Addressable configurations of DNA nanostructures for rewritable memory

Differential electrophoretic mobility of synthetic DNA motifs and duplex DNA in various counter ions

In this work, we analyzed the electrophoretic behavior of a double crossover (DX) DNA motif in various counter ions. The influence of the type and concentration of counter ions on electrophoretic behavior is different for the DX motif compared to a duplex of the same molecular weight. Higher concentrations of divalent ions Mg2+ and Ca2+ in the gel and running buffer reduce the electrophoretic migration of the DX motif. This effect is less pronounced in the monovalent ion Na+ while K+ ion did not have any significant effect on the electrophoretic behavior.

The unusual structural properties and potential biological relevance of switchback DNA

Synthetic DNA motifs form the basis of nucleic acid nanotechnology. The biochemical and biophysical properties of these motifs determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.

The unusual structural properties and potential biological relevance of switchback DNA

Synthetic DNA motifs form the basis of nucleic acid nanotechnology, and their biochemical and biophysical properties determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.

Data Storage Using DNA

The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles.

Processing DNA Storage through Programmable Assembly in a Droplet-Based Fluidics System

DNA can be used to store digital data, and synthetic short-sequence DNA pools are developed to store high quantities of digital data. However, synthetic DNA data cannot be actively processed in DNA pools. An active DNA data editing process is developed using splint ligation in a droplet-controlled fluidics (DCF) system. DNA fragments of discrete sizes (100-500 bps) are synthesized for droplet assembly, and programmed sequence information exchange occurred. The encoded DNA sequences are processed in series and parallel to synthesize the determined DNA pools, enabling random access using polymerase chain reaction amplification. The sequencing results of the assembled DNA data pools can be orderly aligned for decoding and have high fidelity through address primer scanning. Furthermore, eight 90 bps DNA pools with pixel information (png: 0.27-0.28 kB), encoded by codons, are synthesized to create eight 270 bps DNA pools with an animation movie chip file (mp4: 12 kB) in the DCF system.

Parallel molecular computation on digital data stored in DNA

DNA is an incredibly dense storage medium for digital data. However, computing on the stored information is expensive and slow, requiring rounds of sequencing, in silico computation, and DNA synthesis. Prior work on accessing and modifying data using DNA hybridization or enzymatic reactions had limited computation capabilities. Inspired by the computational power of "DNA strand displacement," we augment DNA storage with "in-memory" molecular computation using strand displacement reactions to algorithmically modify data in a parallel manner. We show programs for binary counting and Turing universal cellular automaton Rule 110, the latter of which is, in principle, capable of implementing any computer algorithm. Information is stored in the nicks of DNA, and a secondary sequence-level encoding allows high-throughput sequencing-based readout. We conducted multiple rounds of computation on 4-bit data registers, as well as random access of data (selective access and erasure). We demonstrate that large strand displacement cascades with 244 distinct strand exchanges (sequential and in parallel) can use naturally occurring DNA sequence from M13 bacteriophage without stringent sequence design, which has the potential to improve the scale of computation and decrease cost. Our work merges DNA storage and DNA computing, setting the foundation of entirely molecular algorithms for parallel manipulation of digital information preserved in DNA.

An outlook on the current challenges and opportunities in DNA data storage

Silicon is the gold standard for information storage systems. The exponential generation of digital information will exhaust the global supply of refined silicon. Therefore, investing in alternative information storage materials such as DNA has gained momentum. DNA as a memory material possesses several advantages over silicon-based data storage, including higher storage capacity, data retention, and lower operational energy. Routine DNA data storage approaches encode data into chemically synthesized nucleotide sequences. The scalability of DNA data storage depends on factors such as the cost and the generation of hazardous waste during DNA synthesis, latency of writing and reading, and limited rewriting capacity. Here, we review the current status of DNA data storage encoding, writing, storing, retrieving and reading, and discuss the technology's challenges and opportunities.

Self-Assembly of DNA Nanostructures in Different Cations

The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions that restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions are used so far (typically Mg2+ and Na+ ). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (~134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca2+ , Ba2+ , Na+ , K+ and Li+ and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na+ , K+ and Li+ ) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg2+ , Ca2+ and Ba2+ ). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.

