Transducing Protease Activity into DNA Output for Developing Smart Bionanosensors

Construction of a 3D Quantum Dot Nanoassembly with Two-Step FRET for One-Step Sensing of Human Telomerase RNA in Breast Cancer Cells and Tissues

Telomerase is an important biomarker for early diagnosis of cancers, but current telomerase assays usually rely on measuring the extension products of telomerase substrates, which increases the assay complexity. More evidence indicates that human telomerase RNA (hTR), as a core component of telomerase, is positively correlated with the telomerase activity. Herein, we demonstrate the development of a duplex-specific nuclease (DSN)-propelled 3D quantum dot (QD) nanoassembly with two-step Föster resonance energy transfer (FRET) for the one-step sensing of hTR in breast cancer cells and tissues. This assay involves only one hairpin probe modified with a Cy5 at the sixth base from the 5'-biotin end and a BHQ2 at the 3'-terminus, which integrates three functions of target recognition, target recycling amplification, and signal readout. The anchoring of the hairpin probe on the 605QD surface results in the formation of a 3D 605QD-Cy5-probe-BHQ2 nanoassembly in which two-step FRET occurs among the 605QD, Cy5, and BHQ2 quencher. Notably, the formation of 605QD-Cy5-probe-BHQ2 nanoassembly facilitates the reduction of background signal and the increase of signal-to-background ratio due to its dense, highly oriented nucleic acid shell-induced steric hindrance effect. This assay can achieve one-step and rapid detection of hTR with a detection limit of 2.10 fM, which is the simplest and most rapid hTR assay reported so far. Moreover, this assay can efficiently distinguish single-base mismatched sequences, and it can discriminate the hTR level between breast cancer patients and healthy donors with a high accuracy of 100%, with great prospects for early diagnosis of cancers.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.

Proteolytic Biosensors with Functional Nanomaterials: Current Approaches and Future Challenges

Proteolytic enzymes are one of the important biomarkers that enable the early diagnosis of several diseases, such as cancers. A specific proteolytic enzyme selectively degrades a certain sequence of a polypeptide. Therefore, a particular proteolytic enzyme can be selectively quantified by changing detectable signals causing degradation of the peptide chain. In addition, by combining polypeptides with various functional nanomaterials, proteolytic enzymes can be measured more sensitively and rapidly. In this paper, proteolytic enzymes that can be measured using a polypeptide degradation method are reviewed and recently studied functional nanomaterials-based proteolytic biosensors are discussed. We anticipate that the proteolytic nanobiosensors addressed in this review will provide valuable information on physiological changes from a cellular level for individual and early diagnosis.

Developing FRET Networks for Sensing

Förster resonance energy transfer (FRET) is a widely used fluorescence-based sensing mechanism. To date, most implementations of FRET sensors have relied on a discrete donor-acceptor pair for detection of each analytical target. FRET networks are an emerging concept in which target recognition perturbs a set of interconnected FRET pathways between multiple emitters. Here, we review the energy transfer topologies and scaffold materials for FRET networks, propose a general nomenclature, and qualitatively summarize the dynamics of the competitive, sequential, homoFRET, and heteroFRET pathways that constitute FRET networks. Implementations of FRET networks for sensing are also described, including concentric FRET probes, other single-vector multiplexing, and logic gates and switches. Unresolved questions and future research directions for current systems are discussed, as are potential but currently unexplored applications of FRET networks in sensing.

Peptide probes for proteases - innovations and applications for monitoring proteolytic activity

Proteases are excellent biomarkers for a variety of diseases, offer multiple opportunities for diagnostic applications and are valuable targets for therapy. From a chemistry-based perspective this review discusses and critiques the most recent advances in the field of substrate-based probes for the detection and analysis of proteolytic activity both in vitro and in vivo.

Fluorescence-Based On-Resin Detection of Three Model Proteases

A new approach to on-resin detection of three model proteases (trypsin, chymotrypsin, and thrombin) has been developed, while at the same time already described methodology for simultaneous detection of two enzymes (trypsin and chymotrypsin) has been additionally generalized. Appropriate immobilized substrates, comprising specifically cleavable peptide sequences capped with fluorescent dyes, have been synthesized on Rink Amide PEGA resin or Amino PEGA resin modified with backbone amide linker (BAL). Resulting solid support-bound probes were then dispersed into Tris-HCl buffer solution (pH = 8.0) and subjected to enzymatic cleavage. Liberated fluorophores have been tracked by fluorescence measuring. The competitive activities of studied proteases towards the thrombin probe have been efficiently limited and controlled by employing a Bowman-Birk inhibitor into a system.

