Molecular Beacon Research Articles

A DNA nanowire based-DNAzyme walker for amplified imaging of microRNA in tumor cells.

Sensitive imaging of microRNAs (miRNAs) in tumor cells holds great significance in the domains of pathology, drug development, and personalized diagnosis and treatment. DNA nanostructures possess excellent biostability and programmability and are suitable as carriers for intracellular imaging probes. With its highly controllable motion mechanism and remarkable target recognition specificity, the DNA walker is an ideal tool for living cell imaging. Here, we report a DNA nanowire based-DNAzyme Walker (D-Walker), which loads the DNAzyme based-molecular beacon (D-MB) onto DNA nanowires (NWs) functionalized with aptamers. The experimental results demonstrated that the intracellular target miRNA can specifically activate the pre-locked DNAzyme through a strand displacement reaction, thereby triggering the cleavage of its substrate molecular beacon (MB) and subsequent fluorescence emission. NWs decorated with aptamers can effectively prevent the degradation of the D-Walker by nuclease, and can enter target cells without any transfection reagents, which enhances the stability and reliability of cell imaging. Furthermore, the D-Walker exhibited a remarkable sensitivity with a limit of detection (LOD) of 61 pM and was capable of distinguishing miRNA-21 from other closely related family members. This study provides a novel strategy for intracellular miRNA imaging, offering a promising tool for cancer diagnosis and treatment.

Repair-driven DNA tetrahedral nanomachine combined with DNAzyme for 8-oxo guanine DNA glycosylase activity assay, drug screening and intracellular imaging.

8-oxo guanine DNA glycosylase (8-oxoG DNA glycosylase), a crucial DNA repair enzyme, is essential for maintaining genome integrity and preventing diseases caused by DNA oxidative damage. Imaging 8-oxoG DNA glycosylase in living cells requires a dependable technique. In this study, we designed a DNAzyme-modified DNA tetrahedral nanomachine (DTDN) powered by 8-oxoG restoration. Incorporating a molecular beacon probe (MB), the constructed platform was used for amplified in situ monitoring of 8-oxoG DNA glycosylase. Under normal conditions, duplexing with a complementary strand modified with two 8-oxoG sites inhibited the activity of DNAzyme. The restoration of DNAzyme activity by the repair of intracellular 8-oxoG DNA glycosylase on 8-oxoG bases can initiate a signal amplification reaction. This detection system can detect 8-oxoG DNA glycosylase activity linearly between 0 and 20 U mL-1, with a detection limit as low as 0.52 U mL-1. Using this method, we were able to screen 14 natural compounds and identify 6 of them as 8-oxoG DNA glycosylase inhibitors. In addition, a novel approach was utilized to assess the activity of 8-oxoG DNA glycosylase in living cells. In conclusion, this method provides a universal tool for monitoring the activity of 8-oxoG DNA glycosylase in vitro and in living cells, which holds great promise for elucidating the enzyme's functionality and facilitating drug screening endeavors.

AP endonuclease 1: Biological updates and advances in activity analysis.

Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1, APEX1, REF1, HAP1) is an abasic site-specific endonuclease holding critical roles in numerous biological functions including base excision repair, the DNA damage response, redox regulation of transcription factors, RNA processing, and gene regulation. Pathologically, APE1 expression and function is linked with numerous human diseases including cancer, highlighting the importance of sensitive and quantitative assays to measure APE1 activity. Here, we summarize biochemical and biological roles for APE1 and expand on the discovery of APE1 inhibitors. Finally, we highlight the development of assays to monitor APE1 activity, detailing a recently improved and stabilized DNA Repair Molecular Beacon assay to analyze APE1 activity. The assay is amenable to analysis of purified protein, to measure changes in APE1 activity in cell lysates, to monitor human patient samples for defects in APE1 function, or the cellular and biochemical response to APE1 inhibitors.

Template-controllable rolling circle amplification for dual protein sensitive analysis.

