Multi-arm oligos for Signal-Amplifing Probesf

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Custom Branched Oligonucleotide Synthesis

Multi-arm architectures for multivalent targeting, signal amplification, and multiplex hybridization—engineered to your specifications.

Overview

Branched oligonucleotides incorporate two or more branches extending from a central scaffold or internal branch point, enabling multiple functional groups, labels, or sequence domains on a single molecule. This unlocks high-density signaling, multivalent binding, and true multiplex capability in compact designs.

Bio-Synthesis delivers end-to-end custom branched oligo synthesis—from collaborative design and arm layout to labeling, conjugation, purification, and documentation.

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At-a-Glance

  • Architectures: 2-arm, 3-arm, 4-arm, dendrimeric
  • Chemistries: DNA, RNA, LNA/BNA mixmers, 2′-O-modified, PS backbones
  • Branch points: internal nucleotide cores or synthetic linkers
  • Purification: RP-HPLC (standard), IE-HPLC/PAGE optional
  • Scales: 1 mg to gram quantities
  • QC: MS + analytical HPLC; optional functional/hybridization data

Key Advantages

Multivalency

Present identical or orthogonal binding domains to boost avidity and target capture.

Signal Amplification

Carry multiple dyes/labels on one scaffold to raise signal without increasing probe count.

True Multiplexing

Combine distinct sequences on separate arms for simultaneous hybridization events.

Applications

  • FISH/ISH probes with multi-dye payloads
  • Multiplex mutation/SNP detection
  • Microarrays & biosensors
  • Capture/enrichment (biotinylated multi-arm)
  • Aptamer multivalency & crosslinking studies
  • Nanostructure scaffolds
  • qPCR/probe assemblies
  • Dual-function constructs (targeting + reporting)
  • Research-grade therapeutic prototypes

Branch Architectures

Type Description Typical Uses
2-Arm (Y-shaped) Single branch point dividing into two arms; balanced or asymmetric sequences. Dual labeling, bivalent targeting, capture + reporter on one construct.
3-Arm (Tri-branched) Central node with three independent arms; variable lengths and labels. Multiplex probes, FRET arrays, tri-valent recognition.
4-Arm (Tetra-branched) High-density scaffold for four sequences, labels, or ligands. Signal boosting, multi-epitope capture, biosensor assemblies.
Dendrimeric Hierarchical branching to maximize valency and label count. Ultra-bright probes, nano-assembly, advanced diagnostics.

We can integrate LNA/BNA segments for higher Tm and mismatch discrimination, or PS backbones for stability in complex matrices.

Custom Synthesis Options

Parameter Options
Arm Count 2, 3, 4, dendrimeric (custom)
Chemistry DNA, RNA, LNA/BNA mixmers, 2′-OMe, PS, mixed backbones
Branch Points Internal nucleotide cores, tri-/tetra-functional linkers, PEG hubs
Linkers/Spacers Alkyl (C6/C12), AEEA, Ahx, PEG(n), rigid/aromatic as needed
Purification RP-HPLC (standard), IE-HPLC, PAGE
Scale 1 mg to grams; plates or tubes
Delivery Lyophilized or buffered; ambient/cold per label requirements
QC MS (MALDI/ESI), analytical HPLC; optional hybridization/functional data

Popular Labels & Linkers

Category Examples Typical Uses
Fluorescent Dyes FAM, HEX, JOE, TAMRA, ROX, Cy3/Cy5, ATTO series, Alexa Fluor® Bright multi-dye constructs, FRET arrays, multiplex readouts
Affinity Tags Biotin (C6/TEG/long), Digoxigenin, DNP Capture/enrichment, immunodetection
Reactive Handles Amine, Thiol, Azide/Alkyne (CuAAC/SPAAC), Maleimide Protein/peptide conjugation, surface coupling
Spacers / PEG AEEA, Ahx, miniPEG, PEG(n), C6/C12 Reduce steric hindrance; tune distance and solubility
Quenchers BHQ-1/2/3, Iowa Black, Eclipse Quenched probes & molecular beacons

Need unusual linkers or orthogonal chemistry? Send your schematic—we’ll review feasibility and route.