Delocalized Two-Exciton States in DNA Scaffolded Cyanine Dimers

The engineering and manipulation of delocalized molecular exciton states is a key component for artificial biomimetic light harvesting complexes as well as alternative circuitry platforms based on exciton propagation. Here we examine the consequences of strong electronic coupling in cyanine homodimers on DNA duplex scaffolds. The most closely spaced dyes, attached to positions directly across the double-helix from one another, exhibit pronounced Davydov splitting due to strong electronic coupling. We demonstrate that the DNA scaffold is sufficiently robust to support observation of the transition from the lowest energy (J-like) one-exciton state to the nonlocal two-exciton state, where each cyanine dye is in the excited state. This transition proceeds via sequential photon absorption and persists for the lifetime of the exciton, establishing this as a controlled method for creating two-exciton states. Our observations suggest that DNA-organized dye networks have potential as platforms for molecular logic gates and entangled photon emission based on delocalized two-exciton states.

Fluorescence for biological logic gates

Biological logic gates are smart probes able to respond to biological conditions in behaviors similar to computer logic gates, and they pose a promising challenge for modern medicine. Researchers are creating many kinds of smart nanostructures that can respond to various biological parameters such as pH, ion presence, and enzyme activity. Each of these conditions alone might be interesting in a biological sense, but their interactions are what define specific disease conditions. Researchers over the past few decades have developed a plethora of stimuli-responsive nanodevices, from activatable fluorescent probes to DNA origami nanomachines, many explicitly defining logic operations. Whereas many smart configurations have been explored, in this review we focus on logic operations actuated through fluorescent signals. We discuss the applicability of fluorescence as a means of logic gate implementation, and consider the use of both fluorescence intensity as well as fluorescence lifetime.

Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency

DNA scaffolds enable base-pair-specific positioning of fluorescent molecules, allowing for nanometer-scale precision in controlling multidye interactions. Expanding on this concept, DNA-based molecular photonic wires (MPWs) allow for light harvesting and directional propagation of photonic energy on the nanometer scale. The most common MPW examples exploit Förster resonance energy transfer (FRET), and FRET between the same dye species (HomoFRET) was recently shown to increase the distance and efficiency at which MPWs can function. Although increased proximity between adjacent fluorophores can be used to increase the energy transfer efficiency, FRET assumptions break down as the distance between the dye molecules becomes comparable to their size (∼2 nm). Here we compare dye conjugation with single versus dimer Cy5 dye repeats as HomoFRET MPW components on a double-crossover DNA scaffold. At room temperature (RT) under low-light conditions, end-labeled uncoupled dye molecules provide optimal transfer, while the Cy5 dimers show ultrafast (<100 ps) nonradiative decay that severely limits their functionality. Of particular interest is the observation that through increased excitation fluence as well as cryogenic temperatures, the dimeric MPW shows suppression of the ultrafast decay, demonstrating fluorescence lifetimes similar to the single Cy5 MPWs. This work points to the complex dynamic capabilities of dye-based nanophotonic networks, where dye positioning and interactions can become critical, and could be used to extend the lengths and complexities of such dye-DNA devices, enabling multiparameter nanophotonic circuitry.

Monitoring Proteolytic Activity in Real Time: A New World of Opportunities for Biosensors

Proteases play a pivotal role in several biological processes, from digestion, cell proliferation, and differentiation to fertility. Deregulation of protease metabolism can result in several pathological conditions (i.e., cancer, neurodegenerative disorders, and others). Therefore, monitoring proteolytic activity in real time could have a fundamental role in the early diagnosis of these diseases. Herein, the main approaches used to develop biosensors for monitoring proteolytic activity are reviewed. A comparison of the advantages and disadvantages of each approach is provided along with a discussion of their importance and promising opportunities for the early diagnosis of severe diseases. This new era of biosensors can be characterized by the ability to control and monitor biological processes, ultimately improving the potential of personalized medicine.

