We have now constructed a four-legged DNA walker based on toehold exchange reactions whose movement is controlled by alternating pH changes. A well-characterized, pH-responsive CG-C+ triplex was embedded into tetrameric catalytic hairpin assembly (CHA) walker. The proton-controlled could autonomously move otherwise unprogrammed microparticles surface, and the walking rate steps of were efficiently pH. starting stopping walker, its association dissociation from microparticles, also be...

Programmable and algorithmic behaviors of DNA molecules allow one to control the structures DNA-assembled materials with nanometer precision construct complex networks digital analog behaviors. Here we developed a way integrating DNA-strand-displacement circuit self-assembly spherical nucleic acids, wherein single strand was used initiate catalyze operation upstream circuits release that subsequently triggers acids in downstream circuits, realizing programmable kinetic acids. Through...

CRISPR/Cas9 genome-editing tools have tremendously boosted our capability of manipulating the eukaryotic genomes in biomedical research and innovative biotechnologies. However, current approaches that allow precise integration gene-sized large DNA fragments generally suffer from low efficiency high cost. Herein, we developed a versatile efficient approach, termed LOCK (Long dsDNA with 3'-Overhangs mediated CRISPR Knock-in), by utilizing specially designed 3'-overhang double-stranded (odsDNA)...

A new strategy for single-base polymorphism (SNP) detection based on the assembly of DNA-AuNPs (gold nanoparticles) driven by a DNA-fueled molecular machine, is established and optimized. It highly efficient, works at room temperature, easy to handle. change an oligonucleotide strand unambiguously discriminated either SNPs or insertions deletions (indels). The demonstrated detect mutation in breast cancer gene BRCA1 homogeneous solution temperature.

Toehold-mediated strand displacement reaction, the fundamental basis in dynamic DNA nanotechnology, has proven its extraordinary power programming molecular systems. Programmed activation of toehold a substrate is crucial for building sophisticated devices with digital and behaviors. Here we developed detachable circuit by embedding pH-controlled intermolecular triplex between branch migration domain traditional "linear substrate". The reaction rate "on/off" state can be regulated varying...

Saxitoxin is one of the most harmful paralytic shellfish toxins due to its high toxicity and adverse effects on environment human health. Aptasensors provide simple detection procedures because they have advantages chemical stability, easy synthesis modification, convenience in signal transformation. Surface-enhanced Raman scattering (SERS) an analytical technique that amplifies signals molecules at extremely low concentrations, or even single molecule level, when analyte very close rough...

Escape from metastable states in self-assembly of colloids is an intractable problem. Unlike the commonly adopted approach thermal annealing, recently developed enthalpy-mediated strategy provided a different option to address this dilemma dynamically controllable manner at room temperature. However, it required complex catalytic-assembly DNA strand-displacement circuitry mediate interaction between multiple components. In work, we present simple but effective way achieve DNA-functionalized...

Herein, a class of pH-responsive spherical nucleic acid (SNA) nanostructures prepared by functionalizing gold nanoparticles with DNA nanodevices is presented, which can perform duplex-to-triplex transition upon pH change via pH-sensitive parallel Hoogsteen interactions. The SNA exhibit tunable sensitivity and highly rapid reversible allosteric effect. Furthermore, they exactly image lysosomes in living cells. We next engineered pH-triggered doxorubicin(Dox)-SNA conjugates that could deliver...

This pH-responsive nanomachine can regulate the reaction rate of DNA–AuNPs assembly using pH in an efficient manner.

Significance We developed an enthalpy-mediated strategy to control dynamic pathways in colloidal assembly by working at constant temperature, which provides a different option circumvent metastability that normally causes disordered structures. Using this tractable approach allows bonding be programmed for synchronization with colloid assembly, thereby realizing the optimal programmability of DNA-functionalized colloids. Moreover, conversion identity can easily achieved using method, i.e.,...

Versatile building blocks are essential for complex and scaled-up DNA circuits. In this study, we propose a conceptually new scalable architecture called "junction substrate" (J-substrate) that is linked by prepurified double-stranded molecules. As proof-of-concept, novel type of substrate has been utilized to build multi-input circuits, offering several advantages over the conventional (referred as "linear substrate", L-substrate). First, J-substrate does not require long strands, thus...

