Small Rna Ligation
Small Rna Ligation - Related Videos
11:00
A Model of Disturbed Flow-Induced Atherosclerosis in Mouse Carotid Artery by Partial Ligation and a Simple Method of RNA Isolation from Carotid Endothelium
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Cited by 83 •
2010
This describes a partial carotid ligation surgery, which causes disturbed flow conditions and subsequent atherosclerosis development (in two weeks) with intraplaque neo-vascularization (in four weeks) in the mouse common carotid artery. We also describe a novel method of RNA isolation from the carotid intima, providing high purity endothelial RNA.
07:34
DNA Ligation Reactions
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2023
In molecular biology, ligation refers to the joining of two DNA fragments through the formation of a phosphodiester bond. An enzyme known as a ligase catalyzes the ligation reaction. In the cell, ligases repair single and double strand breaks that occur during DNA replication. In the laboratory, DNA ligase is used during molecular cloning to join DNA fragments of inserts with vectors – carrier DNA molecules that will replicate target fragments in host organisms. This video provides an...
11:32
Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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Cited by 17 •
2017
Here, we detail the method of Sequencing of Psoralen crosslinked, Ligated, and Selected Hybrids (SPLASH), which enables genome-wide mapping of intramolecular and intermolecular RNA-RNA interactions in vivo. SPLASH can be applied to study RNA interactomes of organisms including yeast, bacteria and humans.
11:53
Cecal Ligation Puncture Procedure
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Cited by 200 •
2011
The mouse model of cecal ligation and puncture as a valuable tool for the study of human sepsis.
14:15
Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing
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Cited by 6 •
2014
MicroRNAs (miRNAs) are a widely conserved class of regulatory molecules. Here we describe a miRNA cloning method that relies upon two potent ligation steps followed by high-throughput sequencing. Our method permits accurate genome-wide quantitation of miRNAs.
FAQs
The key chemical requirement is pairing a compatible 5′ phosphate with a 3′ hydroxyl. RNA ligase uses these termini to catalyze phosphodiester bond formation, while ATP may support the reaction. This end dependence explains why substrate chemistry is a central experimental variable rather than a minor technical detail.
Small RNA ligation is sensitive to the chemical groups present at each RNA end. Different molecules may not ligate with equal efficiency when their 5′ phosphate or 3′ hydroxyl is incompatible with the reaction requirements. Researchers therefore evaluate end chemistry when interpreting uneven recovery or sequence-dependent differences in measured RNA abundance.
Adapter design has two linked consequences: it influences how efficiently particular RNA molecules are ligated, and it supplies primer-binding sites for later reverse transcription and amplification. Designs that interact differently with RNA sequences can introduce sequence-dependent bias, so adapter selection affects both library construction and the reliability of RNA diversity measurements.
ATP availability, buffer composition, and temperature are important controlled conditions for the ligation reaction. These factors work alongside RNA end compatibility to determine how efficiently adapters become attached. Maintaining an appropriate combination helps researchers obtain more consistent products for downstream reverse transcription, amplification, and small RNA analysis.
A typical workflow first exposes the small RNA molecules to adapter ligation under selected reaction conditions. The adapter-tagged products then provide primer-binding sites for reverse transcription, followed by amplification. This sequence converts otherwise short RNA molecules into analyzable products whose identities and relative abundance can be examined through sequencing-based analysis.
The approach supports profiling of microRNAs, siRNAs, and other regulatory RNAs. By attaching adapters that enable downstream processing, researchers can examine which small RNA species are present and compare their measured abundance. This makes the technique useful for studying regulatory RNA composition and diversity within biological samples.
Researchers reduce bias by optimizing adapter choices, RNA end compatibility, and reaction conditions rather than treating every RNA molecule as equally recoverable. Careful optimization can lessen sequence-dependent differences in ligation efficiency, improving estimates of RNA abundance and diversity. These controls are especially important when comparing multiple small RNA species in one analysis.