Nascent Rna Folding
Nascent Rna Folding - Related Videos
06:46
Metabolic Labeling of the Nascent Transcriptome in Xenopus Early Embryogenesis
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2026
We provide detailed methods to metabolically label and purify nascent transcripts for transcriptome analysis in Xenopus early embryos using 5-ethynyl-uridine (5-EU).
10:15
Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA
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Cited by 2 •
2012
A technique to identify translational pause sites on mRNA is described. This procedure is based on isolation of nascent polypeptides accumulating on ribosomes during in vitro translation of a target mRNA, followed by the size analysis of the nascent chains using a denaturing gel electrophoresis.
08:26
Transcriptional Analysis by Nascent RNA FISH of In Vivo Trophoblast Giant Cells or In Vitro Short-term Cultures of Ectoplacental Cone Explants
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Cited by 2 •
2016
Trophoblast giant cells (TGCs) play a key role in the placenta to ensure a healthy pregnancy. We present a protocol for assessing the transcriptional status of genes in TGCs by nascent fluorescent in situ hybridization on cryostat sections of post-implantation embryos or short-term cultures of embryonic day 7 ectoplacental cones.
03:00
Molecular Chaperones and Protein Folding
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2020
The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein. The...
01:49
Protein Folding
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2020
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation which is critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.Protein Structure Is Critical to Its Biological FunctionProteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
FAQs
Timing creates a sequence-dependent folding pathway because only part of the transcript is available at any moment. As RNA emerges from RNA polymerase, newly exposed complementary bases can pair into stems and hairpins before downstream sequences appear. Consequently, the order in which segments become available can influence the structures that form and the molecule’s later behavior.
Transcription speed changes the amount of time available for emerging RNA segments to interact before additional sequence is produced. Faster or slower synthesis can therefore shift which complementary regions meet first and which secondary structures become established. In biochemical analysis, transcription rate should be considered alongside sequence because it can help explain differences in folding pathways and resulting RNA function.
Interactions with proteins or ligands can redirect the folding pathway while the RNA is still being synthesized. Their influence adds regulatory information beyond base complementarity and transcription timing, potentially changing which structures become accessible or stable. Considering these interactions helps explain how an emerging RNA can acquire biological activity that depends on its molecular environment.
Hairpins and stems provide early structural states that can affect how the emerging transcript continues to fold. Because their formation depends on complementary base pairing, sequence changes can alter the accessible structures and their timing. Those structural differences matter biochemically because RNA stability, molecular accessibility, and biological activity can all depend on the folding pathway.
Riboswitches illustrate how cotranscriptional folding can connect RNA structure with gene regulation. As the transcript emerges, its sequence-dependent structures may be influenced by ligand interactions, creating a regulatory element whose folding pathway affects biological activity. This makes riboswitches useful examples for examining how timing, molecular interactions, and RNA structure cooperate during transcription.
Biochemists can use this framework to interpret why an RNA may not reach the expected functional structure. Studying the emerging transcript links sequence, transcription speed, and protein or ligand interactions to folding behavior. That perspective supports analysis of RNA misfolding and can guide the design of functional RNAs whose stability, accessibility, or activity depends on controlled structure formation.