Multiplexed Nanopore-Based Nucleic Acid Sensing and Bacterial Identification Using DNA Dumbbell Nanoswitches

Multiplexed nucleic acid sensing methods with high specificity are vital for clinical diagnostics and infectious disease control, especially in the postpandemic era. Nanopore sensing techniques have developed in the past two decades, offering versatile tools for biosensing while enabling highly sensitive analyte measurements at the single-molecule level. Here, we establish a nanopore sensor based on DNA dumbbell nanoswitches for multiplexed nucleic acid detection and bacterial identification. The DNA nanotechnology-based sensor switches from an "open" into a "closed" state when a target strand hybridizes to two sequence-specific sensing overhangs. The loop in the DNA pulls two groups of dumbbells together. The change in topology results in an easily recognized peak in the current trace. Simultaneous detection of four different sequences was achieved by assembling four DNA dumbbell nanoswitches on one carrier. The high specificity of the dumbbell nanoswitch was verified by distinguishing single base variants in DNA and RNA targets using four barcoded carriers in multiplexed measurements. By combining multiple dumbbell nanoswitches with barcoded DNA carriers, we identified different bacterial species even with high sequence similarity by detecting strain specific 16S ribosomal RNA (rRNA) fragments.

Self-assembly of DNA nanostructures in different cations

The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions which restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions have been used so far (typically Mg 2+ and Na + ). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (∼134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca 2+ , Ba 2+ , Na + , K + and Li + and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na + , K + and Li + ) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg 2+ , Ca 2+ and Ba 2+ ). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.

Encoding, Decoding, and Rendering Information in DNA Nanoswitch Libraries

DNA-based construction allows the creation of molecular devices that are useful in information storage and processing. Here, we combine the programmability of DNA nanoswitches and stimuli-responsive conformational changes to demonstrate information encoding and graphical readout using gel electrophoresis. We encoded information as 5-bit binary codes for alphanumeric characters using a combination of DNA and RNA inputs that can be decoded using molecular stimuli such as a ribonuclease. We also show that a similar strategy can be used for graphical visual readout of alphabets on an agarose gel, information that is encoded by nucleic acids and decoded by a ribonuclease. Our method of information encoding and processing could be combined with DNA actuation for molecular computation and diagnostics that require a nonarbitrary visual readout.

Small Molecule-Templated DNA Hydrogel with Record Stiffness Integrates and Releases DNA Nanostructures and Gene Silencing Nucleic Acids

Deoxyribonucleic acid (DNA) hydrogels are a unique class of programmable, biocompatible materials able to respond to complex stimuli, making them valuable in drug delivery, analyte detection, cell growth, and shape-memory materials. However, unmodified DNA hydrogels in the literature are very soft, rarely reaching a storage modulus of 10³  Pa, and they lack functionality, limiting their applications. Here, a DNA/small-molecule motif to create stiff hydrogels from unmodified DNA, reaching 10⁵  Pa in storage modulus is used. The motif consists of an interaction between polyadenine and cyanuric acid-which has 3-thymine like faces-into multimicrometer supramolecular fibers. The mechanical properties of these hydrogels are readily tuned, they are self-healing and thixotropic. They integrate a high density of small, nontoxic molecules, and are functionalized simply by varying the molecule sidechain. They respond to three independent stimuli, including a small molecule stimulus. These stimuli are used to integrate and release DNA wireframe and DNA origami nanostructures within the hydrogel. The hydrogel is applied as an injectable delivery vector, releasing an antisense oligonucleotide in cells, and increasing its gene silencing efficacy. This work provides tunable, stimuli-responsive, exceptionally stiff all-DNA hydrogels from simple sequences, extending these materials' capabilities.

Toehold clipping: A mechanism for remote control of DNA strand displacement

The ability to create stimuli-responsive DNA nanostructures has played a prominent role in dynamic DNA nanotechnology. Primary among these is the process of toehold-based strand displacement, where a nucleic acid molecule can act as a trigger to cause conformational changes in custom-designed DNA nanostructures. Here, we add another layer of control to strand displacement reactions through a 'toehold clipping' process. By designing DNA complexes with a photocleavable linker-containing toehold or an RNA toehold, we show that we can use light (UV) or enzyme (ribonuclease) to eliminate the toehold, thus preventing strand displacement reactions. We use molecular dynamics simulations to analyze the structural effects of incorporating a photocleavable linker in DNA complexes. Beyond simple DNA duplexes, we also demonstrate the toehold clipping process in a model DNA nanostructure, by designing a toehold containing double-bundle DNA tetrahedron that disassembles when an invading strand is added, but stays intact after the toehold clipping process even in the presence of the invading strand. This work is an example of combining multiple physical or molecular stimuli to provide additional remote control over DNA nanostructure reconfiguration, advances that hold potential use in biosensing, drug delivery or molecular computation.

