Engineering molecular beacons for intracellular imaging

Molecular Beacon Probe (MBP)-Based Real-Time PCR

In the advancement of molecular biology techniques, several probe-based techniques, like molecular beacon probe (MBP) assay, TaqMan probe, and minor groove binder (MGB) probe assay, have been reported to identify specific sequences through real-time polymerase chain reaction (PCR). All probe-based methods are more sensitive than the conventional PCR for the detection and quantification of target genes. MBP is a hydrolysis probe that emits fluorescence when getting the specific sequences on the gene. Here, we describe the application of MBP for the identification of the motif sequences present in the promoters of differentially expressed genes.

Quantum Dot-Based Molecular Beacons for Quantitative Detection of Nucleic Acids with CRISPR/Cas(N) Nucleases

Strategies utilizing the CRISPR/Cas nucleases Cas13 and Cas12 have shown great promise in the development of highly sensitive and rapid diagnostic assays for the detection of pathogenic nucleic acids. The most common approaches utilizing fluorophore-quencher molecular beacons require strand amplification strategies or highly sensitive optical setups to overcome the limitations of the readout. Here, we demonstrate a flexible strategy for assembling highly luminescent and colorimetric quantum dot-nucleic acid hairpin (QD-HP) molecular beacons for use in CRISPR/Cas diagnostics. This strategy utilizes a chimeric peptide-peptide nucleic acid (peptide-PNA) to conjugate fluorescently labeled DNA or RNA hairpins to ZnS-coated QDs. QDs are particularly promising alternatives for molecular beacons due to their greater brightness, strong UV absorbance with large emission offset, exceptional photostability, and potential for multiplexing due to their sharp emission peaks. Using Förster resonance energy transfer (FRET), we have developed ratiometric reporters capable of pM target detection (without nucleotide amplification) for both target DNA and RNA, and we further demonstrated their capabilities for multiplexing and camera-phone detection. The flexibility of this system is imparted by the dual functionality of the QD as both a FRET donor and a central nanoscaffold for arranging nucleic acids and fluorescent acceptors on its surface. This method also provides a generalized approach that could be applied for use in other CRISPR/Cas nuclease systems.

Polariton-assisted manipulation of energy relaxation pathways: donor-acceptor role reversal in a tuneable microcavity

Resonant interaction between excitonic transitions of molecules and localized electromagnetic field allows the formation of hybrid light-matter polaritonic states. This hybridization of the light and the matter states has been shown to significantly alter the intrinsic properties of molecular ensembles placed inside the optical cavity. Here, we have observed strong coupling of excitonic transition in a pair of closely located organic dye molecules demonstrating an efficient donor-to-acceptor resonance energy transfer with the mode of a tuneable open-access cavity. Analysing the dependence of the relaxation pathways between energy states in this system on the cavity detuning, we have demonstrated that predominant strong coupling of the cavity photon to the exciton transition in the donor dye molecule can lead not only to an increase in the donor-acceptor energy transfer, but also to an energy shift large enough to cause inversion between the energy states of the acceptor and the mainly donor lower polariton energy state. Furthermore, we have shown that the polariton-assisted donor-acceptor chromophores' role reversal or "carnival effect" not only changes the relative energy levels of the donor-acceptor pair, but also makes it possible to manipulate the energy flow in the systems with resonant dipole-dipole interaction and direct energy transfer from the acceptor to the mainly donor lower polariton state. Our experimental data are the first confirmation of the theoretically predicted possibility of polariton-assisted energy transfer reversal in FRET systems, thus paving the way to new avenues in FRET-imaging, remote-controlled chemistry, and all-optical switching.

Well-Defined DNA-Polymer Miktoarm Stars for Enzyme-Resistant Nanoflares and Carrier-Free Gene Regulation

Herein, we report a star-architectured poly(ethylene glycol) (PEG)-oligonucleotide nanoconjugate of a well-defined molecular structure. Based upon fullerene C₆₀ cores, each star bears precisely 1 DNA strand and 11 polymer chains. The elevated PEG density provides the DNA with steric selectivity: the DNA is significantly more resistant to nuclease digestion while remaining able to hybridize with a complementary sequence. The degree of resistance increases as the centers of mass for the DNA and fullerene are closer together. Such steric selectivity reduces protein-related background signals of the nanoflares synthesized from these miktoarm star polymers. Importantly, the stars improve cellular uptake and regulate gene expression as a non-cytotoxic, single-entity antisense agent without the need for a transfection carrier.

