis of circulating tumor cells (CTCs). It also has the potential to analyze rare cells that exist in small amounts but are of great significance (such as stem cells) in the fields of clinical diagnosis and biomedicine.

Single-Cell Analysis of Highly Metastatic Circulating Tumor Cells by Combining a Self-Folding Induced Release Reaction with a Cell Capture Microchip

Nondestructive analysis of the single-cell molecular phenotype of circulating tumor cells (CTCs) is of great significance to the precise diagnosis and treatment of cancer but is also a huge challenge. To address this issue, here, we develop a facile analysis system that integrates CTCs' capture and molecular phenotype analysis. An isothermal nucleic acid amplification technique named self-folding induced release reaction (sFiR), which has high-efficiency signal amplification capabilities and can run under physiological conditions, is first developed to meet the high requirements for sensitivity and nondestructivity. By combining the sFiR with immune recognition and a single cell capture microchip, the molecular phenotype analysis of a single CTC is realized. As a model, nondestructive analysis of junction plakoglobin (JUP), an overexpressed membrane protein that is closely related to the metastasis of CTCs, is successfully achieved. Results reveal that this sFiR-based analysis system can clearly distinguish the expression of JUP in different cancer cell lines and can present quantitative information on the expression of JUP. Furthermore, the captured and analyzed CTCs maintain their basic physiological activity and can be used for drug sensitivity testing. Considering the excellent performance and ease of operation of the system, it can provide technical support for CTC-based cancer liquid biopsy and drug development.

Nondestructive analysis of tumor-associated membrane protein MUC1 in living cells based on dual-terminal amplification of a DNA ternary complex

Non-destructive analysis of cells at the molecular level is of critical importance for cell research. At present, immunoassay-based and aptamer-based methods can achieve non-structural destructive cell analysis, but still lead to changes in cells at the molecular level. Here, we have proposed a dual-terminal amplification (DTA) strategy, which enables nondestructive analysis of membrane protein MUC1 without the effect on protein expression and cell viability in living cells. Methods: A fluorophore (Cy5)-labeled DNA ternary complex consisting of three oligonucleotides is designed. It can recognize MUC1 through its aptamer region, and thus make the MUC1 of cells visible under a fluorescence microscope. When DNA polymerase is added, dual-terminal amplification is performed. One direction dissociates aptamer from MUC1, and the other direction, also known as rolling circle amplification (RCA), produces long linear DNA strands, which can be further adopted for quantitative analysis of MUC1. In this way, all reagents are removed from the surface of the cells after the analysis, which allows nondestructive analysis. We named this strategy dual-terminal amplification (DTA) analysis. Results: By using the DTA analysis, both in situ fluorescence imaging analysis and ex situ fluorescence quantitative analysis of MUC1 were achieved. In addition, the aptamer-containing DNA ternary complex stays on cell surface only during the analysis and leaves the cell after the analysis is complete. The cells can be maintained in a non-interfering state for the rest of the time. So after the analysis, it is found that there are no effect on the physiological activity of cells and the expression of target protein even after two rounds of repeatable imaging and quantitative analysis. Conclusion: In summary, we have successfully constructed a strategy for nondestructive analysis of membrane protein in living cells. We believe that this method provides a promising way for the analysis of the key membrane proteins of cells and the versatile utilization of precious cell samples.

In situ Analysis of Cancer Cells Based on DNA Signal Amplification and DNA Nanodevices

Cancer is a global disease which has been disturbing researchers in medicine and seriously threatens patients' health and lifetime around the world in the past several decades. Due to the characteristics of cancer cells, such as uncontrollable cell proliferation, cell invasion and metastasis to surrounding tissues, lower grade of differentiation, higher telomerase activity and others, it has been one of the most usual lethal factors, next to heart disease in incidence. Cancer mortality can be decreased by early diagnosis, and the people who with treatment at an early stage have an obvious improved survival rate. Consequently, early detection is significant for better understanding the pathogenesis of cancer and improving the prognosis of patients. In situ detection technique is a vital tool for imaging and cellular pathology research, which can provide effective information about tumor markers in the early cancer detection. In view of low expression of most tumor markers in the early stage of cancers, detection techniques based on DNA signal amplification and DNA nanodevices can provide a strong support for the diagnosis and detection of cancers. In this review, we summarize the research progress of different analytical techniques for detecting various tumor markers that have been reported in recent years. We compare different DNA amplification and nanodevices, then provide guidance and suggestions for better understanding in situ analysis of cancer cells.

