MS Analysis of RNA Pull Down

RNAs and their interacting protein partners form highly dynamic ribonucleoprotein particles, that are involved in many cellular processes such as posttranscriptional events. CD Genomics provides a full range of services in the study of RNA-protein interactions. MS analysis of RNA pull down is a method that combines mass spectrometry and RNA pull down assay for comprehensive, accurate and rapid screening of proteins that bind to RNA in vitro.


Untranslated mRNA regions and non-coding RNAs, such as long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and small nucleolar RNAs (snRNAs), accomplish many of their functions through direct interactions with RNA-binding proteins (RBPs). RNA-protein interactions play a vital role in the regulation of gene expression. And every stage of the RNA life cycle, including RNA synthesis, processing, modification, transport, and decay, is tightly controlled by RBPs. Multiple methods for studying RNA-protein interactions have been developed. To date, in vitro RNA pull down assays have identified most of the known RNA-protein interactions. The significant advances in quantitative mass spectrometry (MS) have enabled the reliable identification of RNA-protein interactions.

CD Genomics provides sample-to-data MS analysis of RNA pull down that theoretically works for all RBPs. The service involves the biotin labeling of RNAs of interest through in vitro transcription, formation of RNA-protein complexes through the incubation with cell/nuclei lysis solution, RNA pull down using streptavidin-coated beads for enrichment of RBPs, elution of RBPs from beads, detection of RBPs by Western blot analysis and/or identification of all of proteins that interact with the RNA of interest by MS analysis. We offer a full range of services in the study of RNA-protein interactions, please don't hesitate to contact me to discuss your project.


Transcriptome-WideBioinformatics AnalysisHigh PerformanceSeamless Integration
Transcriptome-wide profiling of RNA-protein interactions and detection RBPsData QC; encoding activity analysis; validation and functional analysisOptimized experimental procedures, advanced LC-MS system, expertise in operation.Provide a full range of MS- and NGS-based methods for studying RNA-protein interactions

Project Workflow

1. In Vitro RNA Transcription

Biotin labeling of full-or partial-length RNAs of interest through in vitro transcription

2. Incubation with Lysis Solution

Incubate the biotinylated transcripts with cell/nuclei lysis solution to generate RNA-protein complexes

3. Pull Down Assay

Isolation of RNA-protein complexes using streptavidin-coated beads; Elution of RNA-protein complexes from beads

4. Western Blot & Mass Spectrometry

Western blot or mass spectrometry analysis for accurate detection of RNA-binding proteins

Sample Requirements

We work with a wide range of sample types including protein solution, fresh tissue, cultured cells, blood, and microbial sample. Please feel free to contact us for sample size.

Sample Storage: extracted protein should be stored at -80°C. Avoid repeated freezing and thawing.

Shipping Method: When shipping the sample, it is stored in a 1.5 mL Eppendorf tube, sealed with a sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable: data QC report, MS results, integrated experimental report (materials, methodologies, and bioinformatics analysis).


  1. Ramanathan M, Porter D F, Khavari P A. Methods to study RNA–protein interactions. Nature methods, 2019, 16(3): 225-234.
  2. Jazurek M, Ciesiolka A, Starega-Roslan J, et al. Identifying proteins that bind to specific RNAs-focus on simple repeat expansion diseases. Nucleic acids research, 2016, 44(19): 9050-9070.
* For Research Use Only. Not for use in diagnostic procedures.

Research Areas
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