Nanoamplicon Comparator for Live-Cell MicroRNA Imaging

As an investigative tool, live-cell imaging requires superior probe design to guarantee imaging quality and data validity. The ability to simultaneously address the robustness, sensitivity, and consistency issues in a single-assay system is highly desired, but it remains a largely unsolved challenge. We describe herein a probe-design strategy called a nanoamplicon comparator (NAC) and demonstrate its proof-of-concept utility in intracellular microRNA (miRNA) imaging. This novel designer architecture builds upon spherical nucleic acids (SNAs) for robustness, catalytic hairpin assembly (CHA) for sensitivity, and upconversion nanoparticles (UNPs) for consistency. A catalytic circuit comprising a UNP-hairpin-DNA (UNP-HDNA) conjugate and a hairpin-DNA-organic-fluorophore (HDNA-F) conjugate as probe responds to target miRNA and generates the UNP-HDNA-HDNA-F complex as an NAC for quantitative UNP-to-organic-fluorophore-luminescence-resonance-energy-transfer (LRET) imaging against a native UNP-emission reference channel. An imaging application with miR21 shows the ability to monitor miRNA-expression levels across different cell lines and under an external stimulus.

Detection of miRNA cancer biomarkers using light activated Molecular Beacons

Early detection of cancer biomarkers can reduce cancer mortality rate. miRNAs are small non-coding RNAs whose expression changes upon the onset of various types of cancer. Biosensors that specifically detect such biomarkers can be engineered and integrated into point-of-care devices (POC) using label-free detection, high sensibility and compactness. In this paper, a new engineered Molecular Beacon (MB) construct used to detect miRNAs is presented. Such a construct is immobilized onto biosensor surfaces in a covalent and spatially oriented way using the photonic technology Light Assisted Molecular Immobilization (LAMI). The construct consists of a Cy3 labelled MB covalently attached to a light-switchable peptide. One MB construct contains a poly-A sequence in its loop region while the other contains a sequence complementary to the cancer biomarker miRNA-21. The constructs have been characterized by UV-Vis spectroscopy, mass spectrometry and HPLC. LAMI led to the successful immobilization of the engineered constructs onto thiol functionalized optically flat quartz slides and Silicon on Insulator (SOI) sensor surfaces. The immobilized Cy3 labelled MB construct has been imaged using confocal fluorescence microscopy (CFM). The bioavailability of the immobilized engineered MB biosensors was confirmed through specific hybridization with the Cy5 labelled complementary sequence and imaged by CFM and FRET. Hybridization kinetics have been monitored using steady state fluorescence spectroscopy. The label-free detection of miRNA-21 was also achieved by using integrated photonic sensing structures. The engineered light sensitive constructs can be immobilized onto thiol reactive surfaces and are currently being integrated in a POC device for the detection of cancer biomarkers.

Photonic based detection strategies of cancer miRNA biomarkers after Light Assisted Molecular Immobilization (LAMI) of peptide-MB biosensor constructs.

Fluorinated molecular beacons as functional DNA nanomolecules for cellular imaging

Molecular beacons (MBs) are simple, but practical, fluorescent nanoprobes widely used to detect small molecules, nucleic acids and proteins. However, some challenges still remain when MBs are employed in complex biological environments, such as instability and non-target interference. To meet such challenges, we have designed and synthesized fluorinated molecular beacons (FMBs) as functional DNA nanomolecules for cellular imaging, in which the stem sequence is simply composed of artificial nucleotides with 3,5-bis(trifluoromethyl)benzene (F) as the surrogate base of natural A, T, C and G bases. The introduction of F base into MBs significantly increases their hydrophobicity, and the stem is formed by the assembly of self-complementary base F nucleotides through hydrophobic interactions. Fluorescence studies revealed that FMBs confer improved stability over conventional MBs. To demonstrate the application of FMBs for cellular imaging, we constructed an FMB to detect mRNA in MCF-7 cells, and the FMB was proven to be a practical nanoprobe for cellular imaging of mRNA.

Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes

RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.

