A single promoter system co-expressing RNA sensor with fluorescent proteins for quantitative mRNA imaging in living tumor cells

Engineered aptamers for molecular imaging

Molecular imaging, including quantification and molecular interaction studies, plays a crucial role in visualizing and analysing molecular events occurring within cells or organisms, thus facilitating the understanding of biological processes. Moreover, molecular imaging offers promising applications for early disease diagnosis and therapeutic evaluation. Aptamers are oligonucleotides that can recognize targets with a high affinity and specificity by folding themselves into various three-dimensional structures, thus serving as ideal molecular recognition elements in molecular imaging. This review summarizes the commonly employed aptamers in molecular imaging and outlines the prevalent design approaches for their applications. Furthermore, it highlights the successful application of aptamers to a wide range of targets and imaging modalities. Finally, the review concludes with a forward-looking perspective on future advancements in aptamer-based molecular imaging.

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.

High-throughput iSpinach fluorescent aptamer-based real-time monitoring of in vitro transcription

In vitro transcription (IVT) is an essential technique for RNA synthesis. Methods for the accurate and rapid screening of IVT conditions will facilitate RNA polymerase engineering, promoter optimization, and screening for new transcription inhibitor drugs. However, traditional polyacrylamide gel electrophoresis (PAGE) and high-performance liquid chromatography methods are labor intensive, time consuming and not compatible with real-time analysis. Here, we developed an inexpensive, high-throughput, and real-time detection method for the monitoring of in vitro RNA synthesis called iSpinach aptamer-based monitoring of Transcription Activity in Real-time (STAR). STAR has a detection speed at least 100 times faster than conventional PAGE method and provides comparable results in the analysis of in vitro RNA synthesis reactions. It also can be used as an easy and quantitative method to detect the catalytic activity of T7 RNA polymerase. To further demonstrate the utility of STAR, it was applied to optimize the initially transcribed region of the green fluorescent protein gene and the 3T4T variants demonstrated significantly enhanced transcription output, with at least 1.7-fold and 2.8-fold greater output than the wild-type DNA template and common transcription template, respectively. STAR may provide a valuable tool for many biotechnical applications related to the transcription process, which may pave the way for the development of better RNA-related enzymes and new drugs.

Aptamer based probes for living cell intracellular molecules detection

Biosensors have been employed for monitoring and imaging biological events and molecules. Sensitive detection of different biomolecules in vivo can reflect the changes of physiological conditions in real-time, which is of great significance for the diagnosis and treatment of diseases. The detection of intracellular molecules concentration change can indicate the occurrence and development of disease. But the analysis process of the existing detection methods, such as Western blot detection of intracellular protein, polymerase chain reaction (PCR) technique quantitative analysis of intracellular RNA and DNA, usually need to extract the cell lysis which is complex and time-consuming. Fluorescence bioimaging enables in situ monitoring of intracellular molecules in living cells. By combining the specificity of aptamer for intracellular molecules binding, and biocompatibility of fluorescent materials and nanomaterials, biosensors with different nanostructures have been developed to enter into living cells for analysis. This review summarizes the fluorescence detection methods based on aptamer for intracellular molecules detection. The principles, limit of detection, advantages, and disadvantages of different platforms for intracellular molecular fluorescent response are summarized and reviewed. Finally, the current challenges and future developments were discussed and proposed.

Multi-stage responsive peptide nanosensor: Anchoring EMT and mitochondria with enhanced fluorescence and boosting tumor apoptosis

Epithelial-mesenchymal transition (EMT) is closely related to tumor metastasis and invasion. Thereinto, mesenchymal tumor mitochondria are the critical target for tumor inhibition. Therefore, real-time in vivo monitoring of EMT as well as inhibiting mesenchymal tumor mitochondria is of great diagnosis and therapy significance. Herein, we construct a multi-stage recognition and morphological transformable self-assembly-peptide nano biosensor ^NDRP which can response the EMT marker and specifically damage the mesenchymal tumor cell in vivo. This nano-molar-affinity sensor is designed and screened with sensitive peptides containing a molecular switching which could be specifically triggered by the receptor to achieve the vesicle-to-fibril transformation in living system with enhanced fluorescent signal. ^NDRP nanosensor could target the tumor lesion in circulatory system, recognize mesenchymal tumor marker DDR2 (Discoidin domain receptor 2) in cellular level and specifically achieve mitochondria in subcellular level as well as damaged mitochondria which could be applied as a in vivo theranostic platform.