Emerging Approaches to DNA Data Storage: Challenges and Prospects

With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 10¹⁴ GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 10³ GB/mm³. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies.

Construction of Multiple Logic Circuits Based on Allosteric DNAzymes

In DNA computing, the implementation of complex and stable logic operations in a universal system is a critical challenge. It is necessary to develop a system with complex logic functions based on a simple mechanism. Here, the strategy to control the secondary structure of assembled DNAzymes’ conserved domain is adopted to regulate the activity of DNAzymes and avoid the generation of four-way junctions, and makes it possible to implement basic logic gates and their cascade circuits in the same system. In addition, the purpose of threshold control achieved by the allosteric secondary structure implements a three-input DNA voter with one-vote veto function. The scalability of the system can be remarkably improved by adjusting the threshold to implement a DNA voter with 2n + 1 inputs. The proposed strategy provides a feasible idea for constructing more complex DNA circuits and a highly integrated computing system.

Design and Realization of Triple dsDNA Nanocomputing Circuits in Microfluidic Chips

DNA logic gates, nanocomputing circuits, have already implemented basic computations and shown great signal potential for nano logic material application. However, the reaction temperature and computing speed still limit its development. Performing complicated computations requires a more stable component and a better computing platform. We proposed a more stable design of logic gates based on a triple, double-stranded, DNA (T-dsDNA) structure. We demonstrated a half adder and a full adder using these DNA nanocircuits and performed the computations in a microfluidic chip device at room temperature. When the solutions were mixed in the device, we obtained the expected results in real time, which suggested that the T-dsDNA combined microfluidic chip provides a concise strategy for large DNA nanocircuits.

DNA-Based Smart Reagent for Detecting Alzheimer's Associated MicroRNAs

Alzheimer's disease (AD) is the most common neurodegenerative disorder, with significant research efforts devoted to identifying new biomarkers for clinical diagnosis and treatment. MicroRNAs have emerged as likely disease regulators and biomarkers for AD, now implicated as having roles in several biological processes related to progression of the disease. In this work, we use the miRacles assay (microRNA activated conditional looping of engineered switches) for single-step detection of AD-related microRNAs. The technology is based on conformationally responsive DNA nanoswitches that loop upon recognition of a target microRNA and report their on/off status through an electrophoretic readout. Unlike many methods, our approach directly detects native microRNAs without amplification or labeling, eliminating the need for expensive enzymes, reagents, and equipment. For known AD-related microRNA miR-107, we demonstrated sensitivity of ∼8 fM, specificity among four similar microRNAs of the same family, and simultaneous multiplexed detection of those four microRNA targets. Toward clinical use, we screened 56 AD-related microRNAs and found four that showed detectable differences between total RNA extracts derived from human healthy and AD brain samples. In the context of AD, this "smart reagent" could facilitate biomarker discovery, accelerate efforts to understand the role of microRNAs in AD, and have clinical potential as a diagnostic or monitoring tool for validated biomarkers.

A last-in first-out stack data structure implemented in DNA

DNA-based memory systems are being reported with increasing frequency. However, dynamic DNA data structures able to store and recall information in an ordered way, and able to be interfaced with external nucleic acid computing circuits, have so far received little attention. Here we present an in vitro implementation of a stack data structure using DNA polymers. The stack is able to record combinations of two different DNA signals, release the signals into solution in reverse order, and then re-record. We explore the accuracy limits of the stack data structure through a stochastic rule-based model of the underlying polymerisation chemistry. We derive how the performance of the stack increases with the efficiency of washing steps between successive reaction stages, and report how stack performance depends on the history of stack operations under inefficient washing. Finally, we discuss refinements to improve molecular synchronisation and future open problems in implementing an autonomous chemical data structure.

DNA is becoming increasingly used as a medium to store non-genetic information. Here the authors present a dynamic stack data structure implemented as a DNA polymer chemistry able to record and retrieve signals in a last-in first-out order.

