Toehold‐Mediated Displacement of an Adenosine‐Binding Aptamer from a DNA Duplex by its Ligand

DNA is increasingly used to engineer dynamic nanoscale circuits, structures, and motors, many of which rely on DNA strand‐displacement reactions. The use of functional DNA sequences (e.g., aptamers, which bind to a wide range of ligands) in these reactions would potentially confer responsiveness on such devices, and integrate DNA computation with highly varied molecular stimuli. By using high‐throughput single‐molecule FRET methods, we compared the kinetics of a putative aptamer–ligand and aptamer–complement strand‐displacement reaction. We found that the ligands actively disrupted the DNA duplex in the presence of a DNA toehold in a similar manner to complementary DNA, with kinetic details specific to the aptamer structure, thus suggesting that the DNA strand‐displacement concept can be extended to functional DNA–ligand systems.     

Complex Reconfiguration of DNA Nanostructures

Nucleic acids have been used to create diverse synthetic structural and dynamic systems. Toehold‐mediated strand displacement has enabled the construction of sophisticated circuits, motors, and molecular computers. Yet it remains challenging to demonstrate complex structural reconfiguration in which a structure changes from a starting shape to another arbitrarily prescribed shape. To address this challenge, we have developed a general structural‐reconfiguration method that utilizes the modularly interconnected architecture of single‐stranded DNA tile and brick structures. The removal of one component strand reveals a newly exposed toehold on a neighboring strand, thus enabling us to remove regions of connected component strands without the need to modify the strands with predesigned external toeholds. By using this method, we reconfigured a two‐dimensional rectangular DNA canvas into diverse prescribed shapes. We also used this method to reconfigure a three‐dimensional DNA cuboid.     

Fuzzy DNA Strand Displacement: A Strategy to Decrease the Complexity of DNA Network Design

Toehold‐mediated DNA strand displacement endows DNA nanostructures with dynamic response capability. However, the complexity of sequence design dramatically increases as the size of the DNA network increases. We attribute this problem to the mechanism of toehold‐mediated strand displacement, termed exact strand displacement (ESD), in which one input strand corresponds to one specific substrate. In this work, we propose an alternative to toehold‐mediated DNA strand displacement, termed fuzzy strand displacement (FSD), in which one‐to‐many and many‐to‐one relationships are established between the input strand and the substrate, to reduce the complexity. We have constructed four modules, termed converter, reporter, fuzzy detector, and fuzzy trigger, and demonstrated that a sequence pattern recognition network composed of these modules requires less complex sequence design than an equivalent network based on toehold‐mediated DNA strand displacement.     

Antibody Activation using DNA‐Based Logic Gates

Oligonucleotide‐based molecular circuits offer the exciting possibility to introduce autonomous signal processing in biomedicine, synthetic biology, and molecular diagnostics. Here we introduce bivalent peptide–DNA conjugates as generic, noncovalent, and easily applicable molecular locks that allow the control of antibody activity using toehold‐mediated strand displacement reactions. Employing yeast as a cellular model system, reversible control of antibody targeting is demonstrated with low nM concentrations of peptide–DNA locks and oligonucleotide displacer strands. Introduction of two different toehold strands on the peptide–DNA lock allowed signal integration of two different inputs, yielding logic OR‐ and AND‐gates. The range of molecular inputs could be further extended to protein‐based triggers by using protein‐binding aptamers.     

Signal Propagation in Multi‐Layer DNAzyme Cascades Using Structured Chimeric Substrates

Signal propagation through enzyme cascades is a critical component of information processing in cellular systems. Although such systems have potential as biomolecular computing tools, rational design of synthetic protein networks remains infeasible. DNA strands with catalytic activity (DNAzymes) are an attractive alternative, enabling rational cascade design through predictable base‐pair hybridization principles. Multi‐layered DNAzyme signaling and logic cascades are now reported. Signaling between DNAzymes was achieved using a structured chimeric substrate (SCS) that releases a downstream activator after cleavage by an upstream DNAzyme. The SCS can be activated by various upstream DNAzymes, can be coupled to DNA strand‐displacement devices, and is highly resistant to interference from background DNA. This work enables the rational design of synthetic DNAzyme regulatory networks, with potential applications in biomolecular computing, biodetection, and autonomous theranostics.     

