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Branched DNA (bDNA) Amplifier Probes

High-sensitivity, PCR‑free signal amplification for RNA/DNA detection in QuantiGene, ViewRNA, MERFISH, and FISH. Custom design, scalable synthesis, and ISO‑aligned QC.

PCR‑free signal amplification MERFISH / ISH compatible RUO → GMP‑like scale Multiplex‑ready
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Overview How it works Options Specifications FAQ Speak to a scientist

Overview

bDNA amplifier probes (branched DNA) deliver robust, enzyme‑free signal gain by layering pre‑amplifiers, amplifiers, and labeled probes onto a captured target. Unlike PCR—which amplifies the target—bDNA systems amplify the signal, enabling sensitive detection in cells, tissues, or plate‑based assays with low background.

10^2–10^3×
typical signal gain per target
Multiplex
compatible with MERFISH / smFISH panels
PCR‑free
no target amplification required
RUO→GMP‑like
scalable synthesis & QC
Applications: MERFISH readout, smFISH & ViewRNA, plate‑based QuantiGene expression assays, viral RNA panels, oncology biomarkers, miRNA detection.
Design & Technology Considerations
  • Branch factor: amplifier copy per pre‑amplifier and label density per amplifier.
  • Probe tiling: capture/label extenders across target regions to raise occupancy and specificity.
  • Stringency: temperature, formamide/salt to balance kinetics vs background.
  • Label strategy: enzyme (AP/HRP) vs direct dyes (Alexa/Cy series) vs cleavable readouts.
  • Compatibility: co‑design with MERFISH barcoding & imaging rounds.

How bDNA Amplifier Probes Work

Layered hybridization: target capture → pre‑amplifier docking → multiple amplifiers → multiple labeled probes per amplifier.

Target RNA/DNA Capture + Label Extenders Pre-Amplifier Amplifiers (branched) Labeled Probes Target strand Capture/Label Extenders (tile across target) Pre-Amplifier (multiple amplifier docking sites) Amplifier A Amplifier B Amplifier C
Target
RNA/DNA captured on solid support or in situ
Capture / Label Extenders
Probe set tiling the target
Pre‑Amplifier
Scaffold with many amplifier docking sites
Amplifier
Branch molecules that recruit labels
Labeled Probes
Fluorophore/enzyme tags for detection

Options & Formats

Probe Set Architecture
  • Capture & Label Extenders: target‑specific tiling; optional LNA for stability.
  • Pre‑Amplifier / Amplifier: defined branch factor; sequence‑orthogonal for multiplexing.
  • Labels: enzyme (AP/HRP), biotin‑streptavidin, or direct dyes (Alexa, Cy, ATTO).
  • Cleavable Readouts: e.g., disulfide‑linked dyes for strip‑and‑rerun imaging cycles.
Deliverables: lyophilized or liquid; normalized molarity; sequence map; CoA; QC traces.
QC & Documentation
  • LC‑MS, HPLC, PAGE (as applicable)
  • OD260, fluorophore loading where relevant
  • Endotoxin on request; ISO‑aligned documentation
  • RUO default; GMP‑like available for qualified projects

Specifications

Scale:
nmol to multi‑µmol; panel builds on request
Purification:
Desalt, HPLC, PAGE as needed
Storage:
–20 °C (aliquoted, desiccated); protect dyes from light
Compatibility:
Plates, coverslips, tissue sections, cells

FAQ

What is a bDNA amplifier probe?
A hybridization probe system that amplifies signal using branched DNA pre‑amplifiers and amplifiers, rather than amplifying the target itself (PCR).
How does this differ from PCR or rolling‑circle amplification?
PCR amplifies the target; bDNA amplifies the detection signal via layered hybridization. No polymerase is required, which reduces background and preserves spatial context in situ.
Can I use cleavable labels for multi‑round imaging?
Yes. We support disulfide‑linked dyes and other cleavable strategies for MERFISH/smFISH cycles.
What branch factor should I choose?
Typical designs use 1 pre‑amplifier per target, 3–5 amplifiers per pre‑amplifier, and 2–4 labels per amplifier; we tune this for your SNR, kinetics, and imaging constraints.
Do you support RUO → GMP‑like projects?
Yes. We offer ISO‑aligned documentation and phased technical transfers for clinical‑adjacent programs.

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