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1.
Chem Commun (Camb) ; 56(54): 7427-7430, 2020 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-32490866

RESUMO

Homogeneous DNA-only keypad locks were built with multi-stranded scalable junction substrates and a series of double-stranded eliminators to differentially process correctly- and wrongly-added DNA inputs, respectively. Unlike conventional strategies that employed solid-phase platforms, one-pot assay of multiple DNA inputs was achieved, showing merits in fabricating complicated information security systems.

2.
ACS Nano ; 2020 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-32579339

RESUMO

Toehold-mediated strand displacement reaction, the fundamental basis in dynamic DNA nanotechnology, has proven its extraordinary power in programming dynamic molecular systems. Programmed activation of the toehold in a DNA substrate is crucial for building sophisticated DNA devices with digital and dynamic behaviors. Here we developed a detachable DNA circuit by embedding a pH-controlled intermolecular triplex between the toehold and branch migration domain of the traditional "linear substrate". The reaction rate and the "on/off" state of the detachable circuit can be regulated by varying the pHs. Similarly, a two-input circuit composed of three pH-responsive DNA modules was then constructed. Most importantly, a resettable self-assembly system of spherical nucleic acids was built by utilizing the high detachability of the intermolecular triplex structure-based DNA circuit. This work demonstrated a dynamic DNA device that can be repeatedly operated at constant temperature without generating additional waste DNA products. Moreover, this strategy showed an example of recycling waste spherical nucleic acids from a self-assembly system of spherical nucleic acids. Our strategy will provide a facile approach for dynamic regulation of complex molecular systems and reprogrammable nanoparticle assembly structures.

3.
Proc Natl Acad Sci U S A ; 117(11): 5617-5623, 2020 03 17.
Artigo em Inglês | MEDLINE | ID: mdl-32132205

RESUMO

As a strategy for regulating entropy, thermal annealing is a commonly adopted approach for controlling dynamic pathways in colloid assembly. By coupling DNA strand-displacement circuits with DNA-functionalized colloid assembly, we developed an enthalpy-mediated strategy for achieving the same goal while working at a constant temperature. Using this tractable approach allows colloidal bonding to be programmed for synchronization with colloid assembly, thereby realizing the optimal programmability of DNA-functionalized colloids. We applied this strategy to conditionally activate colloid assembly and dynamically switch colloid identities by reconfiguring DNA molecular architectures, thereby achieving orderly structural transformations; leveraging the advantage of room-temperature assembly, we used this method to prepare a lattice of temperature-sensitive proteins and gold nanoparticles. This approach bridges two subfields: dynamic DNA nanotechnology and DNA-functionalized colloid programming.


Assuntos
DNA/química , Nanopartículas Metálicas/química , Polímeros Responsivos a Estímulos/química , Pareamento de Bases , Coloides/química , Ouro/química , Simulação de Dinâmica Molecular , Pressão , Conformação Proteica , Temperatura , Termodinâmica
4.
ACS Nano ; 14(4): 4007-4013, 2020 04 28.
Artigo em Inglês | MEDLINE | ID: mdl-32167282

RESUMO

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 DNA was embedded into a tetrameric catalytic hairpin assembly (CHA) walker. The proton-controlled walker could autonomously move on otherwise unprogrammed microparticles surface, and the walking rate and steps of walking were efficiently controlled by pH. The starting and stopping of the walker, and its association and dissociation from the microparticles, could also be dynamically controlled by pH. The simple, programmable, and robust nature of this proton-controlled walker now provides the impetus for the development of a wide variety of more practical nanomachines.

5.
Chem Commun (Camb) ; 55(77): 11615-11618, 2019 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-31501837

RESUMO

To date, implementation of renewable DNA circuits remains challenging due to issues including reactant depletion and waste accumulation. Herein we simultaneously addressed both issues through nicking enzyme-assisted waste-to-reactant transformation. As a proof-of-concept, a renewable entropy-driven catalytic DNA circuit was implemented, exhibiting a good renewability when replenishing fuel.