基于DNA链置换反应的新型固定化酶反应器制备及应用

建立了一种新型的酶固定化方法,采用DNA链置换反应成功地在单链DNA标记的磁性纳米粒子上实现了酶的链置换无损更替。该技术可实现目标酶的再利用,节约了生产成本。制备的固定化胰蛋白酶微反应器具有较好的重复利用性和高酶切效率,重复使用10次后仍可保持原酶活性的86%;利用链置换反应制备的MNPs@DNATrypsin酶切马心肌红蛋白5 min后,即可获得95%±0%(n=3)的氨基酸序列覆盖率,远超过相同条件下自由酶酶切12 h的结果。实验表明,发展的固定化酶技术具有高磁响应性,便于从反应体系中回收固定化酶和重复使用,同时此技术可显著提高酶活性,因此可用于固定各种重要的酶,同时可将其广泛应用于各种酶促反应中。     

Anomeric DNA Strand Displacement with α-D Oligonucleotides as Invaders and Ethidium Bromide as Fluorescence Sensor for Duplexes with α/β-, β/β- and α/α-D Configuration

DNA strand displacement is a technique to exchange one strand of a double stranded DNA by another strand (invader). It is an isothermal, enzyme free method driven by single stranded overhangs (toeholds) and is employed in DNA amplification, mismatch detection and nanotechnology. We discovered that anomeric (α/β) DNA can be used for heterochiral strand displacement. Homochiral DNA in β-D configuration was transformed to heterochiral DNA in α-D/β-D configuration and further to homochiral DNA with both strands in α-D configuration. Single stranded α-D DNA acts as invader. Herein, new anomeric displacement systems with and without toeholds were designed. Due to their resistance against enzymatic degradation, the systems are applicable to living cells. The light-up intercalator ethidium bromide is used as fluorescence sensor to follow the progress of displacement. Anomeric DNA displacement shows benefits over canonical DNA in view of toehold free displacement and simple detection by ethidium bromide.     

A Molecular Translator that Acts by Binding-Induced DNA Strand Displacement for a Homogeneous Protein Assay

Protein in, DNA out: A "binding-induced molecular translator" is able to convert an input target protein into an output DNA that can be readily detected and potentially be used to assemble DNA nanodevices. Successful molecular translation is mediated by binding-induced DNA assembly on a gold nanoparticle (AuNP) scaffold, thereby achieving efficient target-dependent strand displacement.     

Syntheses, structures and reactivities of designed analogues of cobalt(III)- bleomycinsz : Insight into the mechanism of sequence-specific DNA cleavage upon illumination

Three Co (III) complexes of a designed ligand PMAH that mimics the metal-binding domain of the antitumor antibioticbleomycin (BLM) have been isolated and structurally characterized. The coordination structures of the various forms of Co(III)-BLMs have been established on the basis of spectral similarities between these synthetic analogues and the corresponding Co(III)-BLMs. All three analogues, like Co(III)-BLMs, induce DNA strand scission upon UV illumination. Both DNA cleavage and spin trapping experiments demonstrate that UV irradiation of the analogues generates a C/N-based radical on the ligand framework which rapidly reacts with water to produce -OH radical near the DNA helix and causes strand scission. A similar mechanism could account for the photoactivity of the Co(III)-BLMs. Covalent attachment of DNA-binding groups to these analogues enhances the DNA-affinities and photocleavage efficiencies to a great extent. The hybrid analogues promote sequence-specific DNA photodamage at micromolar concentrations. The metallated cores of the hybrid analogues are the primary determinant of the observed sequence-specificity. Details of the mode of binding of the hybrid analogues to DNA have been explored by NMR techniques.     

Remote toehold: a mechanism for flexible control of DNA hybridization kinetics

Hybridization of DNA strands can be used to build molecular devices, and control of the kinetics of DNA hybridization is a crucial element in the design and construction of functional and autonomous devices. Toehold-mediated strand displacement has proved to be a powerful mechanism that allows programmable control of DNA hybridization. So far, attempts to control hybridization kinetics have mainly focused on the length and binding strength of toehold sequences. Here we show that insertion of a spacer between the toehold and displacement domains provides additional control: modulation of the nature and length of the spacer can be used to control strand-displacement rates over at least 3 orders of magnitude. We apply this mechanism to operate displacement reactions in potentially useful kinetic regimes: the kinetic proofreading and concentration-robust regimes.     

Lineal DNA logic gate for microRNA diagnostics with strand displacement and fluorescence resonance energy transfer

Designing molecular logic gates to operate programmably for molecular diagnostics in molecular computing still remains challenging. Here, we designed a novel linear DNA logic gates for microRNA analysis based on strand displacement and fluorescence resonance energy transfer (FRET). Two labeled strands closed each other produce to FRET through hybridization with a complementary strand to form a basic work unit of logic gate. Two indicators of heart failure (microRNA-195 and microRNA-21) were selected as the logic inputs and the fluorescence mode was used as the logic output. We have demonstrated that the molecular logic gate mechanism worked well with the construction of YES and AND gates.     

