Thermostable Branched DNA Nanostructures as Modular Primers for Polymerase Chain Reaction

Hartman, Mark R.; Yang, Dayong; Tran, Thua N. N.; Lee, Kwang; Kahn, Jason S.; Kiatwuthinon, Pichamon; Yancey, Kenneth G.; Trotsenko, Oleksandr; Minko, Sergiy; Luo, Dan

doi:10.1002/anie.201302175

Cited by 78 publications

(73 citation statements)

References 39 publications

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“…68 Luo and coworkers reported thermostable branched DNA hydrogels combining psoralen crosslinking and branched DNA building blocks. 69 To accomplish this, branched DNA junctions were prepared by a double-stranded core region and single-stranded primer regions (Fig. 2A).…”

Section: Different Strategies For Developing Nucleic Acid-based Hymentioning

confidence: 99%

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

et al. 2016

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Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels.

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Section: Different Strategies For Developing Nucleic Acid-based Hymentioning

confidence: 99%

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

et al. 2016

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“…So far, signal amplification techniques such as Polymerase Chain Reaction (PCR) [17]. Rolling Circle Electronic supplementary material The online version of this article (doi:10.1007/s00604-015-1509-5) contains supplementary material, which is available to authorized users.…”

Section: Introductionmentioning

confidence: 99%

Aptamer biosensor for dopamine based on a gold electrode modified with carbon nanoparticles and thionine labeled gold nanoparticles as probe

Hun

Liu

et al. 2015

Microchim Acta

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We describe a biosensor for dopamine that is based on the use of a gold electrode modified with carbon nanoparticles (CNPs) coupled to thionine labeled gold nanoparticles (AuNPs) acting as signal amplifiers. The biosensor was constructed by first modifying the CNPs on the gold electrode and adsorbing the thionine on the surface of the AuNPs, and then linking the complementary strand of the dopamine aptamer to the AuNPs via gold-thiol chemistry. Next, dopamine aptamer is added and the duplex is formed on the surface. On addition of a sample containing dopamine, it will interact with aptamer and cause the release of the electrochemical probe which then will be adsorbed on the surface of the CNP-modified gold electrode and detected by differential pulse voltammetry. The current is linearly related to the concentration of dopamine in the 30 nM to 6.0 μM ranges. The detection limit is as low as 10 nM, and the RSD is 3.1 % at a 0.3 μM level (for n = 11). The protocol was successfully applied to the determination of dopamine in spiked human urine samples. We perceive that this method holds promise as a widely applicable platform for aptamerbased electrochemical detection of small molecules.

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“…The DNA backbone is unaltered, thus potentially leading to structural limitations, such as the fixed persistence length of double strands. Chemical linkers can change the chemical or structural behaviour of DNA nanostructures . They can, for instance, connect several linear oligonucleotides together and modify the structure of a design by acting as flexible hinges .…”

Section: Introductionmentioning

confidence: 99%

“…Chemical linkers can change the chemical or structuralb ehaviour of DNA nanostructures. [11][12][13][14][15] They can, for instance, connect several linear oligonucleotides together and modify the structure of ad esignb ya cting as flexible hinges. [16][17][18][19][20] The resulting DNA nanoconstructs can be more compact compared to DNA junction-and origami-basedd esigns.…”

Section: Introductionmentioning

confidence: 99%

Flexibility of C_3h‐Symmetrical Linkers in Tris‐oligonucleotide‐Based Tetrahedral Scaffolds

2015

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Flexibility of tris-oligonucleotides is determined by the length of their connecting hydrocarbon chains. Tris-oligonucleotides are branched DNA building blocks with three oligonucleotide arms attached to a C3h -symmetrical linker core at these chains. Four tris-oligonucleotides hybridise into a tetrahedral nanocage by sequence-determined self-assembly. The influence of methylene, ethylene and propylene chains was studied by synthesising sets of tris-oligonucleotides and analysing the relative stability of the hybridisation products against digestion by mung bean nuclease by using gel electrophoresis. Linkers with ethylene chains showed sufficient flexibility, whereas methylene-chain linkers were too rigid. Tris-oligonucleotides based on the latter still formed tetrahedral scaffolds in intermixing experiments with linkers of higher flexibility. Thus, a new generation of versatile isocyanurate-based linkers was established.

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Thermostable Branched DNA Nanostructures as Modular Primers for Polymerase Chain Reaction

Cited by 78 publications

References 39 publications

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

Aptamer biosensor for dopamine based on a gold electrode modified with carbon nanoparticles and thionine labeled gold nanoparticles as probe

Flexibility of C_3h‐Symmetrical Linkers in Tris‐oligonucleotide‐Based Tetrahedral Scaffolds

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Thermostable Branched DNA Nanostructures as Modular Primers for Polymerase Chain Reaction

Cited by 78 publications

References 39 publications

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

Aptamer biosensor for dopamine based on a gold electrode modified with carbon nanoparticles and thionine labeled gold nanoparticles as probe

Flexibility of C3h‐Symmetrical Linkers in Tris‐oligonucleotide‐Based Tetrahedral Scaffolds

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Flexibility of C_3h‐Symmetrical Linkers in Tris‐oligonucleotide‐Based Tetrahedral Scaffolds