Alternating-electric-field-enhanced reversible switching of DNA nanocontainers with pH

Mao, Youdong; Li, Dongsheng; Wang, Shutao; Luo, Songnian; Wang, Wenxing; Yang, Yanlian; Ouyang, Qi; Jiang, Lei

doi:10.1093/nar/gkl1161

Cited by 77 publications

(73 citation statements)

References 47 publications

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“…Among these, the electrochemical detection of DNA hybridization appears promising due to its rapid response time, low cost, and suitability for mass production. 11,12 The E-DNA sensor, [13][14][15][16] which is the electrochemical equivalent of an optical molecular beacon, [17][18][19][20] appears to be a particularly promising approach to oligonucleotide detection because it is rapid, reagentless, and operationally convenient. 21,22 The E-DNA sensor is comprised of a redox-modified "stem-loop" probe that is immobilized on the surface of a gold electrode via self-assembled monolayer chemistry.…”

Section: Introductionmentioning

confidence: 99%

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Effect of Molecular Crowding on the Response of an Electrochemical DNA Sensor

et al. 2007

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E-DNA sensors, the electrochemical equivalent of molecular beacons, appear to be a promising means of detecting oligonucleotides. E-DNA sensors are comprised of a redox-modified (here, methylene blue or ferrocene) DNA stem-loop covalently attached to an interrogating electrode. Because E-DNA signaling arises due to binding-induced changes in the conformation of the stemloop probe, it is likely sensitive to the nature of the molecular packing on the electrode surface. Here we detail the effects of probe density, target length, and other aspects of molecular crowding on the signaling properties, specificity, and response time of a model E-DNA sensor. We find that the highest signal suppression is obtained at the highest probe densities investigated, and that greater suppression is observed with longer and bulkier targets. In contrast, sensor equilibration time slows monotonically with increasing probe density, and the specificity of hybridization is not significantly affected. In addition to providing insight into the optimization of electrochemical DNA sensors, these results suggest that E-DNA signaling arises due to hybridization-linked changes in the rate, and thus efficiency, with which the redox moiety collides with the electrode and transfers electrons.

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Section: Introductionmentioning

confidence: 99%

“…Both E-DNA sensors [13][14][15][16] and related sensors based on the binding-induced folding of DNA aptamers [23][24][25][26][27][28] have been extensively studied in recent years. Nevertheless, key issues in their fabrication and use have not yet been explored in detail.…”

Section: Introductionmentioning

confidence: 99%

Effect of Molecular Crowding on the Response of an Electrochemical DNA Sensor

et al. 2007

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“…In 2004, Mao et al [30] proposed a reversibly switchable DNA nanocompartment on surfaces. In 2007, Mao et al [20] verified this proposition by conducting a series of experiments. They first started with a DNA monolayer possessing a folded four-stranded i-motif structure, which served as a nanocontainer and trapped small molecules (e.g.…”

Section: Smart Surfaces Based On Dnamentioning

confidence: 93%

“…DNA was also designed for the construction of molecular devices or machines that can generate nanoscale movement [15][16][17]. Besides static nanostructures, DNA could be applied to self-assembled structures [18,19] or integrated within other functional systems [20], utilizing properties of DNA such as specific recognition, chain-exchange reactions, specific enzyme reactions and secondary structure transformation to enable precise control of motion at the molecular level [19,21] or change properties at the macro scale [22]. Such responsive and switchable properties allow molecular machine-like devices to be built.…”