Assuntos
DNA Catalítico/química , Endonucleases/química , Redes Reguladoras de Genes , Pareamento Incorreto de Bases , Catálise , Entropia , Corantes Fluorescentes/química , Cinética , Conformação de Ácido Nucleico , Estudo de Prova de Conceito , Espectrometria de Fluorescência
6.
ACS Appl Mater Interfaces ; 11(22): 19724-19733, 2019 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-31083902

RESUMO

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 a DNA-strand-displacement-based DNA circuit with a universal spherical nucleic acid aggregate system was developed for the visible disassembly of spherical nucleic acids. This integrated system exhibited rapid colorimetric response and good sensitivity in the disassembly reaction and demonstrated its capability in the application of single nucleotide polymorphism discrimination. Moreover, an OR logic gate used for multiplex detection was constructed through combining the fixed spherical nucleic acid disassembly system with two DNA circuits. This strategy will have great potential in the fabrication of a portable low-cost DNA diagnostic kit, and it is also a very promising method to be used in other applications, such as complex DNA networks and programmable phase transformation of nanoparticle superlattices.


Assuntos
DNA Catalítico/química , Ácidos Nucleicos/química , Colorimetria , Polimorfismo de Nucleotídeo Único/genética
7.
Langmuir ; 34(49): 14811-14816, 2018 12 11.
Artigo em Inglês | MEDLINE | ID: mdl-30110553

RESUMO

The synthetic DNA hybridization probe has proved its importance in biology and biotechnology. In this study, taking advantage of a novel analytical technique called dual polarization interferometry (DPI), the influence of the toehold strategy of on-chip DNA hybridization probe on the discrimination of single nucleotide polymorphism (SNP) was investigated. Through adjusting the toehold length, the toehold strategies of on-chip toehold exchange probe were thoroughly optimized. For the "6/5" probe, an optimal discrimination factor of 78% against the spurious target was achieved. Moreover, the ability of the on-chip probe in SNP discrimination was significantly enhanced compared to its pure solution counterpart. This simple and rapid detection method for SNP discrimination based on the on-chip toehold exchange probe will show great potential in disease diagnosis.


Assuntos
Sondas de DNA/química , DNA/análise , Polimorfismo de Nucleotídeo Único , DNA/genética , Sondas de DNA/genética , Ácidos Nucleicos Imobilizados/química , Interferometria/instrumentação , Interferometria/métodos , Dispositivos Lab-On-A-Chip , Hibridização de Ácido Nucleico
8.
J Am Chem Soc ; 140(31): 9979-9985, 2018 08 08.
Artigo em Inglês | MEDLINE | ID: mdl-29999319

RESUMO

Versatile building blocks are essential for building complex and scaled-up DNA circuits. In this study, we propose a conceptually new scalable architecture called a "junction substrate" (J-substrate) that is linked by prepurified double-stranded DNA molecules. As a proof-of-concept, this novel type of substrate has been utilized to build multi-input DNA circuits, offering several advantages over the conventional substrate (referred to as a "linear substrate", L-substrate). First, the J-substrate does not require long DNA strands, thus avoiding significant synthetic errors and costs. Second, the traditional PAGE purification method is technically facilitated to obtain high-purity substrates, whereby the initial leakage is effectively eliminated. Third, the asymptotic leakage is eliminated by introducing the "junction". Finally, circuits with the optimized J-substrate architecture exhibit fast kinetics. We believe that the proposed architecture constitutes a sophisticated chassis for constructing complex circuits.


