Biodegradable MnO2 Nanosheet-Mediated Signal Amplification in Living Cells Enables Sensitive Detection of Down-Regulated Intracellular MicroRNA

The monitoring of intracellular microRNAs plays important roles in elucidating the biological function and biogenesis of miRNAs in living cells. However, because of their sequence similarity, low abundance, and small size, it is a great challenge to detect intracellular miRNAs, especially for those with much lower expression levels. To address this issue, we have developed an in cell signal amplification approach for monitoring down-regulated miRNAs in living cells based on biodegradable MnO₂ nanosheet-mediated and target-triggered assembly of hairpins. The MnO₂ nanosheets can adsorb and exhibit an excellent quenching effect to the dye labeled hairpin probes. Besides, due to their biodegradability, the MnO₂ nanosheets feature highly reduced cytotoxicity to the target cells. Upon entering cells, the surface-adsorbed FAM- and Tamra (TMR)-conjugated hairpins can be released due to the displacement reactions by other proteins or nucleic acids and the degradation of the MnO₂ nanosheets by cellular GSH. Subsequently, the down-regulated target miRNA-21 triggers cascaded assembly of the two hairpins into long dsDNA polymers, which brings the fluorescence resonance energy transfer (FRET) pair, FAM (donor), and TMR (acceptor) into close proximity to generate significantly enhanced FRET signals for detecting trace miRNA-21 in living cells. By carefully tailoring the sequences of the hairpins, the developed method can offer new opportunities for monitoring various trace intracellular miRNA targets with low expression levels in living cells.

A versatile size-coded flow cytometric bead assay for simultaneous detection of multiple microRNAs coupled with a two-step cascading signal amplification

A versatile bead size-encoded flow cytometric bead assay (FCBA) is developed for the sensitive and simultaneous detection of multiple microRNAs.

A three-way junction structure-based isothermal exponential amplification strategy for sensitive detection of 3′-terminal 2′-O-methylated plant microRNA

A versatile and general 3WJ-EXPAR strategy is developed for the sensitive detection of 3′-terminal 2′-O-methylated plant microRNAs.

Long-stem shaped multifunctional molecular beacon for highly sensitive nucleic acids determination via intramolecular and intermolecular interactions based strand displacement amplification

LS-MMB based intra-SDA and inter-SDA for amplified gene signaling.

Systematic comparison between toehold exchange and toehold displacement: exploration for highly specific and sensitive DNA detection

The detection of nucleic acid variations with high specificity and sensitivity is essential for the good practice of precision medicine.

A nucleic acid logic gate system that distinguishes different sets of inputs from one miRNA collection with shared members

A proof-of-principle logic system was established to process multi-input and multi-output logic relationships with the aim of identifying the tissue origins of cancer in light of their established relationships with miRNA distributions.

Bivalent Display of Dicysteine on Peptide Nucleic Acids for Homogenous DNA/RNA Detection through in Situ Fluorescence Labelling

Fluorogenic probes that signal the presence of specific DNA or RNA sequences are key enabling tools for molecular disease diagnosis and imaging studies. Usually, at least one fluorophore is attached through covalent bonding to an oligonucleotide probe. However, the additional conjugation step increases costs. Here we introduce a method that avoids the requirement for the preparation of fluorescence-labelled oligonucleotides and provides the opportunity to alter the fluorogenic reporter dye without resynthesis. The method is based on adjacent hybridization of two dicysteine-containing peptide nucleic acid (PNA) probes to form a bipartite tetracysteine motif that binds profluorescent bisarsenical dyes such as FIAsH, ReAsH or CrAsH. Binding is accompanied by strong increases in fluorescence emission (with response factors of up to 80-fold and high brightness up to 50 mL mol^-1  cm^-1 ). The detection system provides sub-nanomolar limits of detection and allows discrimination of single nucleotide variations through more than 20-fold changes in fluorescence intensity. To demonstrate its usefulness, the FIAsH-based readout of the bivalent CysCys-PNA display was interfaced with a rolling-circle amplification (RCA) assay used to detect disease-associated microRNA let-7a.