Conjoint analysis of multiple protein biomarkers can improve the accuracy of disease analysis. Rolling circle amplification (RCA) generates different products by designing circular templates, which can subsequently bind with specific probes to generate various fluorescence signals; thus, it has potential for application in the analysis of various protein biomarkers. Current RCA approaches to detect proteins commonly follow an indirect primer-controlled RCA mode. And the molecular beacon probe combines with RCA products through free collision to generate signals, resulting in lower reaction efficiency. Herein, we propose a direct template-controlled RCA mode using nanosheets as carriers and quenchers for fluorescent probes to simultaneously detect two protein biomarkers. A dual functional magnetic bead was first designed to recognize and capture two proteins while releasing two templates for subsequent RCA. RCA products compete with probes loaded on two-dimensional metal-organic framework nanosheets for hybridization, completing the transition from single-stranded to double-stranded DNA. Double-stranded DNA is far from the nanosheets, and the recovered fluorescence signal can be used to evaluate the concentration of target proteins. This method exhibits excellent analytical performance and can successfully achieve the analysis of Tau and AβO in Alzheimer's disease clinical cerebrospinal fluid samples.

Isolation and characterizations of multidrug-resistant human cancer cells by a biodegradable nano-sensor

Multidrug resistance (MDR) remains a significant challenge in cancer therapy, with inherent and acquired resistance distinct. While conventional drug selection processes enable the isolation of cancer cells with acquired multidrug resistance, identifying cancer cells with inherent drug resistance remains challenging. Herein, we proposed a molecular beacon (MB)-based strategy to identify and isolate the inherent MDR cancer cells. A lipid/PLGA core-shell nanoparticulate system (DNCP) was designed to deliver MB for intracellular MDR1 mRNA imaging. DNCP-MB – possess a surface potential of −8 mV and a size of 150 nm – demonstrated effective delivery of MB, remarkable selectivity towards the selected intracellular mRNA targets, and low cytotoxicity. Following DNCP transfection, fluorescence-activated cell sorting (FACS) was employed to differentiate MCF-7 cells into two distinct sub-populations: the Top 10 cells with a high level of MDR gene expression and the Bottom 10 cells with a low level of MDR gene expression, which represent inherent drug-resistant and non-drug-resistant cells, respectively. Intriguingly, we observed a positive correlation between elevated MDR1 mRNA expression and increased migration, enhanced proliferation rate, and tighter spheroid formation. Moreover, we conducted RNA sequencing analysis on the Top 10, Bottom 10, and MCF-7/ADR cells. The findings revealed a notable disparity in the gene ontology enrichment analysis of differentially expressed genes between the Top 10 and Bottom 10 cells when compared to the Bottom 10 and MCF-7/ADR cells. This novel approach provides a promising avenue for isolating inherent drug-resistant cells and holds significant potential in unraveling the mechanisms underlying inherent drug resistance.

Development of a stable and efficient fluorescence nanosensor for in situ detection of MicroRNA in plant

The detection of microRNA (miRNA), a gene-regulating factor, is crucial for predicting plant growth and development. In this study, we successfully developed a fluorescent nanosensor using nanomaterials and molecular beacons for in situ miRNA detection in plant cells. The molecular beacons were loaded onto 15 nm gold nanoparticles, effectively protecting them from DNase I degradation. The nanosensor exhibits remarkable specificity and detection capability with a detection limit of 1.0 nM, while maintaining stability in plant nutrient solutions. It is readily absorbed and transported by plant through both the symplasmic pathway and apoplastic pathway. Furthermore, it efficiently converts miRNA signals into fluorescent signals, providing valuable insights into the spatial and temporal distribution of miRNA in plants. Although to achieve more accurate detection, the detection limit of the designed nanosensor still needs to be further improved, but this technique offers a convenient and efficient approach, serving as a powerful tool for studying the mechanisms and regulation in plants.

Controlled Surface Functionalization Using Aryldiazonium Salts for the Development of Aptasensing Platforms

