Rna Fragment Circularization
Rna Fragment Circularization - Related Videos
08:25
Identification of Circular RNAs using RNA Sequencing
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Cited by 30 •
2019
Circular RNAs (circRNAs) are non-coding RNAs that may have roles in transcriptional regulation and mediating interactions between proteins. Following assessment of different parameters for construction of circRNA sequencing libraries, a protocol was compiled utilizing stranded total RNA library preparation with RNase R pre-treatment and is presented here.
11:37
Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism
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Cited by 5 •
2017
This article provides a detailed procedure on the solid-phase synthesis, purification, and characterization of dodecamers of RNA modified at the C2'-O-position. UV-vis and circular dichroism photometric analyses are used to quantify and characterize structural aspects, i.e., single-strands or double-strands.
02:31
Habitat Fragmentation
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2020
Habitat fragmentation describes the division of a more extensive, continuous habitat into smaller, discontinuous areas. Human activities such as land conversion, as well as slower geological processes leading to changes in the physical environment, are the two leading causes of habitat fragmentation. The fragmentation process typically follows the same steps: perforation, dissection, fragmentation, shrinkage, and attrition. Perforation and dissection often occur during the initial stages of...
06:13
Electroeluting DNA Fragments
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Cited by 8 •
2010
This procedure allows the purification of DNA fragments with high yield.
09:20
Identification of RNA Fragments Resulting from Enzymatic Degradation using MALDI-TOF Mass Spectrometry
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Cited by 5 •
2022
MALDI-TOF was used to characterize fragments obtained from the reactivity between oxidized RNA and the exoribonuclease Xrn-1. The present protocol describes a methodology that can be applied to other processes involving RNA and/or DNA.
FAQs
Successful joining depends on compatible RNA termini: a 5′-phosphate and a 3′-hydroxyl. End preparation may therefore be necessary before ligation because the RNA ligase requires these chemical groups to form the covalent connection. This requirement makes end chemistry a key control point, since fragments with unsuitable ends are not expected to circularize efficiently.
A complementary splint brings the two RNA termini into proximity and supports their alignment for ligation. This positioning step helps the RNA ligase act on the intended ends rather than relying on random encounters in solution. In practice, splint design is therefore central to promoting the desired circular product from the selected fragment.
Exonuclease resistance can help enrich circular products relative to unwanted linear material and improve detection of sequences that span the circular junction. This is especially valuable when researchers examine low-abundance RNA species, because junction-spanning signals provide evidence that the analyzed molecule contains the joined termini rather than only an internal transcript segment.
A typical workflow prepares the RNA ends, combines the fragment with a complementary splint, and supplies an RNA ligase to join the compatible termini. Subsequent treatment can remove unreacted linear RNA and enrich the circular product. These steps connect chemical readiness, end alignment, ligation, and product cleanup into a focused molecular workflow.
Removing unreacted linear RNA reduces background from molecules that did not undergo the intended joining reaction. Enriching circular products makes downstream observations more attributable to the covalently closed species, including junction-spanning sequences. This cleanup is particularly relevant when the target RNA is scarce or when researchers need clearer evidence of transcript termini and circularization.
In genetics, circularized fragments support investigations of RNA processing, transcript boundaries, and circular RNA formation. The approach can also aid transcript sequence and structure analysis, while junction-spanning detection helps characterize low-abundance RNA species. Together, these applications connect the physical joining of RNA ends with questions about how genetic information is processed and represented in transcripts.