The Application of Tetrahedral Framework Nucleic Acids as a Drug Carrier in Biomedicine Fields

In recent years, tetrahedral Framework Nucleic Acids(tFNAs) have become a hot topic in the field of DNA nanostructures because of their stable structures, nanoscale size, superior mechanical properties and convenient synthesis with high yield. tFNAs are considered promising drug delivery carriers because they can pass through the cellular membrane without any help and they have a good biocompatibility and biodegradability. Besides, they have rich modification sites, they can be modified by kinds of functional groups. The functionalization molecules can be modified on the vertexes, embedded between the double-stranded DNA of the tetrahedron edges, hanged on the edges, or encapsulated in the cage-like structure of the tetrahedron. The structure of tetrahedron can also be intelligently controlled through smart design, such as integrating DNA hairpin loop structure onto the edges. Nowadays, DNA tetrahedron will have a broader development prospect in the application of drug transport carriers and intelligent drug carriers. Therefore, DNA material is a new carrier material with great advantages and has a very broad application prospect in the construction of an intelligent drug transport system.

DNA Microsystems for Biodiagnosis

Researchers are continuously making progress towards diagnosis and treatment of numerous diseases. However, there are still major issues that are presenting many challenges for current medical diagnosis. On the other hand, DNA nanotechnology has evolved significantly over the last three decades and is highly interdisciplinary. With many potential technologies derived from the field, it is natural to begin exploring and incorporating its knowledge to develop DNA microsystems for biodiagnosis in order to help address current obstacles, such as disease detection and drug resistance. Here, current challenges in disease detection are presented along with standard methods for diagnosis. Then, a brief overview of DNA nanotechnology is introduced along with its main attractive features for constructing biodiagnostic microsystems. Lastly, suggested DNA-based microsystems are discussed through proof-of-concept demonstrations with improvement strategies for standard diagnostic approaches.

Target-activated transcription for the amplified sensing of protease biomarkers

Signal amplification is an effective way to achieve sensitive analysis of biomarkers, exhibiting great promise in biomedical research and clinical diagnosis. Inspired by the transcription process, here we present a versatile strategy that enables effective amplification of proteolysis into nucleic acid signal outputs in a homogeneous system. In this strategy, a protease-activatable T7 RNA polymerase is engineered as the signal amplifier and achieves 3 orders of magnitude amplification in signal gain. The versatility of this strategy has been demonstrated by the development of sensitive and selective assays for protease biomarkers, such as matrix metalloproteinase-2 (MMP-2) and thrombin, with sub-picomole sensitivity, which is 4.3 × 10³-fold lower than that of the standard peptide-based method. Moreover, the proposed assay has been further applied in the detection of MMP-2 secreted by cancer cells, as well as in the assessment of MMP-2 levels in osteosarcoma tissue samples, providing a general approach for the monitoring of protease biomarkers in clinical diagnosis.

A transcription-inspired signal amplification strategy that amplifies proteolysis into nucleic acid outputs is presented for the ultrasensitive sensing of protease biomarkers.

Understanding the fate of DNA nanostructures inside the cell

DNA nanostructures are highly tunable and responsive materials for diagnostic and healthcare-related applications, but their intracellular fate remains largely unknown.

Improved Optical Multiplexing with Temporal DNA Barcodes

Many biochemical events of importance are complex and dynamic. Fluorescence microscopy offers a versatile solution to study the dynamics of biology at the mesoscale. An important challenge in the field is the simultaneous study of several objects of interest, referred to as optical multiplexing. For improved multiplexing, some prior techniques used repeated reporter washing or the geometry of nanostructures; however, these techniques require complex nanostructure assembly, multiple reporters, or advanced multistep drift correction. Here we propose a time-based approach, for improved optical multiplexing, that uses readily available inexpensive reporters and requires minimal preparation efforts. We program short DNA strands, referred hereby as DNA devices, such that they undergo unique conformation changes in the presence of the dye-labeled reporters. The universal fluorescent reporter transiently binds with the devices to report their activity. Since each device is programmed to exhibit different hybridization kinetics, their fluorescent time trace, referred to as the temporal barcode, will be unique. We model our devices using continuous-time Markov chains and use stochastic simulation algorithm to generate their temporal patterns. We first ran simulation experiments with a small number of DNA devices, demonstrating several distinct temporal barcodes, all of which use a single dye color. Later, using nanostructure-based devices, we designed a much larger pool of temporal barcodes and used machine learning for classification of these barcodes. Our simulation experiments and design principles can aid in the experimental demonstration of the DNA devices.