It is well known that both the aptamer surface density and surface chemistry can have a strong influence on the analytical performance of aptasensors based on target-induced conformational changes1. In this context, we report here an improved protocol for obtaining aptasensing platforms which allows fine-tuning the DNA aptamer surface coverage. First, glassy carbon substrates were functionalized with ethynylphenyl groups through the electrochemical reduction of silyl-protected ethynylphenyl diazonium tetrafluoroborates followed by deprotection with tetrabutylammonium fluoride2. The successful removal of the protecting groups (triisopropylsilyl-, triphenylsilyl- and tris(biphen-4-yl)silyl-) was confirmed by X-ray photoelectron spectroscopy and cyclic voltammetry in the presence of Fe(CN)6 3-/4- as soluble redox probe. Following “click” post-modification with suitable derivatization reagents, the surface coverage with ethynylphenyl groups was assessed using complementary techniques such as XPS, cyclic voltammetry and chronocoulometry. For example, the F/C surface ratio of substrates derivatized with 1-(2,2,2-trifluoroethoxy)-6-azidohexane provided an indication of the functionalization degree, and the integration of Fc/Fc+ voltammetric peaks for substrates modified with N-(6-azidohexyl)ferrocenecarboxamide allowed a quantitative determination of the surface coverage. Both techniques showed a good correlation between the protective group size and the surface coverage with alkyne groups. Likewise, we observed a similar trend for substrates derivatized with azide-modified oligonucleotides, where the surface packing density was determined based on the chronocoulometric response of Ru(NH3)6 3+, a cationic redox probe which binds with the negatively charged phosphate groups from the oligonucleotide backbone. As proof of concept, we further developed an electrochemical molecular beacon aptasensor employing a ferrocene-labeled quinine aptamer. We demonstrate that the aptamer surface density, and ultimately the analytical performance of molecular beacon aptasensors, can be effectively fine-tuned by employing silyl protecting groups of different sizes.Acknowledgements This work was supported by a grant from the Romanian Ministry of Education and Research, CNCS-UEFISCDI, project number PN-III-P4-ID-PCE-2020-2474, within PNCDI III. References Onaş, A. M., Dascălu, C., Raicopol, M. D. & Pilan, L. Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets. Biosensors 12, (2022).Leroux, Y. R., Fei, H., Noël, J.-M. M., Roux, C. & Hapiot, P. Efficient covalent modification of a carbon surface: Use of a silyl protecting group to form an active monolayer. J. Am. Chem. Soc. 132, 14039–14041 (2010).

An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern

The continued emergence of vaccine-resistant SARS-CoV-2 variants of concern (VOC) requires specific identification of each VOC as it arises. Here, we report an expanded version of our previously described sloppy molecular beacon (SMB) melting temperature (Tm) signature-based assay for VOCs, now modified to include detection of Delta (B.1.617.2) and Omicron (B.1.1.529) sub-variants. The SMB-VOC assay targets the signature codons 501, 484 and 452 in the SARS-CoV-2 spike protein which we show can specifically detect and differentiate all known VOCs including the Omicron subvariants (BA.1, BA.2, BA.2.12.1, BA.4/BA.5). The limit of detection (LOD) of the assay was 20, 22 and 36 genomic equivalents (GE) per reaction with the Delta, Omicron BA.1 and BA.2 respectively. Clinical validation of the 3-codon assay in the LC480 instrument showed the assay detected 94% (81/86) of the specimens as WT or VOCs and 6% (5/86) of the tests producing indeterminate results compared to sequencing. Sanger sequencing also failed for four samples. None of the specimens were incorrectly identified as WT or as a different VOC by our assay. Thus, excluding specimens with indeterminant results, the assay was 100% sensitive and 100% specific compared to Sanger sequencing for variant identification. This new assay concept can be easily expanded to add newer variants and can serve as a robust diagnostic tool for selecting appropriate monoclonal antibody therapy and rapid VOC surveillance.

SPP1 mRNA determination based on molecular beacon for the recurrence prognosis of bladder cancer.

Bladder cancer (BC) has attracted significant attention on account of its recurrence as well as mortality. Tumor recurrence plays a significant role in cancer patients' individual treatment. Secreted phosphoprotein 1 (SPP1) has been recognized as a potential target for treating BC and served as a useful biomarker for prognosis; it is commonly tested by immunohistochemistry (IHC). However, this conventional method has the disadvantage of being time-consuming and costly. This study aimed to develop a molecular beacon (MB) for the detection of SPP1 messenger RNA (mRNA) for the recurrence prognosis of BC. An MB was constructed and applied to image SPP1 mRNA level at both molecular and cellular level. The fluorescence spectra were recorded with a fluorescence spectrophotometer. The effect of SPP1 MB toward the cell viability was performed by Cell Counting Kit-8 (CCK-8) assays. The SPP1 mRNA expression level was measured by quantitative real-time polymerase chain reaction (qRT-PCR). Cancer cells and tissues were analyzed with confocal fluorescence imaging. Correlation, sensitivity, and specificity parameters were calculated. It was demonstrated that both cancer cells and BC tissues expressed high signal which reflected the expression of SPP1. In addition, 42 cases were detected by MB and divided into two groups according to the fluorescence intensity. The results further suggested that highly expressed SPP1 could predict early tumor recurrence in BC. The SPP1 MB could be applied as an appropriate approach to predict BC recurrence and patients' prognosis.