Assuntos
DNA/química , Eletroforese em Gel de Poliacrilamida , Estudo de Prova de Conceito
9.
Spectrochim Acta A Mol Biomol Spectrosc ; 204: 180-187, 2018 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-29933153

RESUMO

Aptamers could be used to construct simple and effective biosensor because the conformational switch of aptamer upon target binding is easy to be transferred to optical or electrochemical signals. Nevertheless, we found that the binding between saxitoxin (STX) and aptamer (M-30f) is not accompanied with conformational switch. Here, the circular dichroism spectra, fluorophore and quencher labeled aptamer, and crystal violet-based assays were used to identify the binding way between STX and aptamer. The results show that the conformation of aptamer is stabilized in PBS buffer (10 mM phosphate buffer, 2.7 mM KCl, 137 mM NaCl, pH 7.4) and this conformation may provide an exactly suitable cave for STX binding. Through the analysis of UV-melting curves and circular dichroism-melting curves, it is found that different concentrations of STX produce different unfolding extents of the aptamer under high temperature. Then, a simple temperature-assisted "turn-on" fluorescent aptasensor was developed to detect STX and the application in real sample detection demonstrates its feasibility. The proposed method provides not only an alternative for STX detection but also a strategy for simple aptasensor design using aptamers that do not switch conformation upon targets binding.


Assuntos
Aptâmeros de Nucleotídeos/metabolismo , Técnicas Biossensoriais/métodos , Corantes Fluorescentes/metabolismo , Saxitoxina/análise , Saxitoxina/metabolismo , Aptâmeros de Nucleotídeos/química , Corantes Fluorescentes/química , Limite de Detecção , Modelos Lineares , Reprodutibilidade dos Testes , Saxitoxina/química
10.
Chem Commun (Camb) ; 54(28): 3520-3523, 2018 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-29564423

RESUMO

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 nanostructures exhibit tunable pH sensitivity and a highly rapid and reversible allosteric effect. Furthermore, they can exactly image lysosomes in living cells. We next engineered pH-triggered doxorubicin(Dox)-SNA conjugates that could deliver Dox molecules into cancer cells and achieve pH-dependent drug release.


Assuntos
Antibióticos Antineoplásicos/química , DNA de Neoplasias/química , Doxorrubicina/química , Sistemas de Liberação de Medicamentos , Nanoestruturas/química , Ácidos Nucleicos/química , Imagem Óptica , Antibióticos Antineoplásicos/farmacologia , Sobrevivência Celular/efeitos dos fármacos , Relação Dose-Resposta a Droga , Doxorrubicina/farmacologia , Ensaios de Seleção de Medicamentos Antitumorais , Fluorescência , Ouro/química , Células HeLa , Humanos , Concentração de Íons de Hidrogênio , Lisossomos/química , Ácidos Nucleicos/farmacologia , Relação Estrutura-Atividade
11.
Chem Commun (Camb) ; 54(1): 106-109, 2017 Dec 19.
Artigo em Inglês | MEDLINE | ID: mdl-29214251

RESUMO

Herein, we designed and prepared a photoresponsive spherical nucleic acid (SNA) conjugate by inserting a photocleavable linker into the recognition sequence of SNA which can block the reactivity of the system temporally until specific UV light (∼365 nm) is introduced. The photoresponsive SNA realizes temporal regulation of a self-assembly reaction circuit and spatial selectivity of microRNA release in a cell population, respectively.


Assuntos
MicroRNAs/metabolismo , Ácidos Nucleicos/química , Carbocianinas/química , Clivagem do DNA/efeitos dos fármacos , Ouro/química , Humanos , Células MCF-7 , Nanopartículas Metálicas/química , Microscopia Confocal , Ácidos Nucleicos/metabolismo , Raios Ultravioleta
12.
Chem Commun (Camb) ; 53(79): 10950-10953, 2017 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-28933793

RESUMO

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. A 10-bp spacer on AuNPs and fourfold amount of fuels were determined for good performance of this model with an optimized toehold strategy. After the reaction at 25 °C for 10 h, a 258 pM target could be identified, which is a remarkable improvement compared with the traditional AuNP-DNA system without fuel. Moreover, this model was also studied to differentiate specific single nucleotide polymorphism on target with superior selection factors. This model may help by introducing a proposition of target detection to guide further investigation.