Image Encoding Using Multi-Level DNA Barcodes with Nanopore Readout

Deoxyribonucleic acid (DNA) nanostructure-based data encoding is an emerging information storage mode, offering rewritable, editable, and secure data storage. Herein, a DNA nanostructure-based storage method established on a solid-state nanopore sensing platform to save and encrypt a 2D grayscale image is proposed. DNA multi-way junctions of different sizes are attached to a double strand of DNA carriers, resulting in distinct levels of current blockades when passing through a glass nanopore with diameters around 14 nm. The resulting quaternary encoding doubles the capacity relative to a classical binary system. Through toehold-mediated strand displacement reactions, the DNA nanostructures can be precisely added to and removed from the DNA carrier. By encoding the image into 16 DNA carriers using the quaternary barcodes and reading them in one simultaneous measurement, the image is successfully saved, encrypted, and recovered. Avoiding any proteins or enzymatic reactions, the authors thus realize a pure DNA storage system on a nanopore platform with increased capacity and programmability.

How to Perform miRacles: A Step-by-Step microRNA Detection Protocol Using DNA Nanoswitches

MicroRNAs are short non-coding RNAs involved in post-transcriptional gene regulation, and are increasingly considered to be biomarkers for numerous biological processes and human diseases. Current techniques used for microRNA detection can be expensive and labor-intensive, and typically require amplification, labeling, or radioactive probes. In this protocol, we describe a DNA nanoswitch-based microRNA detection assay termed  "miRacles": microRNA-activated conditional looping of engineered switches. This method uses conformationally responsive DNA nanoswitches that detect the presence of specific microRNAs with a simple and unambiguous gel-shift assay that can be performed on the benchtop. The assay is low cost, minimalistic, and capable of direct detection of specific microRNAs in unprocessed total RNA samples, with no enzymatic amplification, labeling, or special equipment. The protocol for detection of microRNAs in total RNA can be completed in as little as a few hours, making this assay a compelling alternative to qPCR and Northern blotting. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Preparation of DNA nanoswitches Basic Protocol 2: Detection of microRNAs from total RNA samples Support Protocol 1: Optional nanoswitch purification by PEG precipitation Support Protocol 2: Optional nanoswitch purification by liquid chromatography.

Orthogonal Control of DNA Nanoswitches with Mixed Physical and Biochemical Cues

Nanoscale devices that can respond to external stimuli have potential applications in drug delivery, biosensing, and molecular computation. Construction using DNA has provided many such devices that can respond to cues such as nucleic acids, proteins, pH, light, or temperature. However, simultaneous control of molecular devices is still limited. Here, we present orthogonal control of DNA nanoswitches using physical (light) and biochemical (enzyme and nucleic acid) triggers. Each one of these triggers controls the reconfiguration of specific nanoswitches from locked to open states within a mixture and can be used in parallel to control a combination of nanoswitches. Such dynamic control over nanoscale devices allows the incorporation of tunable portions within larger structures as well as spatiotemporal control of DNA nanostructures.

Novel Modalities in DNA Data Storage

The field of storing information in DNA has expanded exponentially. Most common modalities involve encoding information from bits into synthesized nucleotides, storage in liquid or dry media, and decoding via sequencing. However, limitations to this paradigm include the cost of DNA synthesis and sequencing, along with low throughput. Further unresolved questions include the appropriate media of storage and the scalability of such approaches for commercial viability. In this review, we examine various storage modalities involving the use of DNA from a systems-level perspective. We compare novel methods that draw inspiration from molecular biology techniques that have been devised to overcome the difficulties posed by standard workflows and conceptualize potential applications that can arise from these advances.

DNA Nanoswitch Barcodes for Multiplexed Biomarker Profiling

Molecular biomarkers play a key role in the clinic, aiding in diagnostics and prognostics, and in the research laboratory, contributing to our basic understanding of diseases. Detecting multiple and diverse molecular biomarkers within a single accessible assay would have great utility, providing a more comprehensive picture for clinical evaluation and research, but is a challenge with standard methods. Here, we report programmable DNA nanoswitches for multiplexed detection of up to 6 biomarkers at once with each combination of biomarkers producing a unique barcode signature among 64 possibilities. As a defining feature of our method, we show "mixed multiplexing" for simultaneous barcoded detection of different types of biomolecules, for example, DNA, RNA, antibody, and protein in a single assay. To demonstrate clinical potential, we show multiplexed detection of a prostate cancer biomarker panel in serum that includes two microRNA sequences and prostate specific antigen.