Ionic liquid-caged nucleic acids enable active folding-based molecular recognition with hydrolysis resistance.

Beyond storage and transmission of genetic information in cellular life, nucleic acids can perform diverse interesting functions, including specific target recognition and biochemical reaction acceleration; the versatile biopolymers, however, are acutely vulnerable to hydrolysis-driven degradation. Here, we demonstrate that the cage effect of choline dihydrogen phosphate permits active folding of nucleic acids like water, but prevents their phosphodiester hydrolysis unlike water. The choline-based ionic liquid not only serves as a universal inhibitor of nucleases, exceptionally extending half-lives of nucleic acids up to 6500000 times, but highly useful tasks of nucleic acids (e.g. mRNA detection of molecular beacons, ligand recognition of aptamers, and transesterification reaction of ribozymes) can be also conducted with well-conserved affinities and specificities. As liberated from the function loss and degradation risk, the presence of undesired and unknown nucleases does not undermine desired molecular functions of nucleic acids without hydrolysis artifacts even in nuclease cocktails and human saliva.

DNA four-way junction-driven dual-rolling circle amplification sandwich-type aptasensor for ultra-sensitive and specific detection of tumor-derived exosomes

There is an urgent need to accurately quantify tumor-derived exosomes, which have emerged as promising non-invasive tumor diagnostic biomarkers. Herein, a bispecific-aptamer sandwich-type gold nanoparticle-modified electrochemical aptasensor was developed based on a four-way junction (4-WJ)-triggered dual rolling circle amplification (RCA)-assisted methylene blue (MB)/G-quadruplex strategy for extremely specific and sensitive exosome detection. This aptamer/exosome/aptamer sandwich-type design contained a CD63-specific aptamer and a cancerous mucin-1 (MUC1) protein-specific aptamer. The CD63 aptamer modified on a gold electrode captured exosomes, and then the sandwich-type aptasensor was formed with the addition of the MUC1 aptamer. The MUC1 aptamer's 3′-end sequence facilitated the formation of 4-WJ, assisted by a molecular beacon probe and a binary DNA probe. Subsequently, a dual-RCA reaction was triggered by binding to two cytosine-rich circle DNA templates at both ends of 4-WJ. Ultimately, dual-RCA products containing multiple G-quadruplex conformations were generated with the assistance of K+ to trap abundant MB indicators and amplify electrochemical signals. The aptasensor exhibited high specificity, sensitivity, repeatability, and stability toward MCF-7-derived exosomes, with a detection limit of 20 particles/mL and a linear range of 1 × 102 to 1 × 107 particles/mL. Moreover, it showed excellent applicability in clinical settings to recover exosomes in normal human serum. Our aptasensor is anticipated to serve as a versatile platform for detecting various specific aptamer-based targets in biomedical and bioanalytical applications.

Front Cover: Lanthanide‐FRET Molecular Beacons for microRNA Biosensing, Logic Operations, and Physical Unclonable Functions (Eur. J. Inorg. Chem. 36/2023)

Front Cover: Lanthanide‐FRET Molecular Beacons for microRNA Biosensing, Logic Operations, and Physical Unclonable Functions (Eur. J. Inorg. Chem. 36/2023)

Proximity hybridization induced bipedal DNA walker and rolling circle amplification for label-free electrochemical detection of apolipoprotein A4

Apolipoprotein A4 (Apo-A4) is considered as a prospective molecular biomarker for diagnosis of depression due to its neurosynaptic toxicity. We develop a proximity hybridization-induced DNAzyme-driven bipedal DNA walker strategy for Apo-A4 quantification based on rolling circle amplification (RCA) triggered by poly adenine binding to Ag nanoparticles (AgNPs). With the help of DNAzyme, the free-running bipedal DNA walker can quickly and sequentially shear a molecular beacon that acts as a primer to initiate the RCA process, producing a large number of long DNA strands containing numerous adenines. The long repetitive adenine strands then absorb large amounts of AgNPs on the electrode interface, which is then electrochemically stripped of the AgNPs. The method has a linear detection range of 0.001 ∼ 100 ng mL−1 and a detection limit of 0.46 pg mL−1. The presented detection strategy is label-free, which allows high sensitivity and selectivity for detection of a wide range of protein targets by corresponding DNA-based affinity probes, which have potential applications in bioanalysis.