Assuntos
Técnicas Biossensoriais/métodos , DNA/análise , Ouro/química , Ácidos Nucleicos Imobilizados/química , Nanopartículas Metálicas/química , Nanotecnologia/métodos , Catálise , DNA/genética , Corantes Fluorescentes/química , Nanopartículas Metálicas/ultraestrutura , Polimorfismo de Nucleotídeo Único , Espectrometria de Fluorescência/métodos
13.
Nanoscale ; 9(9): 2981-2985, 2017 Mar 02.
Artigo em Inglês | MEDLINE | ID: mdl-28225119

RESUMO

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


Assuntos
DNA/química , Transferência Ressonante de Energia de Fluorescência , Nanofios , Hibridização de Ácido Nucleico , Fótons
14.
Chem Commun (Camb) ; 52(48): 7556-9, 2016 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-27225943

RESUMO

The toehold-mediated DNA-strand-displacement reaction has unique programmable properties for driving the catalytic assembly of gold nanoparticles (AuNPs). Herein, we introduced a pH-responsive triplex structure into the DNA-strand-displacement-based catalytic assembly system of DNA-AuNPs to add an additional controlling factor, namely the pH. In this catalytic system, the aggregation rate of AuNPs could be regulated by both internal factors (concentrations of substrate, target, etc.) and an external control (pH gradient). This strategy can be used to construct pH-induced DNA logic gates and sophisticated DNA networks as well as to image instantaneous pH changes in living cells.


Assuntos
DNA/química , Ouro/química , Nanopartículas Metálicas/química , Nanoestruturas/química , Catálise , Concentração de Íons de Hidrogênio
15.
Nanotechnology ; 26(42): 425601, 2015 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-26421440

RESUMO

In this work, two DNA nanodevices were constructed utilizing a DNA strand displacement reaction. With the assistance of gold nanoparticles (AuNPs) and gold nanorods (AuNRs), the autonomous reactions can be reflected from the aggregation states of nanoparticles. By sequence design and the two non-overlapping double hump-like UV-vis spectral peaks of AuNPs and AuNRs, two logic gates with multiple inputs and outputs were successfully run with expected outcomes. This method not only shows how to achieve computing with multiple logic calculations but also has great potential for multiple targets detection.


Assuntos
DNA/química , Ouro/química , Nanopartículas Metálicas/química , Nanotecnologia/métodos , Computadores Moleculares , Lógica
16.
J Am Chem Soc ; 137(44): 14107-13, 2015 Nov 11.
Artigo em Inglês | MEDLINE | ID: mdl-26485090

RESUMO

Programmable and algorithmic behaviors of DNA molecules allow one to control the structures of DNA-assembled materials with nanometer precision and to construct complex networks with digital and analog behaviors. Here we developed a way of integrating a DNA-strand-displacement circuit with self-assembly of spherical nucleic acids, wherein a single DNA strand was used to initiate and catalyze the operation of upstream circuits to release a single strand that subsequently triggers self-assembly of spherical nucleic acids in downstream circuits, realizing a programmable kinetic control of self-assembly of spherical nucleic acids. Through utilizing this method, single-nucleotide polymorphisms or indels occurring at different positions of a sequence of oligonucleotide were unambiguously discriminated. We provide here a sophisticated way of combining the DNA-strand-displacement-based characteristic of DNA with the distinct assembly properties of inorganic nanoparticles, which may find broad potential applications in the fabrication of a wide range of complex multicomponent devices and architectures.