Parallel poly(A) homo- and hetero-duplex formation detection with an adapted DNA nanoswitch technique

Polyriboadenylic [poly(rA)] strands of sufficient length form parallel double helices in acidic and/or ammonium-containing conditions. Poly(rA) duplexes in acidic conditions are held together by A⁺-A⁺ base-pairing also involving base interactions with the phosphate backbone. Traditional UV-melting studies of parallel poly(A) duplexes have typically examined homo-duplex formation of a single nucleic acid species in solution. We have adapted a technique utilizing a DNA nanoswitch that detects interaction of two different strands either with similar or differing lengths or modifications. Our method detected parallel duplex formation as a function of length, chemical modifications, and pH, and at a sensitivity that required over 100-fold less concentration of sample than prior UV-melting methods. While parallel polyriboadenylic acid and poly-2'-O-methyl-adenylic acid homo-duplexes formed, we did not detect homo-duplexes of polydeoxyriboadenylic acid strands or poly-locked nucleic acid (LNA)-adenylic strands. Importantly however, a poly-locked nucleic acid (LNA)-adenylic strand, as well as a poly-2'-O-methyl-adenylic strand, formed a hetero-duplex with a polyriboadenylic strand. Overall, our work validates a new tool for studying parallel duplexes and reveals fundamental properties of poly(A) parallel duplex formation. Parallel duplexes may find use in DNA nanotechnology and in molecular biology applications such as a potential poly(rA) tail capture tool as an alternative to traditional oligo(dT) based purification.

Ribonuclease-Responsive DNA Nanoswitches

DNA has been used in the construction of dynamic DNA devices that can reconfigure in the presence of external stimuli. These nanodevices have found uses in fields ranging from biomedical to materials science applications. Here, we report a DNA nanoswitch that can be reconfigured using ribonucleases (RNases) and explore two applications: biosensing and molecular computing. For biosensing, we show the detection of RNase H and other RNases in relevant biological fluids and temperatures, as well as inhibition by the known enzyme inhibitor kanamycin. For molecular computing, we show that RNases can be used to enable erasing, write protection, and erase-rewrite functionality for information-encoding DNA nanoswitches. The simplistic mix-and-read nature of the ribonuclease-activated DNA nanoswitches could facilitate their use in assays for identifying RNase contamination in biological samples or for the screening and characterization of RNase inhibitors.

Processing DNA-Based Molecular Signals into Graphical Displays

DNA is now well-established as a nanoscale building material with applications in fields such as biosensing and molecular computation. Molecular processes such as logic gates, nucleic acid circuits, and multiplexed detection have used different readout strategies to measure the output signal. In biosensing, this output can be the diagnosis of a disease biomarker, whereas in molecular computation, the output can be the result of a mathematical operation carried out using DNA. Recent developments have shown that the output of such processes can be displayed graphically as a macroscopic symbol or an alphanumeric character on multiwell plates, microarray chips, gels, lateral flow devices, and DNA origami surfaces. This review discusses the concepts behind such graphical readouts of molecular events, available display platforms, and the advantages and challenges in adapting such methods for practical use. Graphical display systems have the potential to be used in the creation of intelligent computing and sensing devices by which nanoscale binding events are translated into macroscopic visual readouts.

Dynamic and scalable DNA-based information storage

The physical architectures of information storage systems often dictate how information is encoded, databases are organized, and files are accessed. Here we show that a simple architecture comprised of a T7 promoter and a single-stranded overhang domain (ss-dsDNA), can unlock dynamic DNA-based information storage with powerful capabilities and advantages. The overhang provides a physical address for accessing specific DNA strands as well as implementing a range of in-storage file operations. It increases theoretical storage densities and capacities by expanding the encodable sequence space and simplifies the computational burden in designing sets of orthogonal file addresses. Meanwhile, the T7 promoter enables repeatable information access by transcribing information from DNA without destroying it. Furthermore, saturation mutagenesis around the T7 promoter and systematic analyses of environmental conditions reveal design criteria that can be used to optimize information access. This simple but powerful ss-dsDNA architecture lays the foundation for information storage with versatile capabilities.

The physical architectures of information storage dictate how data is encoded, organised and accessed. Here the authors use DNA with a single-strand overhang as a physical address to access specific data and do in-storage file operations in a scalable and reusuable manner.

Nanopore-Based DNA Hard Drives for Rewritable and Secure Data Storage

Nanopores are powerful single-molecule tools for label-free sensing of nanoscale molecules including DNA that can be used for building designed nanostructures and performing computations. Here, DNA hard drives (DNA-HDs) are introduced based on DNA nanotechnology and nanopore sensing as a rewritable molecular memory system, allowing for storing, operating, and reading data in the changeable three-dimensional structure of DNA. Writing and erasing data are significantly improved compared to previous molecular storage systems by employing controllable attachment and removal of molecules on a long double-stranded DNA. Data reading is achieved by detecting the single molecules at the millisecond time scale using nanopores. The DNA-HD also ensures secure data storage where the data can only be read after providing the correct physical molecular keys. Our approach allows for easy-writing and easy-reading, rewritable, and secure data storage toward a promising miniature scale integration for molecular data storage and computation.