Recent Development of Fluorescent Light-Up RNA Aptamers

Technologies for RNA imaging in live cells play an important role in understanding the function and regulatory process of RNAs. One approach for genetically encoded fluorescent RNA imaging involves fluorescent light-up aptamers (FLAPs), which are short RNA sequences that can bind cognate fluorogens and activate their fluorescence greatly. Over the past few years, FLAPs have emerged as genetically encoded RNA-based fluorescent biosensors for the cellular imaging and detection of various targets of interest. In this review, we first give a brief overview of the development of the current FLAPs based on various fluorogens. Then we further discuss on the photocycles of the reversibly photoswitching properties in FLAPs and their photostability. Finally, we focus on the applications of FLAPs as genetically encoded RNA-based fluorescent biosensors in biosensing and bioimaging, including RNA, non-nucleic acid molecules, metal ions imaging and quantitative imaging. Their design strategies and recent cellular applications are emphasized and summarized in detail.

Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More

The central role of RNA in living systems made it highly desirable to have noninvasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-fluorescent molecules called "fluorogens" that become fluorescent upon binding to genetically encodable RNAs called "light-up aptamers." Yet, the development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications is presented and discussed.

Genetically encoded light-up RNA aptamers and their applications for imaging and biosensing

Intracellular small ligands and biomacromolecules are playing crucial roles not only as executors but also as regulators. It is essential to develop tools to investigate their dynamics to interrogate their functions and reflect the cellular status. Light-up RNA aptamers are RNA sequences that can bind with their cognate nonfluorescent fluorogens and greatly activate their fluorescence. The emergence of genetically encoded light-up RNA aptamers has provided fascinating tools for studying intracellular small ligands and biomacromolecules owing to their high fluorescence activation degree and facile programmability. Here we review the burgeoning field of light-up RNA aptamers. We first briefly introduce light-up RNA aptamers with a focus on the photophysical properties of the fluorogens. Then design strategies of genetically encoded light-up RNA aptamer based sensors including turn-on, signal amplification and ratiometric rationales are emphasized.

A DNA-functionalized biomass nanoprobe for the targeted photodynamic therapy of tumor and ratiometric fluorescence imaging-based visual cancer cell identification/antitumor drug screening

Survivin is widely expressed in tumor tissue, in which the in situ ratiometric fluorescence imaging of intracellular survivin mRNA can provide accurate information for the diagnosis and treatment of cancers, as well as the screening of antitumor drugs. However, the development of a nanoprobe that can be used simultaneously in the diagnosis and treatment of tumors and the screening of antitumor drugs remains a challenge. In an effort to address these requirements, a multifunctional biomass nanoprobe was developed for the photodynamic therapy (PDT) of tumors as well as cancer cell identification and antitumor drug screening based on the ratiometric fluorescence imaging of intracellular survivin mRNA. This nanoprobe was assembled from near-infrared (NIR) biomass quantum dots (BQDs), single-stranded DNA and NIR dye (dylight680) labeled single-stranded DNA. The BQDs contain a large number of chlorophyll molecules, meaning that they can produce a large amount of singlet oxygen under NIR light irradiation, thus realizing the PDT of a tumor. However, the specific binding of the nanoprobe to intracellular survivin mRNA causes the release of dylight680 and reduces the fluorescence resonance energy transfer (FRET) efficiency between the BQDs and dylight680 in the probe, thereby achieving the ratiometric fluorescence imaging of survivin mRNA. Therefore, the prepared nanoprobe can not only be used in the diagnosis of cancers, but also in the targeted PDT of tumors.

