SARS-CoV-2 RNA Pseudoknot Unfolding and Refolding Force-Extension Curves

Force-extension curve data for the frameshift-stimulatory RNA pseudoknot from SARS-CoV-2, measured with optical tweezers. The dataset consists of Excel files containing paired force (pN) and extension (nm) columns for sequential unfolding and refolding measurements. Data was contributed by Krishna Neupane and is hosted on Papers with Code.

Use Cases

• Modeling RNA folding energy landscapes based on force-extension curve data.
• Analyzing the mechanical stability of viral pseudoknots under different conditions (e.g., presence of antisense oligos or absence of Mg ions).
• Training machine learning models to predict RNA unfolding pathways from force spectroscopy traces.
• Comparing the refolding kinetics of RNA constructs with different spacer lengths.

Strengths

• Data includes measurements under varied experimental conditions, such as different spacer lengths and the presence/absence of Mg ions.
• Measurements are organized by molecule, set, and pull number, providing a structured hierarchy for analysis.
• Force and extension data are provided in standard physical units (pN and nm).

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Last update date is unknown; freshness unverified.

Provenance

Source

Krishna Neupane

Collection Method

Measured with optical tweezers.