Quality Assurance

  • Mass spectrometry (MALDI/ESI) for MW confirmation
  • Analytical HPLC purity profile; multi-peak deconvolution as needed
  • Optional functional assays (hybridization/Tm, capture efficiency)
  • Traceable documentation; RUO standard with GLP/cGMP support on request

Typical Turnaround

Standard branched constructs: 2–3 weeks after order confirmation. Complex multi-arm/multi-label designs may require additional time.

Lead time depends on architecture, labels, and purification. Rush options may be available.

How to Order

  1. Share your desired architecture (arms), sequences, and labels.
  2. We optimize linkers, placement, and branch points for performance.
  3. Select scale, purification, and optional functional QC.
  4. Receive a same-day quote and timeline.

RFPs welcome—attach diagrams or prior designs for fastest scoping.

Specs Checklist

  • Arm count and layout (2/3/4/dendrimeric)
  • Sequences (5′→3′) per arm + target Tm
  • Branch point type and desired linkers/spacers
  • Labels/tags per arm; conjugation targets (if any)
  • Scale, purification, and QC requirements
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Branched Oligonucleotide Technology & Benefits

What are Branched Oligonucleotides? Branched oligonucleotides are synthetic nucleic acid constructs in which two or more arms extend from a central branch point or scaffold. These arms may carry identical or different sequences, labels, or ligands, enabling multifunctional capability in a single molecule.

How Branched Oligos Work
  • Central Branch Point: Created using multi-functional linkers or modified nucleotides to generate two, three, or four arms.
  • Independent or Cooperative Arms: Each arm can target a different nucleic acid sequence or work together to bind one target more strongly.
  • Multi-Label Capability: Attach multiple fluorescent dyes, quenchers, or affinity tags for enhanced detection or capture.
  • Structural Versatility: Choose from simple Y-shaped constructs to complex dendrimeric assemblies.
Design Considerations
  • Arm length and sequence for optimal hybridization or interaction.
  • Branch point chemistry to ensure stability and accessibility.
  • Spacer and linker selection to reduce sterics and improve solubility.
Benefits at a Glance
  • Multivalency: Multiple binding events from a single molecule increase avidity and target capture efficiency.
  • Signal Amplification: Carry multiple dyes to significantly boost fluorescence output.
  • True Multiplexing: Incorporate different sequences to detect multiple targets simultaneously.
  • Compact Design: Consolidate multiple functions into one oligo to save assay space and simplify workflows.
  • Customizable Functionality: Integrate affinity tags, reactive handles, or conjugation chemistries.
  • Compatibility: Works with hybridization assays, FISH, PCR/qPCR, capture assays, and nanotechnology applications.

We can optimize branch architecture, arm composition, and label placement to achieve the best balance of stability, specificity, and performance for your assay.

Use Case Why Branched Oligos Help Typical Setup
FISH probes with multi-dye payloads Higher signal intensity without increasing probe count 3-arm construct, each with dye + spacer to minimize quenching
Multiplex mutation detection Detect multiple SNPs in one hybridization Different sequences on each arm, each labeled with distinct fluorophores
Capture & reporter in one molecule Reduces steps and reagents in assay Biotin on one arm, fluorophore on another, target sequence on third
Nanostructure assembly Scaffold multiple binding domains in precise arrangement 4-arm tetra-branched core with defined arm lengths
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FAQ

How do I choose 2 vs. 3 vs. 4 arms?

Match arm count to your function: two arms for bivalency or dual-label; three for multiplex detection; four for maximum signal or multi-epitope capture. Dendrimers amplify density when ultra-high payloads are needed.

Can I mix DNA with LNA/BNA in branched designs?

Yes. Mixmers help tune Tm, specificity, and stability. We can recommend %LNA/BNA by region to hit assay windows.

What about solubility with many labels?

We add PEG/AEEA spacers or longer linkers to improve solubility and minimize quenching/sterics for multi-dye constructs.

Do you support GMP production?

We support RUO through cGMP with appropriate QA oversight. Include your regulatory needs in the request for scoping.

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Complete the form to receive a tailored quote. Your request will be emailed to info@biosyn.com and logged to your CRM endpoint (configure below).

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