Programmable RNA detection with a fluorescent RNA aptamer using optimized three-way junction formation

Angle-controllable RNA tiles for programable array assembly and RNA sensing

Programmed self-assembly of RNA nanostructures presents a strategic approach to developing biomaterials with tailored properties and functionalities. Despite advancements, the variety, complexity, and programmability of de novo engineered RNA nanostructures remain limited. Here, we introduce a category of artificially designed RNA tiles by integrating antiparallel crossovers and T-junctions, featuring a controllable angle of either 65o or 90o. A total of 22 distinct tiles are explored, significantly expanding the collection of artificially designed multi-stranded RNA tiles. We investigate the design strategies that affect array assembly including T-loop configuration, sticky end pairing, structural diversification, and variations in annealing methods. Additionally, one single-stranded TC-RNA tile is designed and folded co-transcriptionally, suggesting promising applications in synthetic biology and molecular engineering. Furthermore, we demonstrate the integration of split broccoli RNA aptamers into the multi-stranded monomer tiles, enabling fluorescence activation along linear arrays for programmable RNA sensing. The facile incorporation with RNA functional nanostructures highlights the vast potential of these RNA tiles in constructing more sophisticated nanostructures for diverse biomaterial applications.

Rapid, Multiplexed, and Enzyme-Free Nucleic Acid Detection Using Programmable Aptamer-Based RNA Switches

Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. We describe a class of aptamer-based RNA switches or aptaswitches that recognize target nucleic acid molecules and initiate folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide an intense fluorescent readout without intervening enzymes, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. Aptaswitches can be used to regulate folding of seven fluorogenic aptamers, providing a general means of controlling aptamers and an array of multiplexable reporter colors. Coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed all-in-one reactions against RNA from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that are readily integrated into rapid diagnostic assays.

Fluorogenic Aptamer-Based Hybridization Chain Reaction for Signal-Amplified Imaging of Apurinic/Apyrimidinic Endonuclease 1 in Living Cells

A fluorogenic aptamer (FA)-based hybridization chain reaction (HCR) could provide a sensitive and label-free signal amplification method for imaging molecules in living cells. However, existing FA-HCR methods usually face some problems, such as a complicated design and significant background leakage, which greatly limit their application. Herein, we developed an FA-centered HCR (FAC-HCR) method based on a remote toehold-mediated strand displacement reaction. Compared to traditional HCRs mediated by four hairpin probes (HPs) and two HPs, the FAC-HCR displayed significantly decreased background leakage and improved sensitivity. Furthermore, the FAC-HCR was used to test a non-nucleic acid target, apurinic/apyrimidinic endonuclease 1 (APE1), an important BER-involved endonuclease. The fluorescence analysis results confirmed that FAC-HCR can reach a detection limit of 0.1174 U/mL. By using the two HPs for FAC-HCR with polyetherimide-based nanoparticles, the activity of APE1 in living cells can be imaged. In summary, this study could provide a new idea to design an FA-based HCR and improve the performance of HCRs in live cell imaging.

Rapid and Multiplexed Nucleic Acid Detection using Programmable Aptamer-Based RNA Switches

Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. Here, we describe a class of aptamer-based RNA switches called aptaswitches that recognize specific target nucleic acid molecules and respond by initiating folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide a fast and intense fluorescent readout, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. We demonstrate that aptaswitches can be used to regulate folding of six different fluorescent aptamer/fluorogen pairs, providing a general means of controlling aptamer activity and an array of different reporter colors for multiplexing. By coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed one-pot reactions against RNA extracted from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that can be readily integrated into rapid diagnostic assays.

