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After scanning and image analysis, the RNA abundance (amount of RNA molecules bound to the complementary probes on the microarray) is analysed and the relative gene expression of the treated sample can be compared to the untreated control.
These results indicated that the antisense oligonucleotides bound to the complementary region of the mRNA encoding β-lactamase, which catalyzes the hydrolysis of the β-lactam ring in the ampicillin molecule, and that the oligonucleotides inhibited translation of the bound mRNAs.
If we neglect some effects such as that secondary structures and cross-hybridization, and there is only specific binding between a given probe and its complimentary allelic strand, and between labeled tag and its corresponding probe, we can deduce that the amount of labeled tag-probe bound to the complementary immobilized allelic sequence is proportional to the fluorescence intensity.
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Hybridization-sensitive fluorescent DNA probes may serve as an effective and simple technology for tag labeling of nucleic acids, because they emit fluorescence only when they bind to the complementary sequences.
The siRNA-RISC complex then binds to the complementary target messenger RNA (mRNA).
ASOs specifically bind to the complementary region of mRNA, leading to enzymatic destruction of mRNA and ultimately to reduction in protein expression.
The gRNA contains 20 nucleotides targeted DNA sequence (known as spacer) that binds to the complementary strand of the target DNA by base-pairing and 79 nucleotides conserved sequence to form a specific hairpin-like fold.
The idea behind the analysis is that signal should be emitted only when the probe is bound to the target complementary fragment of nucleic acid.
However, the indicator strongly interacts with the negatively charged backbone of the complementary oligonucleotide bound to the PNA probe through electrostatic interactions.
A recent work on the impact of single base MMs in RNA-interference (RNAi) – allele-specific gene silencing experiments [ 2] – is interesting in the context of this study, since here the sequence recognition is based on base-pairing between the guide strand (a single RNA strand which is bound to the RISC complex) and a complementary mRNA.
If a gene is active, the RNA in the sample binds to the complementary gene fragment on the slide, and can be detected under ultraviolet light as a coloured dot.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com