Single-molecule microscopy (SiM-KARTS) and chemical probing (SHAPE) of lncRNA

Long noncoding RNAs (lncRNAs) provide a wealth of potential as therapeutic targets and diagnostic biomarkers. Several heart-specific lncRNAs have been identified, including ones that play important roles in heart health and disease. Despite their importance, the mechanisms by which these lncRNAs affect the heart have not been dissected at the molecular level. We propose to utilize single-molecule fluorescence techniques to determine the structure and molecular mechanism of a heart-specific lncRNA, Myheart (Mhrt), which protects the heart under conditions of stress. Mhrt binds to and sequesters a chromatin remodeling enzyme called Brg1, enabling certain key transcripts to be produced at basal levels. This projects intends use a technique called Single-Molecule Analysis of RNA Transient Structure (SiM-KARTS) to probe the structure and folding dynamics of the RNA in isolation. Small model systems based on a heart-specific lncRNA were constructed in order to provide a baseline for rigorous ..., This dataset was collected through analysis of gel electrophoresis, single-molecule fluorescence imaging, and analysis of the protein content of cells., , # Single-molecule microscopy (SiM-KARTS) and chemical probing (SHAPE) of lncRNA

Dataset DOI: [https://doi.org/10.5061/dryad.j9kd51cnp](https://doi.org/10.5061/dryad.j9kd51cnp)

## Description of the data and file structure

AHA_Data_Deposit_2025.zip contains data collected for three experimental efforts, separated into sub-folders:

1. Single-molecule fluorescence microscopy on a segment of the long noncoding RNA* Braveheart*
2. Chemical secondary structure probing of long noncoding RNA* Myheart*
3. Expression of Brg1 protein in SF9 insect cells

### Files and variables

For convenience, each sub-folder contains a PDF describing the file naming conventions, data structure and units of measurement of the files within it. The folders are:

1_single-molecule/Dwell time files (dwell times, in movie frames, in unbound and probe-bound states of the RNA)

1_single-molecule/Movie files (single-molecule fluorescence images and traces)

2_gels (polyacrylamide gel electrophoresis images)

3_prot...,