Label-free detection of microRNA based on coupling multiple isothermal amplification techniques

MicroRNA (miRNA) was a promising class of cancer biomarkers. Here we developed a label-free method for sensitive measurement of let-7d miRNA based on multiple amplification techniques. The primer will bind to the duplex strand DNA that was formed by stem-loop template and target let-7d to initiate strand displacement amplification (SDA) in tandem. The released single strand DNA will be a primer to bind the circular template to initiate rolling circle amplification (RCA). The products based on multiple amplifications will be detected by a standard fluorimeter with N-methyl mesoporphyrin IX (NMM) as the fluorescent indicator. The proposed method exhibited excellent selectivity and high sensitivity with a detection limit of as low as 1.5 × 10⁻¹³ M. Moreover, this methodology was used for the determination of biomolecules in real serum samples with satisfying results.

G-quadruplex fluorescent probe-mediated real-time rolling circle amplification strategy for highly sensitive microRNA detection

Real-time PCR has revolutionized PCR from qualitative to quantitative. As an isothermal DNA amplification technique, rolling circular amplification (RCA) has been demonstrated to be a versatile tool in many fields. Development of a simple, highly sensitive, and specific strategy for real-time monitoring of RCA will increase its usefulness in many fields. The strategy reported here utilized the specific fluorescence response of thioflavin T (ThT) to G-quadruplexes formed by RCA products. Such a real-time monitoring strategy works well in both traditional RCA with linear amplification efficiency and modified RCA proceeded in an exponential manner, and can be readily performed in commercially available real-time PCR instruments, thereby achieving high-throughput detection and making the proposed technique more suitable for biosensing applications. As examples, real-time RCA-based sensing platforms were designed and successfully used for quantitation of microRNA over broad linear ranges (8 orders of magnitude) with a detection limit of 4 aM (or 0.12 zmol). The feasibility of microRNA analysis in human lung cancer cells was also demonstrated. This work provides a new method for real-time monitoring of RCA by using unique nucleic acid secondary structures and their specific fluorescent probes. It has the potential to be extended to other isothermal single-stranded DNA amplification techniques.

Applying DNA rolling circle amplification in fluorescence imaging of cell surface glycans labeled by a metabolic method

Glycans on the cell surfaces are essential for cellular communication. Metabolically labeling glycans can introduce unnatural sugars into cellular glycans, which can facilitate further labeling. We report herein imaging cell surface glycosylation by using click chemistry and DNA rolling circle amplification (RCA) to improve detection sensitivity. Through the RCA amplification, the image resolution of a cell was significantly improved and much fewer unnatural sugars were used than required previously. The advantage of this method is that it avoids introducing too much unnatural sugar, which can interfere with normal, physiological cell function. Simultaneously, the enhanced fluorescence intensity conveniently facilitates the detection of cells' own biosynthetic glycans by simply using a microplate reader. The results indicate that the metabolically labelling ability is different for different carbohydrates and different cells. Next, the RCA technique was adopted in a fluorescence resonance energy transfer (FRET)-based methodology that facilitated the glycan imaging of specific proteins on the cell surface. This method is broadly applicable to imaging the glycosylation of cellular proteins. Our results highlight the applications of RCA in metabolic glycan labeling, which can be used to monitor the glycosylation status on cells, and study the means by which glycosylation regulates cell function.

Sensitive detection of miRNA by using hybridization chain reaction coupled with positively charged gold nanoparticles

Positively charged gold nanoparticles (+)AuNPs can adsorb onto the negatively charged surface of single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA). Herein, long-range dsDNA polymers could form based on the hybridization chain reaction (HCR) of two hairpin probes (H₁ and H₂) by using miRNA-21 as an initiator. (+)AuNPs could adsorb onto the negatively charged surface of such long-range dsDNA polymers based on the electrostatic adsorption, which directly resulted in the precipitation of (+)AuNPs and the decrease of (+)AuNPs absorption spectra. Under optimal conditions, miRNA-21 detection could be realized in the range of 20 pM-10 nM with a detection limit of 6.8 pM. In addition, (+)AuNPs used here are much more stable than commonly used negatively charged gold nanoparticles ((−)AuNPs) in mixed solution that contained salt, protein or other metal ions. Importantly, the assay could realize the detection of miRNA in human serum samples.

