A Contractile Electronic Switch Made of DNA

Huang, Yu Chuan; Sen, Dipankar

doi:10.1021/ja908508j

Cited by 53 publications

(56 citation statements)

References 38 publications

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“…By incorporating a DNA aptamer into the three-way junction elements, Huang et al 55 reported a rationally designed probe architecture for the detection and quantification of thrombin, which is a plasma protein. With the same design principle, Ge et al 56 designed a contractile DNA duplex probe that incorporated two short, separated motifs of G/G mismatches that were flanked by Watson-Crick base-paired DNA. The presence of K þ induced the transition of the duplex DNA to G-quadruplex and changed the charge-conducting properties of the DNA structure.…”

Section: Scaffolded Biosensors H Pei Et Almentioning

confidence: 99%

Scaffolded biosensors with designed DNA nanostructures

et al. 2013

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In addition to its fundamental function as a genetic code carrier, the utilization of DNA in various material applications has been actively explored over the past several decades. DNA is intrinsically an excellent type of self-assembly nanomaterial owing to its predictable base-pairing, high chemical stability and the convenience it possesses for synthesis and modification. Because of these unparalleled properties, DNA is widely used as excellent recognition elements in biosensors and as unique building blocks in nanodevices. A critical challenge in surface-based DNA biosensors lies in the reduced accessibility of target molecules to the DNA probes arranged on heterogeneous surfaces, especially when compared to probe-target recognition in homogeneous solutions. To improve the recognition abilities of these heterogeneous surface-confined DNA probes, much effort has been devoted to controlling the surface chemistry, conformation and packing density of the probe molecules, as well as the size and geometry of the surface. In this review, we aim to summarize the recent progress on the improvement of the probetarget recognition properties by introducing DNA nanostructure scaffolds. A range of new strategies have proven to provide a significantly enhanced range in the spatial positioning and the accessibility of the probes to the surface over previously reported linear structures. We will also describe the applications of DNA nanostructure scaffold-based biosensors. INTRODUCTIONDetection of nucleic acids (DNA or RNA) is an integral step in many applications, including in clinical diagnosis, environmental monitoring and antibioterrorism. 1 With these applications in mind, significant efforts have been made to develop sensitive, selective, rapid and cost-effective DNA (or RNA) biosensors. In parallel, DNAbased devices have also attracted a significant, recent interest owing to their promising applications in nanoelectronics, 2,3 biomolecular computations, 4-8 cellular imaging 9 and drug delivery. [10][11][12] In a typical design of DNA biosensors and nanodevices, oligonucleotides are often used as the molecular recognition layer. Because DNA is comprised of only four bases with A-T and G-C pairing, DNA hybridization processes are highly predictable and can be finely tuned with a rational design of the sequence. In addition, DNA oligonucleotides are usually easy to design, chemically stable and cost-effective.Understanding the physical structure of a DNA probe immobilized on a surface is critical in applications using DNA as a molecular recognition element. The properties of the DNA molecular recognition layer (such as selectivity, sensitivity and reproducibility) highly depend on the structure of the self-assembled DNA film. Modeling studies with thiolated DNA have demonstrated that efficient hybridization occurs in the well-controlled condition of surface-attached probes with large interprobe distances and upright conformations. [13][14][15][16][17][18][19][20][21][22][23][24]

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Section: Scaffolded Biosensors H Pei Et Almentioning

confidence: 99%

Scaffolded biosensors with designed DNA nanostructures

et al. 2013

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“…These non-canonical structures have been implicated in transcription regulation and telomere maintenance; hence, they are targeted for cancer treatment and detection23. Conversely, engineered G4 oligonucleotides can act as drug delivery vehicles456, materials for nanodevices78, support catalysts9 or even drugs for cancer, HIV and other diseases10. For these reasons, there is strong impetus to develop probes to improve our understanding of G4 and their ligand binding characteristics11.…”

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confidence: 99%

Discovery of a Structural-Element Specific G-Quadruplex “Light-Up” Probe

Zhang

Ghosh

et al. 2014

Sci Rep

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The development of a fluorescent probe capable of detecting and distinguishing the wide diversity of G-quadruplex structures is particularly challenging. Herein, we report a novel BODIPY-based fluorescent sensor (GQR) that shows unprecedented selectivity to parallel-stranded G-quadruplexes with exposed ends and four medium grooves. Mechanistic studies suggest that GQR associates with G-quadruplex grooves close to the end of the tetrad core, which may explain the dye's specificity to only a subset of parallel structures. This specific recognition favours the disaggregation of GQR in aqueous solutions thereby recovering the inherent fluorescence of the dye. Due to its unique features, GQR represents a valuable tool for basic biological research and the rapid discovery of novel, specific ligands that target similar structural features of G-quadruplexes.

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“…These bead-like structures are useful molecular scaffolds, self-assembling and self-folding in an ion-dependent manner into thermally stable nano-scaffolds (18). A host of nanotechnology applications have also been demonstrated which employ the G-quadruplex architecture, including catalysts (19–21), sensing devices (22), imaging agents (21–23) and molecular electronics systems (24,25). …”

Section: Introductionmentioning

confidence: 99%

Ball with hair: modular functionalization of highly stable G-quadruplex DNA nano-scaffolds through N2-guanine modification

Lech

Phan

2017

Nucleic Acids Research

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Functionalized nanoparticles have seen valuable applications, particularly in the delivery of therapeutic and diagnostic agents in biological systems. However, the manufacturing of such nano-scale systems with the consistency required for biological application can be challenging, as variation in size and shape have large influences in nanoparticle behavior in vivo. We report on the development of a versatile nano-scaffold based on the modular functionalization of a DNA G-quadruplex. DNA sequences are functionalized in a modular fashion using well-established phosphoramidite chemical synthesis with nucleotides containing modification of the amino (N2) position of the guanine base. In physiological conditions, these sequences fold into well-defined G-quadruplex structures. The resulting DNA nano-scaffolds are thermally stable, consistent in size, and functionalized in a manner that allows for control over the density and relative orientation of functional chemistries on the nano-scaffold surface. Various chemistries including small modifications (N2-methyl-guanine), bulky aromatic modifications (N2-benzyl-guanine), and long chain-like modifications (N2-6-amino-hexyl-guanine) are tested and are found to be generally compatible with G-quadruplex formation. Furthermore, these modifications stabilize the G-quadruplex scaffold by 2.0–13.3 °C per modification in the melting temperature, with concurrent modifications producing extremely stable nano-scaffolds. We demonstrate the potential of this approach by functionalizing nano-scaffolds for use within the biotin–avidin conjugation approach.

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A Contractile Electronic Switch Made of DNA

Cited by 53 publications

References 38 publications

Scaffolded biosensors with designed DNA nanostructures

Scaffolded biosensors with designed DNA nanostructures

Discovery of a Structural-Element Specific G-Quadruplex “Light-Up” Probe

Ball with hair: modular functionalization of highly stable G-quadruplex DNA nano-scaffolds through N2-guanine modification

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