Paper-Supported Photoelectrochemical Biosensor for Dual-Mode miRNA-106a Assay: Integration of Luminescence-Confined Upconversion-Actuated Fluorescent Resonance Energy Transfer and CRISPR/Cas13a-Powered Cascade DNA Circuits.

Near-infrared (NIR)-responsive bioassays based on upconversion nanoparticle (UCNP) incorporating high-performance semiconductors have been developed by researchers, but most lack satisfactory ultrasensitivity for exceedingly trace amounts of target. Herein, for the first time, the CRISPR/Cas13a system is combined with cascade DNA circuits, fluorescent resonance energy transfer (FRET) effect, and luminescence-confined UCNPs-bonded CuInS2/ZnO p-n heterostructures-functionalized paper-working electrode to construct dual-signal-on paper-supported NIR-irradiated photoelectrochemical (PEC) (NIR-PEC) and upconversion luminescence (UCL) bioassay for high-sensitive quantification of miRNA-106a (miR-106a). By constructing an ideal FAM-labeled aminating molecular beacon (FAM-H2) model, a relatively good FRET ratio between the UCNP and FAM (≈85.3%) can be achieved. In the existence of miR-106a, the hairpin-structure FAM-H2 was unwound, bringing about the distance increase of UCNP and FAM and the restraint of FRET. Accordingly, both the NIR-PEC signal and the UCL intensity gradually recovered distinctly. Unlike conventional single-mode PEC sensors, with NIR excitation, the designed dual-mode sensing system could implement minimized misdiagnose assay and quantitative miR-106a determination with low detection limits, that is, 76.54 and 51.36 aM for NIR-PEC and UCL detection, respectively. This work not only broadens the horizon of application of the CRISPR/Cas13a strategy toward biosensing but also constructs a new structure of the UCNP-semiconductor in the exploration of efficient NIR-responsive tools and inspires the construction of a no-misdiagnosed and novel biosensor for dual-mode liquid biopsy.

Construction of a Programmable Feedback Network with Continuously Activatable Molecular Beacon Fluorescence for One-Step Quantification of Long Noncoding RNAs in Clinical Breast Tissues.

Long noncoding RNAs (lncRNAs) are key regulators in numerous pathological and physiological processes, and their aberrant expression is implicated in many diseases. Herein, we develop a programmable feedback network with continuously activatable molecular beacon (MB) fluorescence for one-step quantification of mammalian-metastasis-associated lung adenocarcinoma transcript 1 (lncRNA MALAT1) in clinical breast tissues. We introduce a functional MB with three domains, including a substrate for lncRNA MALAT1 recognition, a template for strand displacement amplification (SDA), and a reporter for signal output with FAM fluorescence being quenched by BHQ1. When MALAT1 is present, it recognizes and unfolds the MB, leading to the recovery of FAM fluorescence. Once the MB is opened, multiple rounds of SDA reaction are automatically initiated by recruiting primer, KF DNA polymerase, and Nt.BbvCI nicking enzyme, inducing the opening of more MBs and the dissociation of more FAM/BHQ1 pairs. Consequently, a feedback network is constructed through multicycle cascade SDA, achieving the exponential accumulation of fluorescence signals for accurate quantification of MALAT1. In this assay, only two oligonucleotides (i.e., MB and primer) are involved for the establishment of a feedback amplification network, greatly simplifying the design of the reaction system. Moreover, this assay requires only one step to realize the isothermal exponential amplification for real-time monitoring of MALAT1 with attomolar sensitivity. This assay displays single-base mismatch selectivity with high anti-interference capability, and it can further quantify endogenous MALAT1 at the single-cell level and differentiate MALAT1 expression between breast cancer patient tissues and healthy person tissues.