Visualization and Quantification of MicroRNA in a Single Cell Using Atomic Force Microscopy

MicroRNAs (miRNAs) play critical roles in controlling various cellular processes, and the expression levels of individual miRNAs can be considerably altered in pathological conditions such as cancer. Accurate quantification of miRNA at the single-cell level will lead to a better understanding of miRNA function. Here, we present a direct and sensitive method for miRNA detection using atomic force microscopy (AFM). A hybrid binding domain (HBD)-tethered tip enabled mature miRNAs, but not premature miRNAs, to be located individually on an adhesion force map. By scanning several sections of a micrometer-sized DNA spot, we were able to quantify the copy number of miR-134 in a single neuron and demonstrate that the expression was increased upon cell activation. Moreover, we visualized individual miR-134s on fixed neurons after membrane removal and observed 2-4 miR-134s in the area of 1.0 × 1.0 μm(2) of soma. The number increased to 8-14 in stimulated neurons, and this change matches the ensemble-averaged increase in copy number. These findings indicate that miRNAs can be reliably quantified at the single cell level with AFM and that their distribution can be mapped at nanometric lateral resolution without modification or amplification. Furthermore, the analysis of miRNAs, mRNAs, and proteins in the same sample or region by scanning sequentially with different AFM tips would let us accurately understand the post-transcriptional regulation of biological processes.

Direct fluorescence detection of microRNA based on enzymatically engineered primer extension poly-thymine (EPEPT) reaction using copper nanoparticles as nano-dye

A new strategy based on enzymatically engineered primer extension poly-thymine (EPEPT) and nanomaterials in situ generation technology is reported for direct detection of microRNA (miRNA) in a fluorescence turn-on format using the sequential and complementary reactions catalyzed by Klenow Fragment exo^- (KFexo^-) and terminal deoxynucleotidyl transferase (TdTase). The short miRNA can be efficiently converted into long poly-thymine (polyT) sequences, which function as template for in situ formation of fluorescence copper nanoparticles (CuNPs) as nano-dye for detecting miRNA. The polyT-CuNPs can effectively form and emit intense red fluorescence under the 340nm excitation. For the proof of concept, microRNA-21 (miR-21) was selected as the model target to testify this strategy as a versatile assay platform. By directly using miR-21 as the primer, the simple, rapid and sensitive miRNA detection was successfully achieved with a good linearity between 1pM and 1nM and a detection limit of 100fM. Thus, the EPEPT strategy holds great potential in biochemical sensing research as an efficient and universal platform.

Sensitive and specific detection of miRNA using an isothermal exponential amplification method using fluorescence-labeled LNA/DNA chimera primers

MicroRNAs (miRNAs) are currently considered as potential biomarkers for various human diseases. In the present study, miRNA-triggered real-time fluorescent isothermal reaction with exponential amplification (ReFIRE) with or without Thermus aquaticus MutS (Taq MutS) was developed to analyze miRNAs using DNA polymerase, a nicking endonuclease, and fluorescently labeled primers. In the absence of Taq MutS, the ReFIRE system permitted the detection of 100 ymol of targeted miRNA in 80 min. However, this system enabled limited differentiation between homologous miRNA family members. Upon addition of Taq MutS to the ReFIRE system, non-specific amplification generated from the mishybridization between primers and primer dimers or primers and the template duplex was eliminated. The addition of Taq MutS enabled the ultrasensitive detection of as little as 10 ymol of targeted miRNAs in 50 min, which corresponds to less than 10 copies of miRNAs in a total volume of 20 μl. Additionally, the assay exhibited a dynamic range of up to 12 orders of magnitude. The ReFIRE system also showed high specificity, enabling differentiation between homologous miRNA family members exhibiting only single-base differences. The sensitivity, specificity, and dynamic range associated with this system were greater than most currently available miRNA isothermal amplification assays. Moreover, when target-specific primers were labeled with different fluorescent reporters, multiplex analysis was easily performed in a single tube, permitting accurate normalization of miRNA expression. This simple, fast, ultrasensitive, highly specific, and easy-to-multiplex method could significantly contribute to research investigations pertaining to the biological roles of miRNA, as well as clinical diagnosis of various diseases that involve miRNA disruptions. Graphical Abstract The principle of ReFIRE system.

Cas9 cleavage assay for pre-screening of sgRNAs using nicking triggered isothermal amplification

CRISPR/Cas9 is a highly efficient genome engineering tool, yet its off-target effects and sequence-dependent cleavage activity across different sgRNAs remain major concerns for its application. Here, we propose a nicking triggered exponential amplification reaction (NTEXPAR), a fast and sensitive in vitro method, to detect the double strand DNA cleaved by down to 10 pM Cas9 with a linear range of 100 pM to 20 nM. With this newly developed amplification method, Cas9 cleavage activity can be quantified in 40 min and the optimal sgRNA design for specific target sequence can be successfully determined. Using the pre-screened sgRNA, we are able to distinguish single nucleotide mismatch in a gene silencing experiment. This fluorescence based isothermal assay provides a versatile tool for the pre-screening of sgRNAs to achieve highly specific and highly efficient CRISPR/Cas9 genome editing.