The fabrication of DNA polymer brushes with spatial resolution onto a solid surface is crucial step for biochip research and related applications, cell‐free gene expression study, even artificial cell fabrication. Here, the first time, brush patterning method reported based on photoactivation an ortho‐nitrobenzyl linker‐embedded hairpin structure subsequent surface‐initiated hybridization chain reaction (HCR). Inert hairpins are exposed to ultraviolet light irradiation generate duplexes two...

The development of self-replicating systems is great importance in research on the origin life. As most iconic molecules, nucleic acids have provided prominent examples fabrication artificial nanostructures. However, it still challenging to construct sophisticated synthetic that can create large-scale or three-dimensionally ordered nanomaterials using By integrating a template system containing DNA-functionalized colloidal seeds with simplified DNA strand-displacement circuit programmed...

Background The DNA strand displacement reaction, which uses flexible and programmable molecules as reaction components, is the basis of dynamic nanotechnology, has been widely used in design complex autonomous behaviors. Results In this review, we first briefly introduce concept toehold‐mediated its kinetics regulation pure solution. Thereafter, review recent progresses circuit, assembly AuNPs driven by molecular machines, detection single nucleotide polymorphism (SNP) using toehold exchange...

Sophisticated dynamic molecular systems with diverse functions have been fabricated by using the fundamental tool of toehold-mediated strand displacement (TMSD) in field DNA nanotechnology. However, simple approaches to reset these TMSD-based are lacking due difficulty creating kinetically favored pathways implement backward resetting reactions. Here, we develop a facile proton-driven strategy achieve complete modular circuit integrating pH-responsive intermolecular CG-C+ triplex and an...

A design of DNA–gold nanoparticle probe-fueled DNA strand displacements for detecting single-base changes on the platform a quartz crystal microbalance with random sequences was developed.

Multi-module dCas9 engineering systems have been developed for controllable transcriptional manipulation such as chemical- or light-induced systems. However, there is still a need separate module that can be used internal control over the CRISPR-dCas9 system. Here, we describe multi-module system in which structured RNA was applied programmable component could dCas9-based gene regulation and achieved higher activation efficiency than dCas9-VPR traditionally used. By introducing microRNA...

In DNA dynamic nanotechnology, a toehold-mediated strand-displacement reaction has demonstrated its capability in building complex autonomous system. most cases, the is performed pure solution that essentially one-phase present work, we systematically investigated heterogeneous media, which strand implements displacing action conjugated on gold nanoparticles. By monitoring kinetics of spherical nucleic acid (SNA) assembly driven by displacement reaction, observed significant differences,...

The programmable toehold-mediated DNA-strand-displacement reaction has demonstrated its extraordinary capability in driving the spherical nucleic acid assembly. Here, a facile strategy of integrating DNA-strand-displacement-based DNA circuit with universal aggregate system was developed for visible disassembly acids. This integrated exhibited rapid colorimetric response and good sensitivity application single nucleotide polymorphism discrimination. Moreover, an OR logic gate used multiplex...

A new model using a gold nanoparticle (AuNP)-DNA system to constrain leakage and improve efficiency of catalytic toehold-mediated strand displacement reactions was outlined. 10-bp spacer on AuNPs fourfold amount fuels were determined for good performance this with an optimized toehold strategy. After the reaction at 25 °C 10 h, 258 pM target could be identified, which is remarkable improvement compared traditional AuNP-DNA without fuel. Moreover, also studied differentiate specific single...

Toehold-mediated strand displacement (TMSD) provides a versatile toolbox for developing DNA digital computing systems. Although different logic circuits with diverse functions have achieved good performance in terms of complexity and scalability, most previous perform information processing only at the molecular level, nonspecific signal leakages are often difficult to avoid. Here, we demonstrate feasibility constructing leakless systems three-dimensionally ordered colloidal supercrystals....

A DNA photonic nanowire with tunable FRET signals was fabricated on the basis of cascaded toehold-mediated strand displacement reactions. Different inputs were added to trigger reaction network, and corresponding obtained. Compared direct hybridization, this design is sensitive for 2 nM targets within 20 min also causes color changes solution blue-light excitation. It could be applied in live cells monitor MicroRNA a simple modification which might become low-cost method further application future.