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Dye-labeled read-out probes, cleavable linkers, bDNA amplifier support, HPLC/UPLC purification, optional LC-MS QC, and per-round kitting for spatial transcriptomics workflows.
Bio-Synthesis offers custom MERFISH read-out probes with cleavable fluorescent dye chemistries, orthogonal barcode-compatible designs, optional bDNA amplifier support, and flexible purification workflows for spatial transcriptomics applications. Our team supports dye selection, linker chemistry, cyclic imaging workflows, pooled probe formats, and QC documentation for MERFISH, cyclic FISH, and multiplex RNA imaging assays.
Typical read-out length
Cleavable linker options
HPLC, UPLC, LC-MS options
Per-round pools available
Read-out probes are short oligos, typically about 20 nt, that are complementary to encoding-probe docking tags. Dyes are commonly attached through a cleavable linker at the 5′ terminus or, when needed, the 3′ terminus for alternate geometry or dual-dye designs.
Use orthogonal 20–25-mers with Tm about 5–8 °C above imaging temperature. Screen docking tags for cross-homology across the full codebook.
Common choices include Alexa Fluor 568/594/647/700/750, Atto 550/647N, Cy5, and other microscope-compatible dyes.
HPLC or UPLC purification is recommended. LC-MS, dye loading review, and cleavage verification can be added when appropriate.
Keep the product offering simple: dye-labeled read-outs, cleavable linker variants, and optional kitting aligned to the customer’s codebook.
Short dye-labeled oligos complementary to encoding-probe docking tags for cyclic imaging rounds.
Disulfide, photocleavable, enzyme-cleavable, or custom linker options for signal removal between rounds.
Per-round pooled mixes matched to the customer’s MERFISH codebook, imaging channels, and workflow.
bDNA amplifier probe sets increase MERFISH signal by building a layered hybridization structure on the target complex. A pre-amplifier binds the capture/encoding scaffold, multiple amplifier branches bind to the pre-amplifier, and each amplifier recruits labeled read-out probes to generate a brighter signal without PCR amplification of the target.
Recruit multiple fluorescent read-outs per target complex.
Use orthogonal amplifier/read-out designs for multi-target assays.
Improve detection when transcripts are weak, sparse, or difficult to image.
Choose the dye/linker format that best fits your cyclic imaging workflow, reset chemistry, tissue compatibility, and microscope channels.
Disulfide is the field-standard reset option for MERFISH and cyclic FISH. Photocleavable and enzyme-cleavable triggers are useful alternatives when fast on-scope reset or sample-specific compatibility is needed.
MERFISH uses sequential hybridization and imaging rounds to identify RNA molecules by barcode. Each cycle adds fluorescent read-out probes, captures the image, and removes the signal before the next round.
Hybridize encoding probes containing docking tags and target-binding regions.
Add fluorescent read-out probes that bind selected docking tags for the current imaging round.
Trigger cleavage by reductive, photo, or enzyme chemistry to remove fluorescence and prepare the next cycle.
This practical workflow summarizes the major steps customers typically plan around when ordering MERFISH read-out probes and cleavable dye formats.
Discuss read-out design, dyes, cleavage mode, bDNA amplification, pooling, or QC requirements.
Include sequences, dyes, linker type, scale, purification, delivery format, and codebook needs.
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