Custom target RNA Interactome MagIC Beads

RNA isolation for interactome studies: RNA-protein, RNA-RNA, and RNA-DNA interactions. Enrich custom RNA targets up to 100 000x directly from cellular or tissue lysates under unprecedentedly strong denaturing and reducing conditions.


Let us know the RNA sequence of interest and receive a custom ready-to-use kit:

  • Custom design for any RNA molecule:
    • Target any transcript or pool of transcripts.
    • We evaluate the feasibility of capturing your target before you place an order. Request a quotation here.
    • We design the probes and prepare the kit containing all the components you need for your experiment.
  • High efficiency and specificity:
    • Enrich target RNA directly from a cellular lysate by over 100.000 fold.
    • No molecular tag related biases.
    • Reproducible and consistent levels of enrichment.
    • Enrichments take place under unprecedentedly stringent conditions, unachievable with biotin based approaches.
  • Simple and time-saving protocol:
    • Below 15 minutes of hands-on time.
    • The whole procedure takes less than 2 hours.
    • No additional components needed.
    • No DNase treatment or sonication of the sample required, no RNA fragmentation.
    • No need for prior isolation, pre-processing, or RNA fragmentation.

An elegant and simple workflow for RNA enrichment

RNA Interactome MagIC Beads workflow


Unmatched enrichment levels:

Relative RNA enrichment - MALAT1
Lysates of UV cross-lined HEK293 cells were incubated with non-targeting or MALAT1 targeting MagIC Beads. RNA-protein complexes attached to the beads were washed and eluted. RNA was isolated and subjected to cDNA synthesis. Levels of MALAT1, ACTB, GAPDH and 18S rRNA were measured in the input and enriched samples with RT-qPCR. The target RNA was enriched from over 10.000 to over 100.000 fold over non-target transcripts by MALAT1 targeting MagIC Beads, but not by the non-targeting beads. 


CDR1AS MagIC Beads
Lysates of UV cross-linked mouse brains were incubated with CDR1AS targeting MagIC Beads. RNA-protein complexes attached to the beads were washed and eluted. RNA was isolated and subjected to cDNA synthesis. Levels of CDR1AS, GAPDH and 18S rRNA were measured in the input and enriched samples with RT-qPCR. The target RNA was enriched from over 100.000 to over 1.000.000 fold over non-target transcripts by CDR1AS targeting MagIC Beads. 

Identify ribonucleoprotein complexes: 

The identification of the compositions of ribonucleoprotein complexes (RNPs) formed by a specific transcript is of great value in RNA studies. It is, however, a challenging task, and is difficult to accomplish with a classic toolbox of biochemical methods. Such studies can be performed on lysates of UV cross-linked cells with sequence-specific target capture utilizing antisense oligonucleotides. Typically systems based on biotinylated oligonucleotides complementary to the sequence of the transcript of interest in combination with streptavidin beads are employed. Proteins co-captured in such procedures can be identified by mass spectrometry.

Directly from cellular or tissue lysates:

MagIC Beads based systems for the study of RNA-protein interactome feature exceptionally efficient hybridization based approach of sequence specific RNP captures free of the weaknesses and shortcomings of biotin-streptavidin based workflows.

The kits consist of the target-specific MagIC Beads and sets of optimized buffers. They feature standardized cell lysis and capture conditions as well as capture probes properties, which ensure uniformly high efficiency of the system on varying RNA targets, independently of their length or secondary structures. The beads provide very high target capture efficiency and enrichment levels.

For any custom target transcript the optimal number of probes is established based on the target length and nucleotide composition. Experimentally validated design approach is used to provide uniformly highly efficient capture probe arrays for any target. Every probe is extensively screened against potential binding to any off-targets in the transcriptome of interest to ensure superb probe specificity.

Downstream application agnostic: 

The enrichment method is downstream application agnostic and the proteins co-captured with the target RNA can be subjected to analysis with various methods, including:

‣ Mass spectrometry
‣ Western blotting
‣ Silver staining on a protein gel

Compared to classic biotinylated probe-based approaches, MagIC Beads provide multiple benefits: 

No probe design burden Reliable arrays of capture probes are designed by ElementZero Biolabs for any target
Reliable performance: No need for RNA fragmentation Efficient capture regardless of the target length or the presence of secondary structures
No sequence capture biases Full length target transcripts are captured, including fragments of the target not covered by probes
No chromatin fragmentation needed: sonication or DNases not necessary  Full-length genomic DNA is not co-captured by the beads
Reduced experimental background due to stringent capture conditions Reduced capture of non-target transcripts and molecules not cross-linked to the target transcript
No background from naturally biotinylated molecules MagIC Beads do not capture non-target biotinylated molecules from the sample
Significantly lower costs RNase inhibitors, DNases, streptavidin beads or additional buffers are not required
Preserved target integrity During the enrichment, nucleases are inactivated by the buffers (no need for RNase inhibitors)
Fast and simple protocol The enrichment procedure can be completed in 1-2h with a reduced number of hands-on steps
No need for additional key components of the experimental setup MagIC Beads enrichment kits are provided as complete, out of the box solution
Expert support Count on active support regarding the use of the kit as well as analysis of planned downstream applications

Additional information:

‣ Supplied with beads, and hybridization and wash buffers.
‣ 1 reaction = 200 pmol of capture probes (50 pmol per 20-50mln of cells).
‣ Shipping condition: room temperature.
‣ Storage Temperature: 4°C.
‣ Durability: 36 months from the date of manufacture.
Protocol – RNA-protein interactome (UV crosslinking)
Protocol – RNA-protein interactome (chemical crosslinking – formaldehyde)
Protocol – RNA-chromatin interactome
Protocol – RNA-RNA interactome