Genetically Encoded Dual-Color Light-Up RNA Sensor Enabled Ratiometric Imaging of MicroRNA

MicroRNAs (miRNAs) play essential roles in regulating gene expression and cell fate. However, it remains a great challenge to image miRNAs with high accuracy in living cells. Here, we report a novel genetically encoded dual-color light-up RNA sensor for ratiometric imaging of miRNAs using Mango as an internal reference and SRB2 as the sensor module. This genetically encoded sensor is designed by expressing a splittable fusion of the internal reference and sensor module under a single promoter. This design strategy allows synchronous expression of the two modules with negligible interference. Live cell imaging studies reveal that the genetically encoded ratiometric RNA sensor responds specifically to mir-224. Moreover, the sensor-to-Mango fluorescence ratios are linearly correlated with the concentrations of mir-224, confirming their capability of determining mir-224 concentrations in living cells. Our genetically encoded light-up RNA sensor also enables ratiometric imaging of mir-224 in different cell lines. This strategy could provide a versatile approach for ratiometric imaging of intracellular RNAs, affording powerful tools for interrogating RNA functions and abundance in living cells.

Activatable CRISPR Transcriptional Circuits Generate Functional RNA for mRNA Sensing and Silencing

CRISPR-dCas9 systems that are precisely activated by cell-specific information facilitate the development of smart sensors or therapeutic strategies. We report the development of an activatable dCas9 transcriptional circuit that enables sensing and silencing of mRNA in living cells using hybridization-mediated structure switching for gRNA activation. The gRNA is designed with the spacer sequence blocked by a hairpin structure, and mRNA hybridization induces gRNA structure switching and activates the transcription of reporter RNA. An mRNA sensor developed using a light-up RNA reporter shows high sensitivity and fast-response imaging of survivin mRNA in cells under drug treatments and different cell lines. Furthermore, a feedback circuit is engineered by incorporating a small hairpin RNA in the reporter RNA, demonstrating a smart strategy for dynamic sensing and silencing of survivin with induced tumor cell apoptosis. This circuit illustrates a broadly applicable platform for the development of cell-specific sensing and therapeutic strategies.

Capture and selective release of multiple types of circulating tumor cells using smart DNAzyme probes

The effective capture, release and reanalysis of circulating tumor cells (CTCs) are of great significance to acquire tumor information and promote the progress of tumor therapy. Particularly, the selective release of multiple types of CTCs is critical to further study; however, it is still a great challenge. To meet this challenge, we designed a smart DNAzyme probe-based platform. By combining multiple targeting aptamers and multiple metal ion responsive DNAzymes, efficient capture and selective release of multiple types CTCs were realized. Sgc8c aptamer integrated Cu2+-dependent DNAzyme and TD05 aptamer integrated Mg2+-dependent DNAzyme can capture CCRF-CEM cells and Ramos cells respectively on the substrate. With the addition of Cu2+ or Mg2+, CCRF-CEM cells or Ramos cells will be released from the substrate with specific selectivity. Furthermore, our platform has been successfully demonstrated in the whole blood sample. Therefore, our capture/release platform will benefit research on the molecular analysis of CTCs after release and has great potential for cancer diagnosis and individualized treatment.

Biodegradable nanosyringes for intracellular amplification-based dual-diagnosis and gene therapy in single living cells

The efficient delivery of biomolecules into living cells as well as their easy biodegradation have been challenges for the application of intracellular amplification for sensitive multiple-diagnosis and gene therapy for cancer. Herein, new strategies of amplification-based dual-detection of cancer biomarkers (Let-7a miRNA and VEGF) and gene therapy for cancers are put forward. These are achieved through biodegradable nanosyringes (NSs), rigid and sharp in vitro but degradable in vivo, which are applied for the efficient loading, delivery and release of biomolecules (enzymes, nucleic acids, and even silencing RNA) into living cells. After penetrating cell membranes and escaping from endosomes through their rigid and sharp tips, NSs release biomolecules for fast and easy "one-step" rolling circle amplification (ring formation and amplification) in single living cells. Therefore, based on signals from two probes, FAM-Probe and Cy5-Probe, that selectively bind to amplification products, 100 aM of Let-7a and 100 fM of VEGF could be detected, which are much lower than reported values. Furthermore, siRNAs can also be delivered by NSs for gene therapy, and their therapeutic effect was evaluated by their in vivo antitumor efficacy in CCRF-CEM subcutaneous xenograft nude mice. Rigid in vitro and degradable in vivo, NSs show potential for achieving fast, sensitive and safe cancer diagnosis and efficient therapy.