Highly specific detection of Neisseria gonorrhoeae based on recombinase polymerase amplification-initiated strand displacement amplification

Neisseria gonorrhoeae is the only pathogen that causes gonorrhea, and can have serious consequences if left untreated. A simple and accurate detection method for N. gonorrhoeae is essential for the diagnosis of gonorrhea and the appropriate prescription of antibiotics. The application of isothermal recombinase polymerase amplification (RPA) to detect this pathogen is advantageous because of its rapid performance, high sensitivity, and minimal dependency on equipment. However, this simplicity is offset by the risk of false-positive signals from primer-dimers and primer-probe dimers. In this study, RPA-initiated strand displacement amplification (SDA) was established for the detection of N. gonorrhoeae, and eliminated false-positive signals from primer–dimers and primer-probe dimers. The developed biosensor allows for the reduced generation of nonspecific RPA amplification through the design of enzyme cleavage sites on primers, introduction of SDA, and detection of the final product using a molecular beacon (MB). Using this system, the DNA double strand is transformed into single-stranded DNA following SDA, thereby providing a more suitable binding substrate and improving the efficiency of MB detection. Amplification can be conducted below 37 °C, and the process can be completed within 90 min. The limit of detection was determined to be 0.81 copies/μL. This system is highly specific for N. gonorrhoeae and exhibits no cross-reactivity with other common urogenital pathogens. The results of this study are consistent with those of real-time PCR performed on clinical specimens of urogenital secretions. In summary, the biosensor is a simple and specific detection method for N. gonorrhoeae.

Cardiomyocyte precursors generated by direct reprogramming and molecular beacon selection attenuate ventricular remodeling after experimental myocardial infarction

BackgroundDirect cardiac reprogramming is currently being investigated for the generation of cells with a true cardiomyocyte (CM) phenotype. Based on the original approach of cardiac transcription factor-induced reprogramming of fibroblasts into CM-like cells, various modifications of that strategy have been developed. However, they uniformly suffer from poor reprogramming efficacy and a lack of translational tools for target cell expansion and purification. Therefore, our group has developed a unique approach to generate proliferative cells with a pre-CM phenotype that can be expanded in vitro to yield substantial cell doses.MethodsCardiac fibroblasts were reprogrammed toward CM fate using lentiviral transduction of cardiac transcriptions factors (GATA4, MEF2C, TBX5, and MYOCD). The resulting cellular phenotype was analyzed by RNA sequencing and immunocytology. Live target cells were purified based on intracellular CM marker expression using molecular beacon technology and fluorescence-activated cell sorting. CM commitment was assessed using 5-azacytidine-based differentiation assays and the therapeutic effect was evaluated in a mouse model of acute myocardial infarction using echocardiography and histology. The cellular secretome was analyzed using mass spectrometry.ResultsWe found that proliferative CM precursor-like cells were part of the phenotype spectrum arising during direct reprogramming of fibroblasts toward CMs. These induced CM precursors (iCMPs) expressed CPC- and CM-specific proteins and were selectable via hairpin-shaped oligonucleotide hybridization probes targeting Myh6/7-mRNA–expressing cells. After purification, iCMPs were capable of extensive expansion, with preserved phenotype when under ascorbic acid supplementation, and gave rise to CM-like cells with organized sarcomeres in differentiation assays. When transplanted into infarcted mouse hearts, iCMPs prevented CM loss, attenuated fibrotic scarring, and preserved ventricular function, which can in part be attributed to their substantial secretion of factors with documented beneficial effect on cardiac repair.ConclusionsFibroblast reprogramming combined with molecular beacon-based cell selection yields an iCMP-like cell population with cardioprotective potential. Further studies are needed to elucidate mechanism-of-action and translational potential.Graphical

DNA integrity under alkaline conditions: An investigation of factors affecting the comet assay.

