1M6 (1-Methyl-6-nitroisatoic anhydride) is a SHAPE reagent for the detection of RNA chemical structures.

I. SHAPE experiment
1. RNA sample preparation: Extract and purify the target RNA sample to ensure that it is not contaminated and can be stably present in the SHAPE experiment.
2. Reagent reaction: Dissolve 1M6 in an appropriate solvent (such as water or buffer) and add it to the RNA sample. Usually, the reaction is carried out at room temperature, and the time can be adjusted according to the experimental design (usually 10-30 minutes).
3. RNA modification: 1M6 reacts with the exposed 2'-OH hydroxyl group in the RNA molecule to form a modified RNA molecule. These modified RNA fragments can be analyzed by different sequencing technologies (such as high-throughput sequencing).
4. Analysis: Analyze RNA modification data, use SHAPE data to generate a structural model of RNA, predict its secondary structure or explore its interaction with other molecules.
II. Study RNA structure and function
1. RNA secondary structure analysis: Use 1M6 to modify the RNA sample, and infer the secondary structure of RNA by analyzing the location of the modification.
2. Interaction study: Combine other experimental methods (such as affinity chromatography or electrophoresis) to study the interaction between RNA and other molecules (such as proteins, small molecule ligands) and evaluate the effects of these interactions on RNA structure.
III. RNA folding dynamics study
1. Dynamic experiment: By adding 1M6 at different time points, the structural changes of different regions of RNA during the folding process are marked. Combined with real-time sequencing technology, the process and intermediates of RNA folding are studied.
2. Temperature gradient experiment: React under different temperature conditions to evaluate the stability of RNA under different thermodynamic conditions.
IV. RNA binding to small molecules study
1. Binding with small molecules: Add small molecules to RNA samples, label them with 1M6, and analyze RNA structural changes.
2. Comparative analysis: By comparing the modification data of 1M6 in untreated and small molecule-treated RNA samples, the structural region that binds to the small molecule is identified.