Dnazyme Nanomachines
Dnazyme Nanomachines - Related Videos
07:16
DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition
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Cited by 3 •
2024
The DNAzyme-based nanomachines can be used for highly selective and sensitive detection of nucleic acids. This article describes a detailed protocol for the design of DNAzyme-based nanomachines with a 10-23 core using free software and their application in the detection of an Epstein-Barr virus fragment as an example.
13:20
Detection of Bacteria Using Fluorogenic DNAzymes
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Cited by 17 •
2012
We have recently reported a novel approach for generating fluorogenic DNAzyme probes that can be applied to set up a simple, "mix-and-read" fluorescent assay for bacterial detection. These special DNA probes catalyze the cleavage of a chromophore-modified DNA-RNA chimeric substrate in the presence of crude extracellular mixture (CEM) produced by a specific bacterium, thereby translating bacterial detection into fluorescence signal generation. In this report we will describe key experimental...
09:12
DNAzyme-dependent Analysis of rRNA 2’-O-Methylation
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2019
Here we present a protocol for DNAzyme-dependent cleavage of RNA. This enables fast and site-dependent analysis of RNA 2’-O-methylation. This approach can be used for the preliminary or major assessment of snoRNA activity.
03:04
Colorimetric Detection of a Bacterial Biomarker Using a Modified Litmus Test
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2025
This video demonstrates a colorimetric E. coli detection method, involving an E. coli biomarker activating a DNAzyme, leading to cleavage of RNA linkage and detachment of a DNAzyme-urease conjugate. A subsequent colorimetric assay detects the E. coli biomarker through ammonia-induced pH changes.
10:05
Colorimetric Detection of Bacteria Using Litmus Test
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Cited by 5 •
2016
We describe a protocol for colorimetric detection of E. coli using a modified litmus test that takes advantage of an RNA-cleaving DNAzyme, urease, and magnetic beads.
FAQs
Sequence recognition establishes which molecular target can activate a DNAzyme nanomachine, while substrate binding positions the reacting nucleic-acid strand for catalysis. These stages are functionally distinct: recognition supplies selectivity, binding organizes the reacting partners, and catalysis generates the chemical event. Together, they determine whether a molecular signal becomes a reliable downstream response.
Cleavage provides a chemical event that can be coupled to a larger nanoscale response. When the selected nucleic-acid substrate is cut, the resulting change can alter strand connections or molecular organization, producing movement, assembly, or a different molecular state. This coupling lets the device translate catalytic activity into an observable structural or mechanical consequence.
The DNAzyme first responds to a molecular signal through sequence recognition and substrate binding. Catalysis then changes the participating nucleic-acid structure, and that change can be designed to influence how components associate or rearrange. In this way, molecular chemistry supplies the trigger, while programmed nucleic-acid architecture determines whether the outcome is movement, assembly, or state switching.
Programmability allows recognition and catalytic activity to be connected with a selected mechanical or computational function. The sequence-dependent interaction determines which signal is addressed, whereas the associated structural arrangement determines how that reaction is expressed. This makes the platform useful for studying how biochemical events can be organized into controlled nanoscale actions rather than remaining isolated chemical reactions.
A useful design must coordinate the recognizing DNAzyme sequence, the nucleic-acid substrate, and the structural feature that produces the intended output. The signal must support substrate binding and catalysis, while the resulting chemical change must be connected to movement, assembly, or molecular-state switching. Considering these elements together links molecular selectivity with device behavior.
Researchers can examine whether a molecular signal leads to the expected catalytic event and whether that event produces a corresponding structural or mechanical change. Relevant outcomes include nucleic-acid cleavage, movement, assembly, or a shift in molecular state. These observations help connect biochemical recognition and catalysis with the nanomachine's functional response.
The platform supports biosensing and molecular diagnostics by linking recognition of a molecular signal to a controlled response. It is also relevant to targeted delivery and responsive therapeutics, where molecular conditions can be connected to changes in device behavior. These applications reflect the broader value of combining catalytic nucleic acids with programmable nanoscale organization.
They provide a compact way to investigate how molecular recognition and chemical catalysis can produce organized behavior at very small scales. By connecting cleavage or another catalytic event with movement, assembly, or state change, these systems make the relationship between reaction chemistry and molecular function easier to examine in a programmable framework.