Detection and Live-Cell Imaging of a Micro-RNA Associated with the Cancer Neuroblastoma

The ability of a molecular beacon to detect miR-132, a microRNA associated with the childhood cancer neuroblastoma, is reported in solution and within live cells. The stem-loop structure comprises a sequence complementary to miR-132, modified with a 6-FAM dye and dabcyl quencher on either end. In the absence of the target, self-binding occurs bringing the luminophore and quencher into close proximity, significantly decreasing the emission intensity. In the presence of miR-132, the signal is greatly enhanced, with a linear increase in intensity for mole ratios of beacon-to-target between 0.25 and 2.00. The structure differentiates between target and mismatched nucleic acid sequences, e.g., in the presence of a single-base mismatch, no increase in emission intensity beyond the background is observed. The stem-loop can be introduced into neuroblastoma cancer cells by electroporation, allowing miR-132 to be imaged within live cells. miR-132 appears to be localized within the nucleus of the cells, where its concentration is of the order of 1 μM. Significantly, transfection of the cells with a miR-132 mimic causes the emission intensity to more than double, demonstrating the sensitivity of the approach to changes in miR-132 concentration in live cells. This behavior opens up significant theranostic applications, such as the possibility of rapidly identifying retinoic acid resistant patients as well as providing a means to monitor therapeutic efficacy.

Direct detection of circulating free DNA extracted from serum samples of breast cancer using locked nucleic acid molecular beacon

As an emerging noninvasive blood biomarker, circulating free DNA (cfDNA) can be utilized to assess diagnosis, progression and evaluate prognosis of cancer. However, cfDNAs are not "naked", they can be part of complexes, or are bound to the surface of the cells via proteins, which make the detection more challenging. Here, a simple method for the detection of Ubiquitin-like with PHD and ring finger domains 1 (UHRF1) DNA exacted from serum of breast cancer (BC) has been developed using a novel locked nucleic acid molecular beacon (LNA-MB). In order to enhance the stability and detection efficiency of the probe in biofluids, we design a shared-stem molecular beacon containing a 27-mer loop and a 4-mer stem with DNA/LNA alternating bases. The fluorescence is released in the presence of target. The detection procedure is simple and can be completed within 1h. This method shows a sensitive response to UHRF1 DNA with a dynamic range of 3 orders of magnitude. The limit of detection is 11nM (S/N=3) with excellent selectivity. It can discriminate UHRF1 DNA from three-base mismatched DNA with a high specificity. More importantly, this method can distinguish the expression of serum UHRF1 DNA among 5 breast cancer patients and 5 healthy controls. The mentioned superiority may suggest that this assay can be served as a promising noninvasive detection tool for early BC diagnosis and monitoring.

Intracellular FRET-based probes: a review

Probes that exploit Förster resonance energy transfer (FRET) in their feedback mechanism are touted for their sensitivity, robustness, and low background, and thanks to the exceptional distance dependence of the energy transfer process, they provide a means of probing lengthscales well below the resolution of light. These attributes make FRET-based probes superbly suited to an intracellular environment, and recent developments in biofunctionalization and expansion of imaging capabilities have put them at the forefront of intracellular studies. Here, we present an overview of the engineering and execution of a variety of recent intracellular FRET probes, highlighting the diversity of this class of materials and the breadth of application they have found in the intracellular environment.

Strength in numbers: quantitative single-molecule RNA detection assays

Gene expression is a fundamental process that underlies development, homeostasis, and behavior of organisms. The fact that it relies on nucleic acid intermediates, which can specifically interact with complementary probes, provides an excellent opportunity for studying the multiple steps—transcription, RNA processing, transport, translation, degradation, and so forth—through which gene function manifests. Over the past three decades, the toolbox of nucleic acid science has expanded tremendously, making high‐precision in situ detection of DNA and RNA possible. This has revealed that many—probably the vast majority of—transcripts are distributed within the cytoplasm or the nucleus in a nonrandom fashion. With the development of microscopy techniques we have learned not only about the qualitative localization of these molecules but also about their absolute numbers with great precision. Single‐molecule techniques for nucleic acid detection have been transforming our views of biology with elementary power: cells are not average members of their population but are highly distinct individuals with greatly and suddenly changing gene expression, and this behavior of theirs can be measured, modeled, and thus predicted and, finally, comprehended. WIREs Dev Biol 2015, 4:135–150. doi: 10.1002/wdev.170

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Conflict of interest: The authors have declared no conflicts of interest for this article.

Fluorescent silver nanocluster DNA probes for multiplexed detection using microfluidic capillary electrophoresis

We tune the electrophoretic mobilities of silver nanocluster DNA probes for Hepatitis A, B and C targets for single-color multiplexing by microfluidic capillary electrophoresis.