Reversibly switchable DNA nanocompartment on surfaces

Mao, Youdong; Luo, Chunxiong; Deng, Wei; Jin, Guangyin; Yu, Xiaomei; Zhang, Zhaohui; Ouyang, Qi; Chen, Runsheng; Yu, Dapeng

doi:10.1093/nar/gnh145

Cited by 19 publications

(23 citation statements)

References 30 publications

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“…If these devices can operate at a few-molecule level, they could eliminate the need for amplification techniques such as polymerase chain reaction (PCR). The ability to synthesize specific DNA sequences has also made it possible to form novel nanostructures from DNA oligonucleotides and composites [5][6][7][8]. These structures may have biotechnological applications but also have several promising materials applications.…”

Section: Introductionmentioning

confidence: 99%

Sequence specific electronic conduction through polyion-stabilized double-stranded DNA in nanoscale break junctions

Mahapatro¹,

Jeong²,

G³

et al. 2007

Nanotechnology

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This paper presents a study of sequence specific electronic conduction through short (15-base-pair) double-stranded (ds) DNA molecules, measured by immobilizing 3 -thiol-derivatized DNAs in nanometre scale gaps between gold electrodes. The polycation spermidine was used to stabilize the ds-DNA structure, allowing electrical measurements to be performed in a dry state. For specific sequences, the conductivity was observed to scale with the surface density of immobilized DNA, which can be controlled by the buffer concentration. A series of 15-base DNA oligonucleotide pairs, in which the centre sequence of five base pairs was changed from G:C to A:T pairs, has been studied. The conductivity per molecule is observed to decrease exponentially with the number of adjacent A:T pairs replacing G:C pairs, consistent with a barrier at the A:T sites. Conductance-based devices for short DNA sequences could provide sensing approaches with direct electrical readout, as well as label-free detection.

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Section: Introductionmentioning

confidence: 99%

Sequence specific electronic conduction through polyion-stabilized double-stranded DNA in nanoscale break junctions

Mahapatro¹,

Jeong²,

G³

et al. 2007

Nanotechnology

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“…DNA-based SAMs have been shown to be capable of producing reversible, well-defined nanometer-scale motions [210][211][212][213][214][215][216]. DNA molecules exhibit negative electric charges due to the phosphates in the sugar-phosphate backbone and, thus, DNA molecules immobilized on a conductive surface (e.g., gold) can be driven away from, or pulled toward the surface, depending on the electrode potential [213][214][215][216].…”

Section: Samsmentioning

confidence: 99%

“…DNA molecules exhibit negative electric charges due to the phosphates in the sugar-phosphate backbone and, thus, DNA molecules immobilized on a conductive surface (e.g., gold) can be driven away from, or pulled toward the surface, depending on the electrode potential [213][214][215][216]. At a negative electrical potential, the DNA molecules were shown to stand straight up on the surface, whereas at positive potentials the molecules lay flat [211,[213][214][215][216]. The appropriate surface coverage, in order to prevent steric interactions between neighboring strands, together with the strength of the electric field were key elements to realize electrically switchable surface-tethered DNA [211,[213][214][215][216].…”

Section: Samsmentioning

confidence: 99%

“…At a negative electrical potential, the DNA molecules were shown to stand straight up on the surface, whereas at positive potentials the molecules lay flat [211,[213][214][215][216]. The appropriate surface coverage, in order to prevent steric interactions between neighboring strands, together with the strength of the electric field were key elements to realize electrically switchable surface-tethered DNA [211,[213][214][215][216]. Based on the electrical manipulation of surface-confined DNA molecules, elegant methods to detect label-free oligonucleotide [55] and protein targets [217] have been recently developed.…”

Section: Samsmentioning

confidence: 99%

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Stimuli‐Responsive Surfaces in Biomedical Applications

Pranzetti¹,

Preece²,

Mendes³

2013

Intelligent Stimuli‐Responsive Materials

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Nature provides mechanisms that are able to dynamically control specific and nonspecific interactions between cells and biological surfaces [1,2]. Scientists have long tried to reproduce these dynamic biological events and have recently made an important step in that direction by creating artificial stimuli-responsive surfaces [3][4][5][6][7]. These smart substrates present modulatory surface properties that are able to respond to external chemical/biochemical [8][9][10][11][12], thermal [13][14][15], electrical [16][17][18][19][20], and optical stimuli [21][22][23][24][25][26][27][28][29][30][31]. Due to their dynamic nature such substrates are very appealing for applications in the biomedical field [32]. Progress to date has led to control over biomolecule activity [33] and immobilization of a diverse array of proteins, including enzymes [34] and antibodies [35]. These prior achievements have encouraged researchers to take the challenge of using dynamic surfaces to modulate larger and more complex systems, such as bacteria [36] and mammalian cells [37].Achieving control over surface properties could provide new insights in the understanding of cell behavior and can offer distinct benefits with regard to the development of medical devices. For instance, the modulation of cell attachment and detachment could lead to the prevention of unwanted bacteria fouling on implants, reducing the risk of infections and rejection [38][39][40][41][42]. Furthermore, dynamic surfaces able to present on demand regulatory signals to a cell could provide unprecedented opportunities in studies of cell responses in real-time. Cells in tissues adhere to and interact with their extracellular environment via specialized cell-cell and cell-extracellular

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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.…”

Section: Smart Surfaces Based On Dnamentioning

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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Reversibly switchable DNA nanocompartment on surfaces

Cited by 19 publications

References 30 publications

Sequence specific electronic conduction through polyion-stabilized double-stranded DNA in nanoscale break junctions

Sequence specific electronic conduction through polyion-stabilized double-stranded DNA in nanoscale break junctions

Stimuli‐Responsive Surfaces in Biomedical Applications

DNA-based switchable devices and materials

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