Assuntos
DNA de Cadeia Simples/química , Conformação de Ácido Nucleico , Algoritmos , DNA de Cadeia Simples/síntese química , Humanos , Cinética , Polimorfismo de Nucleotídeo Único
17.
Small ; 11(43): 5800-6, 2015 Nov 18.
Artigo em Inglês | MEDLINE | ID: mdl-26382921

RESUMO

The fabrication of DNA polymer brushes with spatial resolution onto a solid surface is a crucial step for biochip research and related applications, cell-free gene expression study, and even artificial cell fabrication. Here, for the first time, a DNA polymer brush patterning method is reported based on the photoactivation of an ortho-nitrobenzyl linker-embedded DNA hairpin structure and a subsequent surface-initiated DNA hybridization chain reaction (HCR). Inert DNA hairpins are exposed to ultraviolet light irradiation to generate DNA duplexes with two active sticky ends (toeholds) in a programmable manner. These activated DNA duplexes can initiate DNA HCR to generate multifunctional patterned DNA polymer brushes with complex geometrical shapes. Different multifunctional DNA polymer brush patterns can be fabricated on certain areas of the same solid surface using this method. Moreover, the patterned DNA brush surface can be used to capture target molecules in a desired manner.


Assuntos
Sondas de DNA/síntese química , DNA/química , Hibridização In Situ/métodos , Impressão Molecular/métodos , Polímeros/química , Adsorção , DNA/genética , DNA/efeitos da radiação , Sondas de DNA/genética , Sondas de DNA/efeitos da radiação , Luz , Teste de Materiais , Fotoquímica/métodos , Propriedades de Superfície/efeitos da radiação
18.
Langmuir ; 31(25): 7055-61, 2015 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-26057346

RESUMO

In DNA dynamic nanotechnology, a toehold-mediated DNA strand-displacement reaction has demonstrated its capability in building complex autonomous system. In most cases, the reaction is performed in pure DNA solution that is essentially a one-phase system. In the present work, we systematically investigated the reaction in a heterogeneous media, in which the strand that implements a displacing action is conjugated on gold nanoparticles. By monitoring the kinetics of spherical nucleic acid (SNA) assembly driven by toehold-mediated strand displacement reaction, we observed significant differences, i.e., the abrupt jump in behavior of an "off/on switch", in the reaction rate when the invading toehold was extended to eight bases from seven bases. These phenomena are attributed to the effect of steric hindrance arising from the high density of invading strand conjugated to AuNPs. Based on these studies, an INHIBIT logic gate presenting good selectivity was developed.


Assuntos
DNA/química , Ouro/química , Nanopartículas Metálicas/química , Nanotecnologia/métodos , Computadores Moleculares , Cinética , Lógica , Prata/análise , Propriedades de Superfície
19.
Chem Commun (Camb) ; 51(22): 4670-3, 2015 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-25690314

RESUMO

A design of DNA-gold nanoparticle probe-fueled DNA strand displacements for detecting single-base changes on the platform of a quartz crystal microbalance with random sequences was developed. After optimizing and testing the detection system, it has been successfully applied to detect mutation of a realistic sequence associated with human cancer, thereby indicating that this method has potential applicability in general.


Assuntos
Técnicas Biossensoriais , Sondas de DNA/química , DNA/química , Ouro/química , Nanopartículas Metálicas/química , Técnicas de Microbalança de Cristal de Quartzo , Análise Mutacional de DNA , Humanos , Mutação
20.
Adv Mater ; 26(35): 6181-5, 2014 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-25066311

RESUMO

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 is highly efficient, works at room temperature, and is easy to handle. A single-base change on an oligonucleotide strand is unambiguously discriminated for either SNPs or insertions and deletions (indels). The strategy is demonstrated to detect a mutation in the breast cancer gene BRCA1 in homogeneous solution at room temperature.


Assuntos
DNA/química , Ouro/química , Nanopartículas Metálicas/química , Proteína BRCA1/genética , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Catálise , Feminino , Genótipo , Humanos , Polimorfismo de Nucleotídeo Único , Espectrofotometria Ultravioleta
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