FRET probe for detecting two mutations in one EGFR mRNA

Technologies for visualizing and tracking RNA are essential in molecular biology, including in disease-related fields. In this study, we propose a novel probe set (DAt-probe and T-probe) that simultaneously detects two mutations in the same RNA using fluorescence resonance energy transfer (FRET). The DAt-probe carrying the fluorophore Atto488 and the quencher Dabcyl were used to detect a cancer mutation (exon19del), and the T-probe carrying the fluorophore Tamra was used to detect drug resistance mutations (T790M) in epidermal growth factor receptor (EGFR) mRNA. These probes were designed to induce FRET when both mutations were present in the mRNA. Gel electrophoresis confirmed that the two probes could efficiently bind to the mutant mRNA. We measured the FRET ratios using wild-type and double-mutant RNAs and found a significant difference between them. Even in living cells, the FRET probe could visualize mutant RNA. As a result, we conclude that this probe set provides a method for detecting two mutations in the single EGFR mRNA via FRET.

A light-up fluorescence platform based DNA: RNA hybrid G-quadruplet for detecting single nucleotide variant of ctDNA and miRNA-21

The nucleic acid assay is an area of great concern in the diagnosis and treatment of breast cancer. Here, we developed a DNA: RNA hybrid G-quadruplet (HQ) detection platform based on strand displacement amplification (SDA) and Baby Spinach RNA aptamer for single nucleotide variant (SNV) of circulating tumor DNA (ctDNA) and miRNA-21. This was the first in vitro construction of HQ for the biosensor. It found that HQ had much stronger ability to switch on fluorescence of DFHBI-1T than Baby Spinach RNA alone. Taking advantage of the platform and the FspI enzyme with high specificity, the biosensor achieved ultra-sensitive detection of SNV of the ctDNA (PIK3CA ^H1047R gene) and miRNA-21. The light-up biosensor had high anti-interference ability in complex actual samples. Hence, the label-free biosensor provided a sensitive and accurate method for early diagnosis of breast cancer. Moreover, it opened a new application model for RNA aptamers.

Monitoring Molecular Properties of a Fluorescence Light-Up Aptamer Using Fluorescence Cross-Correlation Spectroscopy

Fluorescence light-up aptamers (FLAPs) are tools for RNA imaging, wherein the RNA of interest is appended with a FLAP sequence that can bind to a corresponding small-molecule fluorogen and enhance its fluorescence. The fluorescence properties of FLAPs have mostly been analyzed in bulk and described as the average of a large number of RNA–fluorogen complexes. In this study, we evaluated the feasibility of fluorescence correlation spectroscopy (FCS)- and fluorescence cross-correlation spectroscopy (FCCS)-based quantifications of FLAPs in a solution using Broccoli, a common FLAP, and its corresponding fluorogen, DFHBI-1T. We investigated the folding efficiency, photostability, and photophysical properties of the Broccoli–DFHBI-1T complex using their FCS/FCCS characteristics. With FCS, we observed that the fluorescence was affected by the affinity between Broccoli and DFHBI-1T and the folding (maturation) state of Broccoli RNA. Moreover, the FCCS measurement of ATTO647N-labeled Broccoli and its complex with DFHBI-1T revealed the proportion of the mature Broccoli–DFHBI-1T complex. The current FCS/FCCS-based study of Broccoli–DFHBI-1T provides a model for analyzing FLAPs and their fluorogen pairs at the single-molecule level.

The dynamicity of light-up aptamers in one-pot in vitro diagnostic assays

Light-up aptamers are aptamers that ignite the fluorescence emission of certain dyes upon binding. Widely harnessed in in vivo imaging, the binding capacity of the light-up aptamers can also be deployed in in vitro diagnostic assays, engendering a mix-and-read format. Intrigued by this, I intend to provide an overview of the various formats of diagnostic assays developed using light-up aptamers from the direct modulation of the light-up aptamers, split aptamer-based configuration, strand displacement, in vitro transcription-based one-pot diagnostic assay, CRISPR-Cas system to the measurement of the ion reliance. The incorporation of the light-up aptamers into each configuration is expounded and further supported by describing the exemplary assays developed thus far. It is anticipated that the present study can be enlightening to any researchers who aspire to embark on the development of one-pot in vitro diagnostic assays based on light-up aptamers.

