Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers
Pre-miRNA-377 is a hairpin-shaped regulatory RNA associated with heart failure. Here, we use single-molecule optical tweezers to unzip pre-miRNA-377 and study its stability and dynamics. We show that magnesium ions have a strong stabilizing effect, and that sodium ions stabilize the hairpin more tha...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/16/9008 |
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| author | Anna Wypijewska del Nogal Vinoth Sundar Rajan Fredrik Westerlund L. Marcus Wilhelmsson |
| author_facet | Anna Wypijewska del Nogal Vinoth Sundar Rajan Fredrik Westerlund L. Marcus Wilhelmsson |
| author_sort | Anna Wypijewska del Nogal |
| collection | DOAJ |
| description | Pre-miRNA-377 is a hairpin-shaped regulatory RNA associated with heart failure. Here, we use single-molecule optical tweezers to unzip pre-miRNA-377 and study its stability and dynamics. We show that magnesium ions have a strong stabilizing effect, and that sodium ions stabilize the hairpin more than potassium ions. The hairpin unfolds in a single step, regardless of buffer composition. Interestingly, hairpin folding occurs either in a single step (type 1) or through the formation of intermediates, in multiple steps (type 2) or gradually (type 3). Type 3 occurs only in the presence of both sodium and magnesium, while type 1 and 2 take place in all buffers, with type 1 being the most prevalent. By reducing the size of the native hairpin loop from fourteen to four nucleotides, we demonstrate that the folding heterogeneity originates from the large size of the hairpin loop. Further, while efficient pre-miRNA-377 binders are lacking, we demonstrate that the recently developed C2 ligand displays bimodal activity: it enhances the mechanical stability of the pre-miRNA-377 hairpin and perturbs its folding. The knowledge regarding pre-miRNA stability and dynamics that we provide is important in understanding its regulatory function and how it can be modulated to achieve a therapeutic effect, e.g., in heart failure treatment. |
| first_indexed | 2024-03-10T08:43:48Z |
| format | Article |
| id | doaj.art-4eabb0c60e764564b19a2b3e2d50b101 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T08:43:48Z |
| publishDate | 2021-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-4eabb0c60e764564b19a2b3e2d50b1012023-11-22T08:03:59ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-08-012216900810.3390/ijms22169008Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical TweezersAnna Wypijewska del Nogal0Vinoth Sundar Rajan1Fredrik Westerlund2L. Marcus Wilhelmsson3Division of Chemistry and Biochemistry, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, SwedenDivision of Chemistry and Biochemistry, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, SwedenDivision of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, SwedenDivision of Chemistry and Biochemistry, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, SwedenPre-miRNA-377 is a hairpin-shaped regulatory RNA associated with heart failure. Here, we use single-molecule optical tweezers to unzip pre-miRNA-377 and study its stability and dynamics. We show that magnesium ions have a strong stabilizing effect, and that sodium ions stabilize the hairpin more than potassium ions. The hairpin unfolds in a single step, regardless of buffer composition. Interestingly, hairpin folding occurs either in a single step (type 1) or through the formation of intermediates, in multiple steps (type 2) or gradually (type 3). Type 3 occurs only in the presence of both sodium and magnesium, while type 1 and 2 take place in all buffers, with type 1 being the most prevalent. By reducing the size of the native hairpin loop from fourteen to four nucleotides, we demonstrate that the folding heterogeneity originates from the large size of the hairpin loop. Further, while efficient pre-miRNA-377 binders are lacking, we demonstrate that the recently developed C2 ligand displays bimodal activity: it enhances the mechanical stability of the pre-miRNA-377 hairpin and perturbs its folding. The knowledge regarding pre-miRNA stability and dynamics that we provide is important in understanding its regulatory function and how it can be modulated to achieve a therapeutic effect, e.g., in heart failure treatment.https://www.mdpi.com/1422-0067/22/16/9008single-molecule force spectroscopyoptical tweezersRNA dynamicsRNA folding heterogeneitymiRNApre-miRNA |
| spellingShingle | Anna Wypijewska del Nogal Vinoth Sundar Rajan Fredrik Westerlund L. Marcus Wilhelmsson Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers International Journal of Molecular Sciences single-molecule force spectroscopy optical tweezers RNA dynamics RNA folding heterogeneity miRNA pre-miRNA |
| title | Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers |
| title_full | Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers |
| title_fullStr | Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers |
| title_full_unstemmed | Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers |
| title_short | Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers |
| title_sort | complex conformational dynamics of the heart failure associated pre mirna 377 hairpin revealed by single molecule optical tweezers |
| topic | single-molecule force spectroscopy optical tweezers RNA dynamics RNA folding heterogeneity miRNA pre-miRNA |
| url | https://www.mdpi.com/1422-0067/22/16/9008 |
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