Rna-cleaving Dnazyme
Rna-cleaving Dnazyme - Related Videos
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...
01:23
RNA Interference
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2019
RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated. This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
01:32
RNA Splicing
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2019
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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.
02:53
Ribosomal RNA Synthesis
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2020
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells. Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
FAQs
The complementary binding arms recognize matching regions in the RNA substrate and help hold the target in a defined geometry. This positioning brings the RNA-containing junction into the catalytic core, where cleavage can occur. The arrangement links sequence recognition to catalytic activity, so changing the target sequence or arm design can alter which RNA is engaged.
Specificity depends not only on recognizing an RNA sequence but also on placing a susceptible ribonucleotide junction at the intended cutting site. When the arms position that junction within the core, cleavage can be directed to a selected location rather than occurring indiscriminately. This feature makes the approach useful for examining consequences of cutting particular RNA regions.
Divalent metal ions support the chemistry of phosphodiester-bond cleavage within the catalytic core. Their presence helps the DNAzyme promote cutting after the RNA substrate has been correctly positioned, connecting molecular recognition with catalytic output. Consequently, ion conditions are a key part of the system’s operating environment and can influence whether sequence recognition produces detectable cleavage.
A design begins with a single-stranded DNA molecule containing a catalytic core and complementary binding arms, together with an RNA substrate that presents the intended junction. The setup must also account for divalent metal ions, which support cleavage chemistry. Researchers can then evaluate whether recognition and positioning lead to cutting at the selected RNA site.
Biologists can use these molecules to investigate RNA function and gene regulation when they need sequence-selective cleavage without relying on a protein enzyme. Directing cleavage toward a chosen RNA sequence can help connect that RNA to a regulatory or functional outcome. The approach is therefore relevant to studies that ask how particular RNA molecules influence cellular biology.
In biosensor designs, target-RNA recognition can be converted into a measurable signal through the cleavage reaction, allowing molecular detection to be linked to catalytic activity. The same programmable specificity, compact design, and stability make RNA-cleaving DNAzymes candidates for therapeutic and diagnostic research. These uses extend the method beyond mechanistic RNA studies into signal generation and applied development.