DNA‐Programmed Dynamic Assembly of Quantum Dots for Molecular Computation

Despite the widespread use of quantum dots (QDs) for biosensing and bioimaging, QD‐based bio‐interfaceable and reconfigurable molecular computing systems have not yet been realized. DNA‐programmed dynamic assembly of multi‐color QDs is presented for the construction of a new class of fluorescence resonance energy transfer (FRET)‐based QD computing systems. A complete set of seven elementary logic gates (OR, AND, NOR, NAND, INH, XOR, XNOR) are realized using a series of binary and ternary QD complexes operated by strand displacement reactions. The integration of different logic gates into a half‐adder circuit for molecular computation is also demonstrated. This strategy is quite versatile and straightforward for logical operations and would pave the way for QD‐biocomputing‐based intelligent molecular diagnostics.     

Label‐Free Logic Modules and Two‐Layer Cascade Based on Stem‐Loop Probes Containing a G‐Quadruplex Domain

A simple, versatile, and label‐free DNA computing strategy was designed by using toehold‐mediated strand displacement and stem‐loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two‐layer logic cascade were constructed. The probes contain a G‐quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light‐up fluorescent signal of G‐quadruplex/NMM complex was used as the output readout. The inputs are the disease‐specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label‐free and modular strategy might be adapted in multi‐target diagnosis through DNA hybridization and aptamer‐target interaction.     

A Reconfigurable DNA Accordion Rack

DNA nanostructure‐based mechanical systems that control the distance between elements of interest have demonstrated great potential for various applications, including nanoplasmonic systems, molecular reactors, and other nanotechnology platforms. However, previously reported systems could not collectively manipulate a 2D or 3D nanoscale network of elements to various forms in multiple stages. A reconfigurable DNA accordion rack structure is introduced that is a DNA beam lattice that changes its conformation with a small amount of short‐length DNA locks as the controlling input. The lattice shape of the 2D DNA accordion rack and the diameter and the height of the 3D DNA nanotubular structure made of the DNA accordion rack could be controlled. Furthermore, by sequentially repeating the detachment and the attachment of the different DNA locks using strand displacement, the shape reconfiguration was repeatedly carried out.     

Solving probability reasoning based on DNA strand displacement and probability modules

In computation biology, DNA strand displacement technology is used to simulate the computation process and has shown strong computing ability. Most researchers use it to solve logic problems, but it is only rarely used in probabilistic reasoning. To process probabilistic reasoning, a conditional probability derivation model and total probability model based on DNA strand displacement were established in this paper. The models were assessed through the game “read your mind.” It has been shown to enable the application of probabilistic reasoning in genetic diagnosis.     

Massively parallel display of genomic DNA fragments by rolling-circle amplification and strand displacement amplification on chip

Massively parallel genomic DNA fragments display on chip plays a key role in the new generation DNA sequencing. Here, we developed a new technology to display the parallel genomic DNA fragment massively based on two-step reaction with Ф29 DNA polymerase. The genomic DNA fragments were firstly amplified by rolling-circle amplification (RCA) reaction in liquid phase, and then amplified further on the chip by the strand displacement of Ф29 DNA polymerase. In our experiments, through DNA colonies produced by two-step amplification reaction T7 genomic DNA fragments are displayed massively and parallely on the chip, which has been verified through hybridizing the probe labeled with fluorescence or extension reaction with fluorescent-dNTP. The significant difference of fluourescence signals between background and displayed DNA fragments could be obtained. Our results show that the method has good reproducibility in experiments, which may be hopeful to serve the high-throughput sequencing.     

Photoresponsive DNA Nanocapsule Having an Open/Close System for Capture and Release of Nanomaterials

A photofunctionalized square bipyramidal DNA nanocapsule (NC) was designed and prepared for the creation of a nanomaterial carrier. Photocontrollable open/close system and toehold system were introduced into the NC for the inclusion and release of a gold nanoparticle (AuNP) by photoirradiation and strand displacement. The reversible open and closed states were examined by gel electrophoresis and atomic force microscopy (AFM), and the open behavior was directly observed by high‐speed AFM. The encapsulation of the DNA‐modified AuNP within the NC was carried out by hybridization of a specific DNA strand (capture strand), and the release of the AuNP was examined by addition of toehold‐containing complementary DNA strand (release strand). The release of the AuNP from the NC was achieved by the opening of the NC and subsequent strand displacement.     

Chemical approaches untangling sequence-specific DNA binding by proteins

Structure-based design of novel DNA-binding proteins provides an ultimate test of our understanding of protein-DNA interactions. A combination of synthetic, organic, biochemical and molecular biological approaches has been developed to study the principle of molecular recognition associated with the protein-DNA interactions. The strategies enabled a specific formation of noncovalent peptide dimers and determination of the preferential DNA-binding sequence of short peptides.