A mutation-resistant deoxyribozyme OR gate for highly selective detection of viral nucleic acids

Kamar, Ola; Sun, Sin-Cih; Lin, Chih-Long; Chung, Wan-Yu; Lee, Min-Shi; Liao, Yu-Chieh; Kolpashchikov, Dmitry M.; Chuang, Min‐Chieh

doi:10.1039/c7cc05576e

Cited by 15 publications

(10 citation statements)

References 63 publications

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“…In 2017, Kamar et al designed an OR logic gate consisting of three DNAzyme‐specific biosensors, each of which had a binding site to the viral genome sequences (Figure 3b). [ 14 ] It could fluorescently report the presence of different types of enterovirus 71 (EV71), covering 90% of known EV71 mutation strains. Vijayakumar et al fused the complementary sequences of Lyssavirus to the structures of ribozymes and built a series of YES gates for Lyssavirus diagnosis (Figure 3c).…”

Section: Construction Of Dna Logic Gates As the Basic Computing Componentsmentioning

confidence: 99%

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DNA Computing: Principle, Construction, and Applications in Intelligent Diagnostics

Zhang

et al. 2021

Small Structures

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Demands on faster information processing speed and denser data storage are catalyzing new computation modes. DNA, as an important biomolecule that carries genetic information, has shown its potential in information processing and storage due to its predictable base pairings and nanoscale size for programmable and high‐throughput coding, as well as computing. More importantly, DNA also plays key biological roles, including regulating gene expression and monitoring biochemical reactions in the cells. When these capabilities are combined, the result is the development of new fields of DNA computing in biology and biomedicine. Herein, the most recent and important developments in DNA‐based computing for biomedical applications are presented, mainly from the perspective of biosensing related to diagnostics. The design and implementation of DNA computing systems from all stages in the pipeline are also discussed. The aim is to present DNA computing as a serious tool for intelligent diagnostics.

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Section: Construction Of Dna Logic Gates As the Basic Computing Componentsmentioning

confidence: 99%

Section: Construction Of Dna Logic Gates As the Basic Computing Componentsmentioning

confidence: 99%

DNA Computing: Principle, Construction, and Applications in Intelligent Diagnostics

Zhang

et al. 2021

Small Structures

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“…Multicomponent probes can also be designed to tolerate SNVs , or to detect a selected SNV, while being tolerant to other SNVs in the analyzed sequences . The latter is important to maintain binding affinity to highly mutagenic viral sequences.…”

Section: Addressing the Selectivity Issuementioning

confidence: 99%

Evolution of Hybridization Probes to DNA Machines and Robots

Kolpashchikov

2019

Acc. Chem. Res.

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Hybridization probes are RNA or DNA oligonucleotides or their analogs that bind to specific nucleotide sequences in targeted nucleic acids (analytes) via Watson−Crick base pairs to form probe−analyte hybrids. Formation of a stable hybrid would indicate the presence of a DNA or RNA fragment complementary to the known probe sequence. Some of the well-known technologies that rely on nucleic acid hybridization are TaqMan and molecular beacon (MB) probes, fluorescent in situ hybridization (FISH), polymerase chain reaction (PCR), antisense, siRNA, and CRISPR/cas9, among others. Although invaluable tools for DNA and RNA recognition, hybridization probes suffer from several common disadvantages including low selectivity under physiological conditions, low affinity to folded single-stranded RNA and double-stranded DNA, and high cost of dye-labeled and chemically modified probes. Hybridization probes are evolving into multifunctional molecular devices (dubbed here "multicomponent probes", "DNA machines", and "DNA robots") to satisfy complex and often contradictory requirements of modern biomedical applications. In the definition used here, "multicomponent probes" are DNA probes that use more than one oligonucleotide complementary to an analyzed sequence. A "DNA machine" is an association of a discrete number of DNA strands that undergoes structural rearrangements in response to the presence of a specific analyte. Unlike multicomponent probes, DNA machines unify several functional components in a single association even in the absence of a target. DNA robots are DNA machines equipped with computational (analytic) capabilities. This Account is devoted to an overview of the ongoing evolution of hybridization probes to DNA machines and robots. The Account starts with a brief excursion to historically significant and currently used instantaneous probes. The majority of the text is devoted to the design of (i) multicomponent probes and (ii) DNA machines for nucleic acid recognition and analysis. The fundamental advantage of both designs is their ability to simultaneously address multiple problems of RNA/DNA analysis. This is achieved by modular design, in which several specialized functional components are used simultaneously for recognition of RNA or DNA analytes. The Account is concluded with the analysis of perspectives for further evolution of DNA machines into DNA robots.

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“…Notably, the signal appears only in the presence of the DNA/RNA analyte species which are needed for assembling the catalytic BiDZ core. A BiDZ sensor was applied for molecular diagnostics of diseases [21][22][23]. The MaBiDZ system, which includes DNA-functionalized magnetic nanoparticles, was developed for the detection of a specific biomarker inside cancer cells.…”

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confidence: 99%

Towards Nanomaterials for Cancer Theranostics: A System of DNA-Modified Magnetic Nanoparticles for Detection and Suppression of RNA Marker in Cancer Cells

et al. 2019

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Theranostics of cancer using smart biocompatible materials can enable early cancer diagnostics and treatment. Here, we report on a DNA-nanoparticle functional material, which can simultaneously report the presence of an mRNA cancer biomarker and trigger its degradation in cultured cells. The nanodevice consists of two species of magnetic beads, each of which is conjugated with different components of a multicomponent deoxyribozyme (DZ) sensor. The system is activated only under two conditions: (i) in the presence of a specific target mRNA and (ii) when a magnetic field is applied. We demonstrate that delivery of such a system is markedly enhanced by the application of a magnetic field. The system not only fluorescently detects target mRNA in cultured MCF-7 cancer cells, but also induces its downregulation. Thus, the two-component magnetic nanoparticle system has characteristics of a material that can be used for cancer theranostics.

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A mutation-resistant deoxyribozyme OR gate for highly selective detection of viral nucleic acids

Cited by 15 publications

References 63 publications

DNA Computing: Principle, Construction, and Applications in Intelligent Diagnostics

DNA Computing: Principle, Construction, and Applications in Intelligent Diagnostics

Evolution of Hybridization Probes to DNA Machines and Robots

Towards Nanomaterials for Cancer Theranostics: A System of DNA-Modified Magnetic Nanoparticles for Detection and Suppression of RNA Marker in Cancer Cells

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