Protein-free RNA Structure Characterization Service | Cryo-EM

RNA functions far beyond being a passive messenger of genetic information. It actively mediates catalysis, gene regulation, structural scaffolding, and signal transmission. Characterizing RNA in its unbound state—without associated proteins—offers critical insights into its intrinsic folding, dynamic behavior, and regulatory mechanisms.

 

Traditional techniques such as X-ray crystallography and NMR have contributed significantly to RNA structural studies but face limitations when applied to large, flexible, or heterogeneous RNAs. Recent advancements in Cryogenic Electron Microscopy (Cryo-EM) have opened new opportunities for visualizing RNA structures in their native, protein-free forms. To address this need, MtoZ Biolabs offers Protein-free RNA Structure Characterization Service based on Cryo-EM that enables high-resolution structural mapping of biologically relevant RNA entities.

 

Services at MtoZ Biolabs

MtoZ Biolabs provides an end-to-end Protein-free RNA Structure Characterization Service based on Cryo-EM, covering the entire workflow from RNA sample preparation to atomic-resolution 3D reconstruction. The service accommodates a broad range of RNA types, including:

– Catalytic RNAs (ribozymes) such as hammerhead, group I/II introns, and hairpin motifs, ideal for resolving catalytic centers and self-cleaving domains

– Long non-coding RNAs (lncRNAs)

– Aptamers and antisense RNAs

– Precursor miRNAs and siRNAs

– Structurally heterogeneous or conformationally flexible RNA fragments

 

Each project is tailored according to the molecular weight, structural complexity, and conformational flexibility of the RNA, with customized strategies for data acquisition, image processing, and 3D modeling.

 

Analysis Workflow

1. Sample preparation and quality assessment

Evaluate RNA integrity, aggregation tendency, and secondary structure consistency.

 

2. Negative-stain TEM screening

Rapid visualization of particle monodispersity and detectability.

 

3. Cryo-EM grid preparation

Optimize ice thickness and particle distribution for effective vitrification.

 

4. High-throughput Cryo-EM imaging and classification

Acquire large-scale datasets and perform 2D/3D classification to resolve conformational heterogeneity.

 

5. 3D reconstruction and conformational landscape analysis

Generate high-resolution models and map RNA folding behavior using free energy-based interpretations.

 

Why Choose MtoZ Biolabs?

✅ Native conformation captured without protein interference: Enables structural interpretation of RNA in its physiologically relevant, unbound form

✅ Crystallization-free approach for large and flexible RNA molecules: Overcomes the limitations of XRC and NMR, especially for complex or highly dynamic RNAs

✅ Conformational diversity resolved in small-to-medium RNAs: Heterogeneity classification and polymorphic modeling reveal dynamic ensembles

✅ Broad compatibility with RNA modifications: Supports chemically modified, probe-labeled, and endogenously altered RNA species

✅ One-time-charge: Our pricing is transparent, no hidden fees or additional costs.

 

Applications

Protein-free RNA Structure Characterization Service based on Cryo-EM is applicable to a wide range of scientific and translational use cases:

·  Structural and functional analysis of naturally occurring functional RNAs, such as ribozymes, ribosomal RNAs, and regulatory elements

·  Investigation of RNA folding kinetics and conformational heterogeneity

·  Structural validation and optimization of novel RNA-based therapeutics

·  Conformational analysis of viral RNA domains (e.g., SARS-CoV-2, HCV)

·  Evaluation of artificially designed RNA structures in synthetic biology

·  Monitoring the assembly efficiency of RNA-based nanostructures

 

Case Study

Case 1: Scaffold-assisted Cryo-EM for High-Resolution Structure of Small RNAs

Due to their size and flexibility, protein-free RNAs have historically posed challenges for structural determination via Cryo-EM. In a landmark Nature study (2021), researchers fused small RNAs to a group II intron scaffold to stabilize imaging targets. This approach enabled the visualization of the thiamine pyrophosphate riboswitch and raiA ncRNA at 2.5 Å resolution, uncovering key conformational states and ligand-binding modes.

 



Su, Z. et al. Nature.2021. 

 

Building on this precedent, MtoZ Biolabs integrates scaffold engineering with high-throughput Cryo-EM, offering dedicated services for resolving the structure of free-state RNAs including non-coding RNAs, regulatory elements, and synthetic constructs.

 

FAQ

Q1: Can small RNA molecules be resolved using Cryo-EM?

Yes. For RNAs under 100 nucleotides, we apply RNA scaffold fusion techniques to increase mass and rigidity, significantly improving imaging contrast and enabling atomic-level reconstruction.

 

Q2: What if the RNA is unstable or unsuitable for direct imaging?

We provide structure stabilization strategies such as scaffold selection, end modification, or site-specific mutation, based on RNA folding prediction and thermodynamic profiling. Low-input vitrification methods are also available for precious or low-concentration samples.

 

Q3: Must the RNA sample be of natural origin?

No. We accept RNA from diverse sources, including in vitro transcription, chemical synthesis, or cellular expression systems. Purity and conformational integrity are the primary criteria to ensure high-quality structural output.

 

MtoZ Biolabs offers cutting-edge RNA Cryo-EM solutions designed to support both discovery and therapeutic development. With a robust platform and expert team, our Protein-free RNA Structure Characterization Service based on Cryo-EM empowers researchers to explore RNA structure and dynamics with confidence. Contact us today for consultation.