Stem-loop Unfolding
Stem-loop Unfolding - Related Videos
01:37
The Unfolded Protein Response
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2023
The ER is the hub of protein synthesis in a cell. It has robust systems to quality control protein folding and also for degradation of terminally misfolded proteins. Under normal conditions, a small proportion of misfolded proteins that cannot be salvaged need to be transported to the cytoplasm by the ER-associated degradation or ERAD pathways. However, if the ERAD cannot handle the misfolded proteins, the cell activates the unfolded protein response or UPR to adjust the protein folding...
09:48
Neural Activity Propagation in an Unfolded Hippocampal Preparation with a Penetrating Micro-electrode Array
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Cited by 2 •
2015
We have developed an in vitro unfolded hippocampus which preserves CA1-CA3 array of neurons. Combined with the penetrating micro-electrode array, neural activity can be monitored in both the longitudinal and transverse orientations. This method provides advantages over hippocampal slice preparations as the propagation in the entire hippocampus can be recorded simultaneously.
02:38
Assessing Bacterial Chaperone Activity via Thermal Unfolding of a Model Protein
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2025
Source: Dahl, J. et al. Detection of the pH-dependent Activity of Escherichia coli Chaperone HdeB In Vitro and In Vivo. J. Vis. Exp. (2016)This video demonstrates a fluorescence spectrophotometer-based assay to evaluate chaperone activity on a substrate protein under acid and heat stress. It outlines the steps for monitoring substrate unfolding and aggregation through light scattering, comparing conditions with and without the chaperone.
03:25
Recording Neural Activity of Unfolded Hippocampal Tissue Using Penetrating Microelectrode Array
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2025
This video demonstrates the procedure to set up a recording chamber with a penetrating microelectrode array (PMEA) to capture neural signals from an unfolded hippocampus. This method allows us to study the speed and direction of propagation of neural activity within the unfolded hippocampus in vitro.
01:31
Regulation of the Unfolded Protein Response
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2023
Inositol-requiring kinase one or IRE1 is the most conserved eukaryotic unfolded protein response (UPR) receptor. It is a type I transmembrane protein kinase receptor with a distinctive site-specific RNase activity. As the binding mechanics of the misfolded proteins with the N-terminal domain of IRE-1 are unclear, three binding models — direct, indirect, and allosteric -- are proposed for receptor activation. Nevertheless, it is known that once a misfolded protein associates with IRE1, it...
FAQs
Stem-loop unfolding can be driven by heat, chemical conditions, mechanical force, or proteins such as helicases. These influences destabilize the base pairing that holds the paired regions together. As those interactions are disrupted, the nucleic acid can shift from a compact hairpin arrangement toward a more extended conformation, linking environmental or molecular inputs to structural change.
The stem’s paired regions provide the structural constraint that maintains the hairpin. When their base pairing becomes sufficiently destabilized, the strand can no longer retain the same compact arrangement and begins to extend. Studying this transition helps connect nucleic acid structure with changes in behavior, including effects on translation, transcription, splicing, and molecular recognition.
Heat, chemical conditions, and mechanical force act as external destabilizing influences, whereas a helicase is a protein-based factor that can promote separation of paired regions. Comparing these triggers helps researchers distinguish whether a structural transition reflects environmental conditions or active molecular intervention. That distinction is useful when interpreting nucleic acid regulation and designing assays that examine controlled unfolding.
Two central outcomes are folding stability and structural transitions. Folding stability indicates how well the hairpin arrangement persists, while a structural transition records movement toward a less paired, more extended state. Single-molecule assays are relevant because they can examine these changes at the level of individual nucleic acid molecules, complementing broader experimental analysis.
Unfolding studies provide information about how nucleic acid structures respond when their base pairing is destabilized. That information can guide the use of structural changes in biosensors and nucleic acid probes, where a conformational response is useful. The same measurements support single-molecule assay design by linking observed signals to folding stability and structural transitions.
Because hairpin structure can change, unfolding studies help explain how RNA structure participates in translation, transcription, splicing, and molecular recognition. The biological value lies not only in observing strand extension, but also in relating a structural transition to regulation or interaction. This makes the topic relevant to questions about how nucleic acid conformation influences cellular processes.
Experimental analysis can connect changes in hairpin stability or structure with biological functions attributed to RNA conformation. By examining how paired regions separate under different influences, researchers can investigate structural contributions to translation, transcription, splicing, and molecular recognition. These observations provide a framework for relating physical unfolding events to broader regulatory behavior in biology.