Simple and universal signal labeling of cell surface for amplified detection of cancer cells via mild reduction

Membrane protein, a novel surface biomarker, plays an important role in cell recognition and disease diagnosis. Accurate recognition of membrane protein ensure high specificity of cell identification, while introducing signal molecules onto cell membrane is critical to achieve high sensitivity. In this work, we introduced a simple and universal signal labeling approach for cancer cell detection based on mild reduction-mediated cell engineering. This approach included the mild reduction of disulfide bonds within membrane proteins and the introduction of DNA bridge complex-templated silver nanoclusters (DNA bridge-AgNCs) through the thiol-maleimide conjugation. The mild reduction reactions on the cell surface significantly increased the binding sites for signal labeling, and DNA bridge-AgNCs served as a scaffold of signal amplification, resulting in a wide linear range from 50-2 × 10⁶ cells, and a detection limit of 15 cells. In addition, the method also showed good selectivity in complex environment. Therefore, this method may have great application space in the field of cell detection and even disease diagnosis in the near future.

Molecular Engineering of Functional Nucleic Acid Nanomaterials toward In Vivo Applications

Recent advances in nanotechnology and engineering have generated many nanomaterials with unique physical and chemical properties. Over the past decade, numerous nanomaterials are introduced into many research areas, such as sensors for environmental monitoring, food safety, point-of-care diagnostics, and as transducers for solar energy transfer. Meanwhile, functional nucleic acids (FNAs), including nucleic acid enzymes, aptamers, and aptazymes, have attracted major attention from the biomedical community due to their unique target recognition and catalytic properties. Benefiting from the recent progress of molecular engineering strategies, the physicochemical properties of nanomaterials are endowed by the target recognition and catalytic activity of FNAs in the presence of a target analyte, resulting in numerous smart nanoprobes for diverse applications including intracellular imaging, drug delivery, in vivo imaging, and tumor therapy. This progress report focuses on the recent advances in designing and engineering FNA-based nanomaterials, highlighting the functional outcomes toward in vivo applications. The challenges and opportunities for the future translation of FNA-based nanomaterials into clinical applications are also discussed.

RNA-Cleaving DNAzymes: Old Catalysts with New Tricks for Intracellular and In Vivo Applications

DNAzymes are catalytically active DNA molecules that are normally isolated through in vitro selection methods, among which RNA-cleaving DNAzymes that catalyze the cleavage of a single RNA linkage embedded within a DNA strand are the most studied group of this DNA enzyme family. Recent advances in DNA nanotechnology and engineering have generated many RNA-cleaving DNAzymes with unique recognition and catalytic properties. Over the past decade, numerous RNA-cleaving, DNAzymes-based functional probes have been introduced into many research areas, such as in vitro diagnostics, intracellular imaging, and in vivo therapeutics. This review focus on the fundamental insight into RNA-Cleaving DNAzymes and technical tricks for their intracellular and in vivo applications, highlighting the recent progress in the clinical trial of RNA-Cleaving DNAzymes with selected examples. The challenges and opportunities for the future translation of RNA-cleaving DNAzymes for biomedicine are also discussed.

DNA Nanotechnology for Cancer Diagnosis and Therapy

Cancer is one of the leading causes of mortality worldwide, because of the lack of accurate diagnostic tools for the early stages of cancer. Thus, early diagnosis, which provides important information for a timely therapy of cancer, is of great significance for controlling the development of the disease and the proliferation of cancer cells and for improving the survival rates of patients. To achieve the goals of early diagnosis and timely therapy of cancer, DNA nanotechnology may be effective, since it has emerged as a valid technique for the fabrication of various nanoscale structures and devices. The resultant DNA-based nanoscale structures and devices show extraordinary performance in cancer diagnosis, owing to their predictable secondary structures, small sizes, and high biocompatibility and programmability. In particular, the rapid development of DNA nanotechnologies, such as molecular assembly technologies, endows DNA-based nanomaterials with more functionalization and intellectualization. Here, we summarize recent progress made in the development of DNA nanotechnology for the fabrication of functional and intelligent nanomaterials and highlight the prospects of this technology in cancer diagnosis and therapy.