Ultrasensitive electrochemical detection of miRNA-21 by using an iridium(III) complex as catalyst

The ultrasensitive electrochemical detection of miRNA-21 was realized by using a novel redox and catalytic "all-in-one" mechanism with an iridium(III) complex as a catalyst. To construct such a sensor, a capture probe (CP) was firstly immobilized onto the gold electrode surface. In the presence of miRNA-21, a sandwiched DNA complex could form between CP and a methylene blue (MB) labeled G-rich detection probe modified onto a gold nanoparticle (AuNP) surface (DP-AuNPs). Upon addition of K(+), the structure of DP changed to a G-quadruplex. Then, the iridium(III) complex could selectively interact with the G-quadruplex, catalyzing the reduction of H2O2, which was accompanied by an electrochemical signal change using MB as an electron mediator. Under optimal conditions, the electrochemical signal of MB reduction peak was proportional to miRNA concentration in the range from 5.0 fM to 1.0 pM, with a detection limit of 1.6 fM. In addition, satisfactory results were obtained for miRNA-21 detection in human serum samples, indicating a potential application of the sensor for bioanalysis.

Self-assembly of nucleic acid molecular aggregates catalyzed by a triple-helix probe for miRNA detection and single cell imaging

We herein report a novel finding that nucleic acid molecular aggregates (NAMAs) self-assembled on graphene oxide nanoplates (GONPs) as a result of DNA rolling circle amplification (RCA) and a functionalized triple-helix probe (THP) in single cells. The functionalized THP containing the aptamer region for target recognition and the trigger DNA region for RCA was firstly used to activate RCA for miRNA imaging in single cells. Interestingly, NAMAs with the fluorescent labels were hybridized by both the RCA products and FAM-DNA, and could partly self-assemble on GONPs; meanwhile, NAMAs could extend from the GONPs, which led to the quenched fluorescence being renewed. Significantly, the NAMAs were successfully applied for low-abundance miRNA detection and imaging in single cells. The self-assembled NAMAs could generate prominent and agminated fluorescence-bright spots in single cancer cells, which will effectively drive cell imaging into a new era.

Asymmetric exponential amplification reaction on a toehold/biotin featured template: an ultrasensitive and specific strategy for isothermal microRNAs analysis

The sensitive and specific analysis of microRNAs (miRNAs) without using a thermal cycler instrument is significant and would greatly facilitate biological research and disease diagnostics. Although exponential amplification reaction (EXPAR) is the most attractive strategy for the isothermal analysis of miRNAs, its intrinsic limitations of detection efficiency and inevitable non-specific amplification critically restrict its use in analytical sensitivity and specificity. Here, we present a novel asymmetric EXPAR based on a new biotin/toehold featured template. A biotin tag was used to reduce the melting temperature of the primer/template duplex at the 5′ terminus of the template, and a toehold exchange structure acted as a filter to suppress the non-specific trigger of EXPAR. The asymmetric EXPAR exhibited great improvements in amplification efficiency and specificity as well as a dramatic extension of dynamic range. The limit of detection for the let-7a analysis was decreased to 6.02 copies (0.01 zmol), and the dynamic range was extended to 10 orders of magnitude. The strategy enabled the sensitive and accurate analysis of let-7a miRNA in human cancer tissues with clearly better precision than both standard EXPAR and RT-qPCR. Asymmetric EXPAR is expected to have an important impact on the development of simple and rapid molecular diagnostic applications for short oligonucleotides.

Two-wheel drive-based DNA nanomachine and its sensing potential for highly sensitive analysis of cancer-related gene

With the biological significance and important advances of nano-scale DNA devices, scientific activities have been directed toward developing molecular machinery. In this work, we present a novel two-wheel drive-based DNA nanomachine composed of one signaling recognition probe (SRP), one label-free recognition probe (LRP), and one driving primer (DP). Target DNA hybridization can activate LRP-based wheel driving by resorting to DP-mediated polymerization/nicking/displacement cycles. This in turn results in the accumulation of nicked strand 1 (NS1) that can initiate extended SRP-based wheel driving. As a result, the hairpin structure of SRP is stretched and pre-quenched fluorescence is restored. Meanwhile, lots of nicked strand 2 (NS2) are produced, which could hybridize perfectly with SRP and lead to further fluorescence amplification. It is worth noting that, because the nanomachine operation relies strongly on inputted target trigger, the unwanted background is completely eliminated. The detection limit of 1 pM and an excellent capability to recognize the single-base mutation were achieved. Significantly, the interrogating of target trigger extracted from cancer cells is already available, reflecting the potential for practical applications. As a proof-of-concept building, the unique analytical properties would significantly benefit the DNA nanomachines and reveal great promise in biochemical and biomedical studies.