Split light up aptamers as a probing tool for nucleic acids

Aptamers that bind non-fluorescent dyes and increase their fluorescence can be converted to fluorescent sensors. Here, we discuss and provide guidance for the design of split (binary) light up aptameric sensors (SLAS) for nucleic acid analysis. SLAS consist of two RNA or DNA strands and a fluorogenic organic dye added as a buffer component. The two strands hybridize to the analyzed DNA or RNA sequence and form a dye-binding pocket, followed by dye binding, and increase in its fluorescence. SLAS can detect nucleic acids in a cost-efficient label-free format since it does not require conjugation of organic dyes with nucleic acids. SLAS design is preferable over monolith fluorescent sensors due to simpler assay optimization and improved selectivity. RNA-based SLAS can be expressed in cells and used for intracellular monitoring and imaging biological molecules.

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.

In Vivo Production of RNA Aptamers and Nanoparticles: Problems and Prospects

RNA aptamers are becoming increasingly attractive due to their superior properties. This review discusses the early stages of aptamer research, the main developments in this area, and the latest technologies being developed. The review also highlights the advantages of RNA aptamers in comparison to antibodies, considering the great potential of RNA aptamers and their applications in the near future. In addition, it is shown how RNA aptamers can form endless 3-D structures, giving rise to various structural and functional possibilities. Special attention is paid to the Mango, Spinach and Broccoli fluorescent RNA aptamers, and the advantages of split RNA aptamers are discussed. The review focuses on the importance of creating a platform for the synthesis of RNA nanoparticles in vivo and examines yeast, namely Saccharomyces cerevisiae, as a potential model organism for the production of RNA nanoparticles on a large scale.

Perspective on the Future Role of Aptamers in Analytical Chemistry

It has been almost 30 years since the invention of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology and the description of the first aptamers. In retrospect over the past 30 years, advances in aptamer development and application have demonstrated that aptamers are potentially useful reagents that can be employed in diverse areas within analytical chemistry, biotechnology, biomedicine, and molecular biology. While often touted as artificial antibodies with an ability to be selected for any target, aptamer development, unfortunately, lags behind development of analytical methodologies that employ aptamers, hindering deeper integration into the application of analytical tool development. This perspective covers recent advances in SELEX methodology for improving efficiency of the SELEX procedure and enhancing affinity and specificity of the selected aptamers, what we view as a critical barrier in the future role of aptamers in analytical chemistry. We discuss postselection modifications that can be used for enhancing performance of the selected aptamers in an analytical device by including understanding intermolecular interaction forces in the binding domain. While highlighting promising properties of aptamers that enable several analytical advances, we provide discussion on the challenges of penetration of aptamers in the analytical field.

A highly efficient Baby Spinach-based minimal modified sensor (BSMS) for nucleic acid analysis

Molecular recognition between nucleic acids has proven to be a powerful tool for designing hybridization probes for the detection of DNA and RNA sequences. Most detection probes rely on the conjugation of small molecule dyes to nucleic acids for fluorescence output, which is not cost-effective and also limits their applications in vivo, as they are not genetically encodable. More affordable sensors devoid of any chemical labeling are needed that show high fluorescence output and are genetically encodable. Here, we have designed a label-free Baby Spinach-based minimal modified sensor (BSMS) for the analysis of nucleic acids. The minimal modification in the sensor design reduces the complexity of the design, and provides additional stabilization after binding the target nucleic acids, leading to a high fluorescence output. BSMS is able to detect both DNA and RNA of potentially any lengths and is based on a Baby Spinach aptamer that binds and enhances the fluorescence of a small molecule dye. BSMS shows specificity towards its analyte in the presence of other sequences and selectively differentiates between closely related sequences. BSMS comprises genetically encodable unmodified RNA and has been shown to function at ambient temperature, and thus is anticipated to provide nucleic acid monitoring in vivo.