DNA nanotechnology in the undergraduate laboratory: Analysis of molecular topology using DNA nanoswitches

There is a disconnect between the cutting-edge research done in academic labs, such as nanotechnology, and what is taught in undergraduate labs. In the current undergraduate curriculum, very few students get a chance to do hands-on experiments in nanotechnology-related experiments most of which are through selective undergraduate research programs. In most cases, complicated synthesis procedures, expensive reagents, and requirement of specific instrumentation prevent broad adaptation of nanotechnology-based experiments to laboratory courses. DNA, being a nanoscale molecule, has recently been used in bottom-up nanotechnology with applications in sensing, nano-robotics, and computing. In this article, we propose a simple experiment involving the synthesis of a DNA nanoswitch that can change its shape from a linear "off" state to a looped "on" state in the presence of a target DNA molecule. The experiment also demonstrates the programmable topology of the looped state of the nanoswitch and its effect on gel migration. The experiment is easy to adapt in an undergraduate laboratory, requires only agarose gel electrophoresis, a minimal set-up cost for materials, and can be completed in a 3-hour time frame.

DNA circuits driven by conformational changes in DNAzyme recognition arms

DNA computing plays an important role in nanotechnology due to the unique programmability and parallelism of DNA molecules. As an important tool to realize DNA computation, various logic computing devices have great application potential. The application of DNAzyme makes the achievements in the field of logical computing more diverse. In order to improve the efficiency of the logical units run by DNAzyme, we proposed a strategy to regulate the DNA circuit by the conformational change of the E6-type DNAzyme recognition arms driven by Mg2+. This strategy changes the single mode of DNAzyme signal transmission, extends the functions of E6-type DNAzyme, and saves the time of signal transmission in the molecular scale. To verify the feasibility of this strategy, first, we constructed DNA logic gates (YES, OR, and AND). Second, we cascade different logic gates (YES-YES, YES-AND) to prove the scalability. Finally, a self-catalytic DNA circuit is established. Through the experimental results, we verified that this DNAzyme regulation strategy relatively reduces the cost of logic circuits to some extent and significantly increases the reaction rate, and can also be used to indicate the range of Mg2+ concentrations. This research strategy provides new thinking for logical computing and explores new directions for detection and biosensors.

DNA logic circuits based on FokI enzyme regulation

A series of DNA logic devices was constructed based on the allosteric strategy of the enzyme-assisted cleavage regulation system, which are simple in scale, modular, and work efficiently.

Programmable DNA Nanoswitch Sensing with Solid-State Nanopores

Sensing performance of solid-state nanopores is limited by the fast kinetics of small molecular targets. To address this challenge, we translate the presence of a small target to a large conformational change of a long polymer. In this work, we explore the performance of solid-state nanopores for sensing the conformational states of molecular nanoswitches assembled using the principles of DNA origami. These programmable single-molecule switches show great potential in molecular diagnostics and long-term information storage. We investigate the translocation properties of linear and looped nanoswitch topologies using nanopores fabricated in thin membranes, ultimately comparing the performance of our nanopore platform for detecting the presence of a DNA analogue to a sequence found in a Zika virus biomarker gene with that of conventional gel electrophoresis. We found that our system provides a high-throughput method for quantifying several target concentrations within an order of magnitude by sensing only several hundred molecules using electronics of moderate bandwidth that are conventionally used in nanopore sensing systems.

Encrypted Oligonucleotide Arrays for Molecular Authentication

Counterfeiting is an incredibly widespread problem, with some estimates placing its economic impact above 2% of worldwide GDP. The scale of the issue suggests that current preventive measures are either technologically insufficient or too impractical and costly to be widely adopted. High-density arrays of biomolecules are explored here as security devices that can be coupled to a valuable commodity as proof of its authenticity. Light-directed DNA array fabrication technology is used to synthesize arrays that are designed to resist analysis with sequencing-by-hybridization approaches. A relatively simple sequence design strategy forces a counterfeiter to undertake a prohibitively high number of complex experiments to decipher the array sequences employed.

