A DNA minimachine for selective and sensitive detection of DNA

Lyalina, Tatiana; Goncharova, Ekaterina A.; Prokofeva, Nadezhda Y; Ворошилина, Е. С.; Kolpashchikov, Dmitry M.

doi:10.1039/c8an02274g

Cited by 12 publications

(9 citation statements)

References 58 publications

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“…Recently, we have proposed an approach for direct detection of dsDNA amplicons using sophisticated hybridization probes that can force displacement of the complementary DNA strands. [35] However, this approach is applicable only for fluorescent probes with LOD down to 10 pM. LOD demonstrated by biPxD sensors is about 60 nM, [36] unless additional amplification steps are added.…”

Section: Resultsmentioning

confidence: 99%

“…At step 2, we converted a dsDNA amplicon into a ssDNA analyte to enable its efficient binding to the hybridization probes at the 3rd step. Recently, we have proposed an approach for direct detection of dsDNA amplicons using sophisticated hybridization probes that can force displacement of the complementary DNA strands [35] . However, this approach is applicable only for fluorescent probes with LOD down to 10 pM.…”

Section: Resultsmentioning

confidence: 99%

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Towards Point of Care Diagnostics: Visual Detection of Meningitis Pathogens Directly from Cerebrospinal Fluid

et al. 2020

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Rapid and cost‐efficient methods for diagnostics of infectious diseases can expedite prescription of adequate treatment, thus shortening the patients’ recovery and reducing adverse side effects. In this study, we developed a procedure for visual detection of bacterial pathogens Gram‐negative Neisseria meningitidis and Gram‐positive Streptococcus pneumoniae directly from human samples of cerebrospinal fluid (CSF). The assay uses hybridization probes that can efficiently recognize folded single‐stranded DNA analytes due to their split design. The assay includes the following stages: PCR amplification of N. meningitidis and S. pneumoniae targeted sequences; λ exonuclease treatment of the polymerase chain reaction (PCR) amplicons, and detection of the amplicons by hybridization probes with visual signal output. The assay requires 2.0 h with hands‐on time of about 40 min, and a regular PCR thermal cycler. It detects down to 10 bacteria in 2 μL of cerebrospinal fluid. The assay works for both gram‐positive and gram‐negative bacteria and does not require optimization of PCR conditions. This development creates a basis for the point‐of‐care diagnostics of bacterial meningitis with visual signal output.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Towards Point of Care Diagnostics: Visual Detection of Meningitis Pathogens Directly from Cerebrospinal Fluid

et al. 2020

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“…Strand Dz a is attracted to the association from solution in the presence of the analyzed DNA target. (D) Detection of HPV16 PCR amplicon by machine 2 or the correspondent BiDz probe . Panels C and D are adopted with permission from ref .…”

Section: Dna Machines For Nucleic Acid Analysismentioning

confidence: 99%

Section: Dna Machines For Nucleic Acid Analysismentioning

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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“…[23] Furthermore, attachment of several functional components to ac ommon DNA platform can positionm ultiple functional units in close proximity to each other and increases their cooperation in nucleic acid binding and detection. [24] Recently,w eu sed these principles to design an association of three DNA stands (T1, T2 and T3 in Scheme 3), which collectively constitute aD NA nanomachine with the following functions: [25] 1) The machine can recognize ac ancerm arker sequence (blue in Scheme 3);2 )bind and unwind secondary structure of targeted RNA using arms 1a nd 4; 3) recognize the cleavage site with high selectivity using arms 2a nd 3; and 4) cleave RNA by the RCDZ catalytic core. Such DNA constructions can be easily assembled by annealing the constituent DNA strands( e.g.,T 1, T2, and T3 in Scheme 3).…”

Section: Cancer-marker-dependent Activation Of Nucleic Acid Enzymesmentioning

confidence: 99%

Deoxyribozyme‐Based DNA Machines for Cancer Therapy

et al. 2019

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Soon after their discovery, RNA‐cleaving deoxyribozymes (RCDZ) were explored as anticancer gene therapy agents. Despite low toxicity found in clinical trials, there is no clinically significant anticancer RCDZ‐based therapy. Some of the reported disadvantages of RCDZ agents include poor accessibility to folded nucleic acids, low catalytic efficiency inside cells, and problems of intracellular delivery. On the other hand, structural DNA nanotechnology provides an opportunity to build multifunctional nano‐associations that can address some of these problems. Herein we discuss the possibility of building RCDZ‐based multifunctional DNA nanomachines equipped with RNA unwinding, cancer marker recognition, and RCDZ‐based RNA‐cleavage functions. An important advantage of such “nanomachines” is the possibility to cleave a housekeeping gene mRNA in a cancer‐cell‐specific manner. The proposed design could become a starting point for building sophisticated DNA‐based nanodevices for cancer treatment.

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A DNA minimachine for selective and sensitive detection of DNA

Abstract: Synthetic molecular machines have been explored to manipulate matter at the molecular level.

Cited by 12 publications

References 58 publications

Towards Point of Care Diagnostics: Visual Detection of Meningitis Pathogens Directly from Cerebrospinal Fluid

Towards Point of Care Diagnostics: Visual Detection of Meningitis Pathogens Directly from Cerebrospinal Fluid

Evolution of Hybridization Probes to DNA Machines and Robots

Deoxyribozyme‐Based DNA Machines for Cancer Therapy

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