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confidence: 99%

DNA-based switchable devices and materials

2011

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Studies on DNA molecules have long been focused on its biological functions, since the discovery of the molecular structure of DNA by Watson and Crick [1] in 1953. DNA is known to be composed of adenine (A), guanine (G), cytosine (C) and thymine (T), and the Watson-Crick interaction of A-T and C-G base-pairing leads to the formation of the double-helix structure when sequences are complementary; this base-pairing process is also referred to as hybridization. Single-stranded DNA (ssDNA) is considered flexible, whereas double-stranded DNA (dsDNA) has a persistence length of about 50 nm. In the early 1980s [2], scientists started reconsidering the chemical composition of DNA, examining details such as chain structure, adjustable persistence length at the nanoscale, base-pair formation and programmable sequence. DNA quickly gained fresh recognition beyond strict biological roles and was rapidly introduced into the field of nanoscience as a new type of building block [3][4][5][6][7][8]. For example, DNA was used to fabricate nanostructures [9-14] from two-dimensional DNA nanostructures to three-dimensional curved nanostructures, as complex as spheres, ellipsoids, and flasks utilizing DNA origami techniques. DNA was also designed for the construction of molecular devices or machines that can generate nanoscale movement [15][16][17]. Besides static nanostructures, DNA could be applied to self-assembled structures [18,19] or integrated within other functional systems [20], utilizing properties of DNA such as specific recognition, chain-exchange reactions, specific enzyme reactions and secondary structure transformation to enable precise control of motion at the molecular level [19,21] or change properties at the macro scale [22]. Such responsive and switchable properties allow molecular machine-like devices to be built. [5,6] in the past several years. The present review focuses on DNA-based devices and smart materials that can respond to external stimuli, resulting in conformational changes to DNA structures at the nanoscale and detectable changes in properties such as volume, wettability at the macroscopic scale or transduction of force to move objects. This responsiveness is recoverable on removal of the external stimulus. DNA-based devices are introduced relating to smart surfaces and nanopores/nanochannels, while DNA-based smart materials are related to newly developed pure and hybrid DNA hydrogels. Figure 1 shows a typical example of a DNA device or motor. In 2003, Liu and Balasubramanian [19] proposed a pH-driven molecular motor system that is strong and swift. It comprises a 21mer ssDNA sequence X containing four stretches of three cytosines and a 17mer single-stranded DNA sequence Y, which is partially complementary to X. At pH 5, via the formation of C·CH+ base-pairs, sequence X folds into a compact 4-stranded i-motif structure with the 3' and 5' ends close to each other, representing the closed state of the motor. Changing the pH to 8 results in X unfolding and forming an extended DNA duplex structure XY, c...

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“…i-Motive können auch durch elektrochemische Stimuli effizient zwischen ihrem gefalteten und entfalteten Zustand hin-und hergeschaltet werden. [119] Unlängst wurden neuere Ausführungen i-Motiv-basierter Schalter konstruiert, bei denen die Strangbewegung auf zwei koaxial gestapelte DNA-Duplexe übertragen wird, was zu einer nanoskaligen Hebelbewegung zweiter Ordnung führt (Abbildung 9). [121,122] Eine Schlüsselentwicklung ist die erste Demonstration einer i-Motiv-Faltung und -Entfaltung als [107] B) Ein Oligonukleotid in Form eines G-Quadruplexes positioniert Liganden in einer zweizähnigen Weise, wodurch kooperatives Binden an das Zielprotein erreicht wird.…”

Section: I-motiv-schalterunclassified

Nukleinsäure‐basierte molekulare Werkzeuge

2011

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In der Biologie sind die Nukleinsäuren die Träger der molekularen Information: Die DNA‐Basensequenz speichert und vermittelt genetische Anweisungen, während die RNA‐Sequenz der Weitergabe der Information sowie der Regulation der Genexpression dient. Als Biopolymere haben Nukleinsäuren auch interessante physikochemische Eigenschaften, die sich darüber hinaus auf unzählige Weise über die Basensequenz rational verändern lassen. Es verwundert daher nicht, dass Nukleinsäuren in den letzten Jahren wichtige Bausteine für die Bottom‐up‐Nanotechnologie geworden sind: als Moleküle für die Selbstorganisation molekularer Nanostrukturen, aber auch als Material zum Aufbau maschinenähnlicher Nanobauteile. In diesem Aufsatz werden wir die wichtigsten Entwicklungen auf dem wachsenden Gebiet der Nukleinsäure‐Nanobauteile zusammenfassen. Wir werden auch einen Überblick über die biochemischen und biophysikalischen Hintergründe des Gebiets sowie über die “historischen” Einflüsse, von denen es geprägt wurde, geben. Besonderes Augenmerk wird molekularen DNA‐Motoren, der molekularen Robotik, der molekularen Datenverarbeitung sowie Anwendungen von Nukleinsäure‐Nanobauteilen in der Biologie gelten.

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Alternating-electric-field-enhanced reversible switching of DNA nanocontainers with pH

Cited by 77 publications

References 47 publications

Effect of Molecular Crowding on the Response of an Electrochemical DNA Sensor

Effect of Molecular Crowding on the Response of an Electrochemical DNA Sensor

DNA-based switchable devices and materials

Nukleinsäure‐basierte molekulare Werkzeuge

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