Entropy-driven DNA logic circuits regulated by DNAzyme

The catalytic DNA circuits play a critical role in engineered biological systems and molecular information processing. Actually, some of the natural or synthetic DNA circuits were triggered by covalent modifications, where conformational changes were induced to facilitate complex DNA engineering functions and signal transmissions. However, most of the reported artificial catalytic DNA circuits were regulated by the toehold-mediated reaction. Therefore, it is significant to propose a strategy to regulate the catalytic DNA circuit not only by the toehold-mediated mechanism, but also by involving the conformational changes induced by the covalent modification. In this study, we developed the catalytic DNA logic circuits regulated by DNAzyme. Here, a regulation strategy based on the covalent modification was proposed to control the DNA circuit, combing two reaction mechanisms: DNAzyme digestion and entropy-driven strand displacement. The DNAzyme and DNA catalyst can participate into the reactions alternatively, thus realizing the cascading catalytic circuits. Using the DNAzyme regulation, a series of logic gates (YES, OR and AND) were constructed. In addition, a two-layer cascading circuit and a feedback self-catalysis circuit were also established. The proposed DNAzyme-regulated strategy shows great potentials as a reliable and feasible method for constructing more complex catalytic DNA circuits.

Nucleic Acid Databases and Molecular-Scale Computing

DNA outperforms most conventional storage media in terms of information retention time, physical density, and volumetric coding capacity. Advances in synthesis and sequencing technologies have enabled implementations of large synthetic DNA databases with impressive storage capacity and reliable data recovery. Several robust DNA storage architectures featuring random access, error correction, and content rewritability have been constructed with the potential for scalability and cost reduction. We survey these recent achievements and discuss alternative routes for overcoming the hurdles of engineering practical DNA storage systems. We also review recent exciting work on in vivo DNA memory including intracellular recorders constructed by programmable genome editing tools. Besides information storage, DNA could serve as a versatile molecular computing substrate. We highlight several state-of-the-art DNA computing techniques such as strand displacement, localized hybridization chain reactions, and enzymatic reaction networks. We summarize how these simple primitives have facilitated rational designs and implementations of in vitro DNA reaction networks that emulate digital/analog circuits, artificial neural networks, or nonlinear dynamic systems. We envision these modular primitives could be strategically adapted for sophisticated database operations and massively parallel computations on DNA databases. We also highlight in vivo DNA computing modules such as CRISPR logic gates for building scalable genetic circuits in living cells. To conclude, we discuss various implications and challenges of DNA-based storage and computing, and we particularly encourage innovative work on bridging these two areas of research to further explore molecular parallelism and near-data processing. Such integrated molecular systems could lead to far-reaching applications in biocomputing, security, and medicine.

A Molecular Hero Suit for In Vitro and In Vivo DNA Nanostructures

Precise control of DNA base pairing has rapidly developed into a field full of diverse nanoscale structures and devices that are capable of automation, performing molecular analyses, mimicking enzymatic cascades, biosensing, and delivering drugs. This DNA-based platform has shown the potential of offering novel therapeutics and biomolecular analysis but will ultimately require clever modification to enrich or achieve the needed "properties" and make it whole. These modifications total what are categorized as the molecular hero suit of DNA nanotechnology. Like a hero, DNA nanostructures have the ability to put on a suit equipped with honing mechanisms, molecular flares, encapsulated cargoes, a protective body armor, and an evasive stealth mode.

Integration of a photocleavable element into DNA nanoswitches

Reconfigurable DNA nanostructures can be designed to respond to external stimuli such as nucleic acids, pH, small molecules and enzymes. In this study, we incorporated photocleavable linkers in DNA strands that trigger a conformational change in binary DNA nanoswitches. We demonstrate control of the output using UV light, with potential applications in biosensing and molecular computation.

pH-Operated Triplex DNA Device on MoS2 Nanosheets

We report a triplex-based DNA device coupled with molybdenum disulfide (MoS₂) nanosheets for use as a pH-sensing platform. The device transitions from a duplex state at pH 8 to a triplex state at pH 5. The interaction of the device with MoS₂ nanosheets in the two states is read out as a fluorescence signal from a pH-insensitive dye attached to the device. We characterized the operation of the DNA device on MoS₂ nanosheets, analyzed the pH response, and tested the reversibility of the system. Our strategy can lead to the creation of a suite of biosensors where the sensing element is a triplex DNA device and the signal response is modulated by inorganic nanomaterials.