Live Cell MicroRNA Imaging Using Exonuclease III-Aided Recycling Amplification Based on Aggregation-Induced Emission Luminogens

Enzyme-assisted detection strategies of microRNAs (miRNAs) in vitro have accomplished both great sensitivity and specificity. However, low expression of miRNAs and a complex environment in cells induces big challenges for monitoring and tracking miRNAs in vivo. The work reports the attempt to carry miRNA imaging into live cells, by enzyme-aided recycling amplification. We utilize facile probes based yellow aggregation-induced emission luminogens (AIEgens) with super photostable property but without quencher, which are applied to monitor miRNAs not only from urine sample extracts (in vitro) but also in live cells (in vivo). The assay could distinguish the cancer patients' urine samples from the healthy urine due to the good specificity. Moreover, the probe showed much higher fluorescence intensity in breast cancer cells (MCF-7) (miR-21 in high expression) than that in cervical cancer cells (HeLa) and human lung fibroblast cells (HLF) (miR-21 in low expression) in more than 60 min, which showed the good performance and super photostability for the probe in vivo. As controls, another two probes with FAM/Cy3 and corresponding quenchers, respectively, could perform miRNAs detections in vitro and parts of in vivo tests but were not suitable for the long-term cell tracking due to the photobleach phenomena, which also demonstrates that the probe with AIEgens is a potential candidate for the accurate identification of cancer biomarkers.

Detecting miRNA by producing RNA: a sensitive assay that combines rolling-circle DNA polymerization and rolling circle transcription

Target miRNA was detected by producing RNA: rolling circle polymerization (RCP) and rolling circle transcription (RCT) were interlinked to provide dual amplification, producing multiplied malachite green (MG) aptamers, and a signal was generated by the SERS (surface-enhanced Raman scattering) quantification of the MG molecules that were bound to the transcripts.

Sensitive and homogeneous microRNA detection using branched cascade enzymatic amplification

This assay, termed branched cascade enzymatic amplification (BCEA), can be a novel and straightforward method for sensitive and specific microRNA detection in crude cellular extracts of cancer cells at physiological temperature, by coupling two ordinary polymerases, Klenow fragment exo(-) and terminal deoxynucleotidyl transferase.

Graphene oxide surface blocking agents can increase the DNA biosensor sensitivity

Graphene oxide adsorbs single-strand fluorescent probe DNA, and the adsorbed probe can be desorbed by adding the complementary target DNA. Using this method, many biosensor studies have been carried out. We recently proposed a two-step mechanism for this sensing reaction: non-specific probe displacement followed by hybridization in the solution. Only about one out of six added target DNA is hybridized with the adsorbed probe to generate signal, leading to relatively low sensitivity. In this work, we aim to test whether surface blocking agents can minimize non-specific target adsorption and increase hybridization efficiency. Over ten blocking agents (polymers, surfactants, and DNA) were screened based on their effect on probe DNA adsorption and target DNA induced probe desorption. DNA oligonucleotides show significant and controllable enhancement in sensor sensitivity. The effect of DNA length and sequence was systematically investigated. Under optimized conditions, the sensor sensitivity was enhanced by nearly 10-fold. Using the same blocking method, sensitivity enhancement of other targets was also achieved, including adenosine and Hg(2+) with DNA aptamer probes. This reported surface blocking strategy can generally improve graphene oxide and potentially other surface adsorption based biosensors for metal ions, small molecules, and DNA.