The effect of pH on DNA integrity was assessed using a three-step approach. The comet assay was used on a whole genome level, with three different protocols: neutral (no alkaline unwinding), flash (pH 12.5 with 2.5min unwinding), and the conventional alkaline protocol (pH>13 with 40min unwinding). Real-time quantitative PCR (RT-qPCR) was then used to study the isolated DNA, revealing that gene amplification decreased with increasing pH, indicating DNA degradation. Specially designed molecular beacons were used to examine DNA at the molecular level, with or without alkali-labile site (ALS) insertions. At pH 12.5, fluorescence in the hairpins with ALS started to increase after 30min, while at pH>13, this increase was already observed after 5min, indicating a significant increase in DNA strand breaks. Liquid chromatography analysis was also used, demonstrating that the hairpins remained intact up to pH 10, even after 1h exposure, whereas, at pH 12.5, partial conversion into strand breaks occurred after 30min. At pH>13, the hairpins were almost completely degraded after 30min. The flash protocol effectively detects DNA single- and double-strand breaks and identified these damages after 2.5min of alkaline treatment at pH 12.5. When the hairpins were exposed to pH 12.5 for 60min, ALS were converted to strand breaks, demonstrating the sensitivity of this approach to detect changes in DNA structure. These findings indicate that pH poses a substantial risk to DNA integrity, leading to significantly higher background levels of DNA damage compared to conditions closer to neutrality. Our study demonstrates the importance of understanding the influence of pH on DNA stability and provides insights into risks associated with alkaline environments, especially at pH>13.

Lanthanide‐FRET Molecular Beacons for microRNA Biosensing, Logic Operations, and Physical Unclonable Functions

AbstractTime‐resolved or time‐gated (TG) biosensing and bioimaging with luminescent lanthanide probes and Förster resonance energy transfer (FRET) have significantly advanced bioanalytical chemistry. However, the development of lanthanide‐based molecular beacons (MBs) has been rather limited. Here, we designed DNA stem‐loop MB probes against two different microRNAs (miR‐21 and miR‐27b) using Tb and Eu FRET donors and quenching (BHQ2) and fluorescent (Cy3) FRET acceptors. Limits of detection down to 190 pM and duplexed miR‐21/miR‐27b quantification at low nanomolar concentrations with Tb‐BHQ2 and Eu‐BHQ2 TG‐FRET MBs demonstrated the versatility and high analytical performance of lanthanide‐based MBs. The particular donor‐acceptor distances in the Tb‐Cy3 MB resulted in inverted nucleic acid target concentration‐dependent TG PL intensities in short (e. g., 0 to 40 μs) and long (e. g., 0.1 to 2.1 ms) TG detection windows after pulsed excitation. We showed that this specific feature of our TG‐FRET MBs can be adapted to the design of molecular logic devices (NOR, OR, NAND, AND, XNOR, XOR, IMPLEMENT, and INHIBIT). Moreover, the almost unlimited choice of TG detection windows and the distinct spectral features of Tb and Cy3 over a broad visible spectral range could be exploited to devise biophotonic physical unclonable functions for highly secure authentication and identification. Our study manifests the versatility of lanthanides for advanced biophotonic applications.

Interaction of a Dimeric Single-Stranded DNA-Binding Protein (G5P) with DNA Hairpins. A Molecular Beacon Study.

Gene-V protein (G5P/GVP) is a single-stranded (ss)DNA-binding protein (SBP) of bacteriophage f1 that is required for DNA synthesis and repair. In solution, it exists as a dimer that binds two antiparallel ssDNA strands with high affinity in a cooperative manner, forming a left-handed helical protein-DNA filament. Here, we report on fluorescence studies of the interaction of G5P with different DNA oligonucleotides having a hairpin structure (molecular beacon, MB) with a seven base-pair stem (dT24-stem7, dT18-stem7), as well as with DNA oligonucleotides (dT38, dT24) without a defined secondary structure. All oligonucleotides were end-labeled with a Cy3-fluorophore and a BHQ2-quencher. In the case of DNA oligonucleotides without a secondary structure, an almost complete quenching of their strong fluorescence (with about 5% residual intensity) was observed upon the binding of G5P. This implies an exact alignment of the ends of the DNA strand(s) in the saturated complex. The interaction of the DNA hairpins with G5P led to the unzipping of the base-paired stem, as revealed by fluorescence measurements, fluorescence microfluidic mixing experiments, and electrophoretic mobility shift assay data. Importantly, the disruption of ssDNA's secondary structure agrees with the behavior of other single-stranded DNA-binding proteins (SBPs). In addition, substantial protein-induced fluorescence enhancement (PIFE) of the Cy3-fluorescence was observed.