Controlled disassembly of a DNA tetrahedron using strand displacement

In this study, we assembled a DNA tetrahedron containing single stranded extensions in the middle of the struts. Using these extensions as toeholds, the tetrahedron can be disassembled by nucleic acid triggers via strand displacement. The release mechanism is sequence specific, is functional in biological fluids such as serum and urine, and the kinetics of the disassembly process can be controlled by different molar ratios of the release strand. Such DNA nanostructures that respond to external stimuli have potential use in biosensing and drug delivery, and we demonstrate a proof-of-concept of this approach for microRNA detection.

Allosteric DNAzyme-based DNA logic circuit: operations and dynamic analysis

Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers. However, those regulations required to change the sequences of whole DNAzyme, as separating parts and inserting extra DNA sequence. Inspired by the allosteric regulation of proteins in nature, a new allosteric strategy is proposed to regulate the activity of DNAzyme without DNA sequences changes. In this strategy, DNA strand displacement was used to regulate the DNAzyme structure, through which the activity of DNAzyme was well controlled. The strategy was applied to E6-type DNAzymes, and the operations of DNA logic circuit (YES, OR, AND, cascading and feedback) were established and simulated with the dynamic analyses. The allosteric regulation has potential to construct more complicated molecular systems, which can be applied to bio-sensing and detection.

Digital Data Storage Using DNA Nanostructures and Solid-State Nanopores

Solid-state nanopores are powerful tools for reading the three-dimensional shape of molecules, allowing for the translation of molecular structure information into electric signals. Here, we show a high-resolution integrated nanopore system for identifying DNA nanostructures that has the capability of distinguishing attached short DNA hairpins with only a stem length difference of 8 bp along a DNA double strand named the DNA carrier. Using our platform, we can read up to 112 DNA hairpins with a separating distance of 114 bp attached on a DNA carrier that carries digital information. Our encoding strategy allows for the creation of a library of molecules with a size of up to 5 × 10³³ (2¹¹²) that is only built from a few hundred types of base molecules for data storage and has the potential to be extended by linking multiple DNA carriers. Our platform provides a nanopore- and DNA nanostructure-based data storage method with convenient access and the potential for miniature-scale integration.

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

A roadmap towards a functional paradigm for learning & memory in plants

In plants, the acquisition, processing and storage of empirical information can result in the modification of their behavior according to the nature of the stimulus, and yet this area of research remained relatively understudied until recently. As the body of evidence supporting the inclusion of plants among the higher organisms demonstrating the adaptations to accomplish these tasks keeps increasing, the resistance by traditional botanists and agricultural scientists, who were at first cautious in allowing the application of animal models onto plant physiology and development, subsides. However, the debate retains much of its heat, a good part of it originating from the controversial use of nervous system terms to describe plant processes. By focusing on the latest findings on the cellular and molecular mechanisms underlying the well established processes of Learning and Memory, recognizing what has been accomplished and what remains to be explored, and without seeking to bootstrap neuronal characteristics where none are to be found, a roadmap guiding towards a comprehensive paradigm for Learning and Memory in plants begins to emerge. Meanwhile the applications of the new field of Plant Gnosophysiology look as promising as ever.

Systematic Investigation of Two-Dimensional DNA Nanoassemblies for Construction of a Nonspecific Sensor Array

We have performed a systematic study to analyze the effect of ssDNA length, nucleobase composition, and the type of two-dimensional nanoparticles (2D-nps) on the desorption response of 36 two-dimensional nanoassemblies (2D-NAs) against several proteins. The studies were performed using fluorescently labeled polyA, polyC, and polyT with 23, 18, 12, and 7 nucleotide-long sequences. The results suggest that the ssDNAs with polyC and longer sequences are more resistant to desorption, compared to their counterparts. In addition, 2D-NAs assembled using WS₂ were least susceptible to desorption by the proteins tested, whereas nGO 2D-NAs were the most susceptible nanoassemblies. Later, the results of these systematic studies were used to construct a sensor array for discrimination of seven model proteins (BSA, lipase, alkaline phosphatase, acid phosphatase, protease, β-galactosidase, and Cytochrome c). Neither the ssDNAs nor the 2D-nps have any specific interaction with the proteins tested. Only the displacement of the ssDNAs from the 2D-np surface was measured upon the disruption of the existing forces within 2D-NAs. A customized sensor array with five 2D-NAs was developed as a result of a careful screening/filtering process. The sensor array was tested against 200 nM of protein targets, and each protein was discriminated successfully. The results suggest that the systematic studies performed using various ssDNAs and 2D-nps enabled the construction of a sensor array without a bind-and-release sensing mechanism. The studies also demonstrate the significance of systematic investigations in the construction of two-dimensional DNA nanoassemblies for functional studies.