Cascade Signal Amplification Based on Copper Nanoparticle-Reported Rolling Circle Amplification for Ultrasensitive Electrochemical Detection of the Prostate Cancer Biomarker

An ultrasensitive and highly selective electrochemical assay was first attempted by combining the rolling circle amplification (RCA) reaction with poly(thymine)-templated copper nanoparticles (CuNPs) for cascade signal amplification. As proof of concept, prostate specific antigen (PSA) was selected as a model target. Using a gold nanoparticle (AuNP) as a carrier, we synthesized the primer-AuNP-aptamer bioconjugate for signal amplification by increasing the primer/aptamer ratio. The specific construction of primer-AuNP-aptamer/PSA/anti-PSA sandwich structure triggered the effective RCA reaction, in which thousands of tandem poly(thymine) repeats were generated and directly served as the specific templates for the subsequent CuNP formation. The signal readout was easily achieved by dissolving the RCA product-templated CuNPs and detecting the released copper ions with differential pulse stripping voltammetry. Because of the designed cascade signal amplification strategy, the newly developed method achieved a linear range of 0.05-500 fg/mL, with a remarkable detection limit of 0.020 ± 0.001 fg/mL PSA. Finally, the feasibility of the developed method for practical application was investigated by analyzing PSA in the real clinical human serum samples. The ultrasensitivity, specificity, convenience, and capability for analyzing the clinical samples demonstrate that this method has great potential for practical disease diagnosis applications.

Nitrogen-doped carbon nanoparticle modulated turn-on fluorescent probes for histidine detection and its imaging in living cells

In this work, nitrogen-doped carbon nanoparticle (N-CNP) modulated turn-on fluorescent probes were developed for rapid and selective detection of histidine. The as synthesized N-CNPs exhibited high fluorescence quantum yield and excellent biocompatibility. The fluorescence of N-CNPs can be quenched selectively by Cu(II) ions with high efficiency, and restored by the addition of histidine owing to the competitive binding of Cu(II) ions and histidine that removes Cu(II) ions from the surface of the N-CNPs. Under the optimal conditions, a linear relationship between the increased fluorescence intensity of N-CNP/Cu(II) ion conjugates and the concentration of histidine was established in the range from 0.5 to 60 μM. The detection limit was as low as 150 nM (signal-to-noise ratio of 3). In addition, the as-prepared N-CNP/Cu(II) ion nanoprobes showed excellent biocompatibility and were applied for a histidine imaging assay in living cells, which presented great potential in the bio-labeling assay and clinical diagnostic applications.

Visual Detection of Multiplex MicroRNAs Using Cationic Conjugated Polymer Materials

A simple, visual, and specific method for simultaneous detection of multiplex microRNAs (miRNAs) has been developed by integrating duplex-specific nuclease (DSN)-induced amplification with cationic conjugated polymer (CCP) materials. The probe DNA with a complementary sequence to target miRNA is labeled with fluorescein dye (FAM). Without target miRNA, the single-strand DNA probe cannot be digested by DSN. Upon adding CCPs, efficient fluorescence resonance energy transfer (FRET) from CCP to FAM occurs owing to strong electrostatic interactions between CCP and the DNA probe. In the presence of target miRNA, the DNA probe hybridizes with target miRNA followed by digestion to small nucleotide fragments by DSN; meanwhile, the miRNA is released and subsequently interacts again with the probe, resulting in the cycled digestion of the DNA probe. In this case, weak electrostatic interactions between oligonucleotide fragments and CCP lead to inefficient FRET from CCP to FAM. Thus, by triggering the FRET signal from CCP to FAM, miRNA can be specially detected, and the fluorescence color change based on FRET can be visualized directly with the naked eye under an UV lamp. Furthermore, an energy transfer cascade can be designed using CCP and DNA probes labeled at the 5'-terminus with FAM and Cy3 dyes, and the multistep FRET processes offer the ability of simultaneous detection of multiplex miRNAs.

ATP-Releasing Nucleotides: Linking DNA Synthesis to Luciferase Signaling

A new strategy is reported for the production of luminescence signals from DNA synthesis through the use of chimeric nucleoside tetraphosphate dimers in which ATP, rather than pyrophosphate, is the leaving group. ATP-releasing nucleotides (ARNs) were synthesized as derivatives of the four canonical nucleotides. All four derivatives are good substrates for DNA polymerase, with Km values averaging 13-fold higher than those of natural dNTPs, and kcat values within 1.5-fold of those of native nucleotides. Importantly, ARNs were found to yield very little background signal with luciferase. DNA synthesis experiments show that the ATP byproduct can be harnessed to elicit a chemiluminescence signal in the presence of luciferase. When using a polymerase together with the chimeric nucleotides, target DNAs/RNAs trigger the release of stoichiometrically large quantities of ATP, thereby allowing sensitive isothermal luminescence detection of nucleic acids as diverse as phage DNAs and short miRNAs.