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Branch Peptide Synthesis

Multivalent peptide architectures beyond lysine MAP, engineered for epitope density and avidity.

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Overview Capabilities Architectures Beyond MAP Design guidance Workflow Specifications QC & deliverables FAQs Contact

Overview

Branched peptides: what they are (and why they’re used)

Branch peptide synthesis (also called branched peptide synthesis) produces peptides with two or more peptide chains attached to a single branching point—most commonly via lysine α/ε amino groups or dendrimeric scaffolds. This format increases valency and epitope density, which can improve functional binding (avidity) and immune recognition compared with a single linear peptide.

Bio-Synthesis manufactures branched peptides, including lysine-branched peptides and Multiple Antigen Peptides (MAP) such as MAP-2, MAP-4, and MAP-8, using orthogonal protecting-group strategies and coupling protocols designed to preserve branch-point fidelity and reduce mixed-arm products.

Lysine-branched (MAP) peptides Dendrimeric peptides Fit-for-purpose Services ISO 9001:2015/ISO13485:2016 45+ Years of Expertise U.S. Facilities - Texas
Higher avidity

Multiple copies or motifs can increase binding strength through multivalent interactions.

Epitope density

MAP formats concentrate epitopes without a carrier protein—useful for immunology workflows.

Controlled branching

Orthogonal protecting groups help reduce mixed products and improve reproducibility.

Branched peptide synthesis schematic showing a lysine branching core with two to eight peptide arms (MAP-2, MAP-4, MAP-8) and dendrimer for multivalent epitope presentation.

Figure: Lysine-branched (MAP) and dendrimeric peptide architectures—multivalent formats used to increase epitope density and/or binding avidity.

MAP Lysine-branched peptides Dendrimeric peptides Backbone branching Cysteine-based branching Hybrid branching

Related services: Custom Peptide Synthesis, Peptide Modifications, Peptide Bioconjugation. For ready-made options, browse Catalog Peptides.

Common requests: MAP-2/4/8 peptide synthesis, hetero-branched peptides, multivalent ligP / probe constructs, and dendrimeric peptide designs (project-dependent).

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Capabilities at a glance

Architectures
  • Lysine-branched (Y / star)
  • MAP-2 / MAP-4 / MAP-8
  • Dendrimeric & multivalent (project-dependent)
Options
  • Biotin, fluorophores, PEG/spacers
  • Click handles (azide/alkyne), cleavable linkers
  • Isotope labels (project-dependent)
Deliverables
  • MS identity confirmation
  • HPLC profile / purity (where feasible)
  • COA + supporting documentation

Need help choosing a branching strategy? Send your sequence(s), copy number/valency target, and downstream use—we’ll recommend a practical synthesis, purification, and QC plan.

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Branched peptide architectures we support

Lysine-branched peptides (α/ε branching)

Classic branch-point designs using lysine side-chain and backbone amino groups. Ideal for Y-shaped and star-like constructs when you need two or more arms.

  • Homo-branched (same sequence on each arm)
  • Hetero-branched (different sequences per arm)
  • Optional spacing/linkers to reduce steric crowding
MAP peptides (MAP-2 / MAP-4 / MAP-8)

Multiple Antigen Peptides (MAP) display multiple copies of an epitope on a dendrimeric lysine core to increase immune recognition and assay signal.

  • Copy number and spacing control
  • Carrier-free immunogen format (project-dependent)
  • Common in antibody production and epitope screening
Multivalent & dendrimeric designs

Higher-valency constructs for receptor clustering, multivalent binding, and biomaterials research where avidity matters.

  • Custom branching cores (case-dependent)
  • PEG/spacer options to tune solubility and presentation
  • Labels/handles integrated when compatible

Beyond lysine MAP: branched peptide design strategies

Branched peptides are not limited to lysine-based MAP constructs

MAP peptides (MAP-2 / MAP-4 / MAP-8) are a popular subset of branched peptides because lysine provides a convenient α/ε branching point. However, branched architectures can also be built using alternative amino acid branch points, dendrimeric or small-molecule cores, and post-synthetic ligation chemistries. We recommend the strategy based on spacing/geometry, steric congestion risk, solubility, stability, and downstream use.

Diamino acid branching (non-lysine)

Branching via diamino acids such as Dap, Dab, or Ornithine to tune arm spacing and reduce steric crowding compared with lysine.

Dendrimeric peptide cores

Higher-valency, generation-defined dendrimeric designs (case-dependent) for multivalent binding, clustering, or biomaterials research.

Backbone (N-substituted) branching

Advanced architectures that introduce branching through backbone features (peptidomimetic-style). Useful for stability-focused designs when appropriate for the application.

Cysteine / thioether branching

Post-synthetic branching via cysteine chemistry (e.g., thioether) or reversible disulfides for redox-responsive or modular constructs.

Click-chemistry branching

Branching via azide–alkyne coupling (CuAAC/SPAAC) to build peptide–peptide or peptide–non-peptide multivalent constructs with strong orthogonality to SPPS.

Small-molecule scaffold cores

Rigid cores (project-dependent) to control arm angle/geometry for multivalent ligands, SAR studies, or probe design.

Diamino acid branching (Dap/Dab/Orn) Dendrimeric peptides Backbone branching Cysteine / thioether Click-chemistry branching Small-molecule scaffolds
Comparison: choosing the right branched peptide strategy

Different branching approaches solve different problems (spacing/geometry, steric congestion, solubility, and downstream chemistry). The table below helps you pick a strategy quickly and reduces rework during synthesis.

Strategy Best for Strengths Watch-outs Typical choices
Lysine MAP / Lys-branch Epitope density (immunology), multivalent display, “carrier-free” formats (project-dependent) Well-established SPPS workflows; clear copy-number options (MAP-2/4/8); efficient for homo-branched designs Steric crowding near branch point at high valency; arm-to-arm heterogeneity risk if conditions aren’t optimized MAP-2 / MAP-4 / MAP-8; Y-shaped; star-like
Diamino acids (Dap/Dab/Orn) When lysine spacing is suboptimal or steric congestion is limiting yield/purity Tunable arm spacing; can reduce crowding vs lysine; useful for difficult / hydrophobic arms Project-dependent feasibility; may require more design input to hit geometry goals Dap, Dab, Orn branch cores
Dendrimeric cores Higher-valency clustering, multivalent binding, materials/probe designs needing defined valency Generation-defined valency; flexible mixing of arms (case-dependent); strong avidity potential Purification and analytics can be more complex; solubility management often required Generation-style dendrimers; custom scaffolds
Click-chemistry branching Post-synthetic modular assembly; peptide–peptide or peptide–non-peptide hybrids Orthogonal to SPPS; flexible assembly order; enables modular libraries and handles Requires compatible handles and downstream chemistry plan; linkers may affect presentation Azide/alkyne (CuAAC/SPAAC), modular ligation

If you’re comparing providers, ask how they control branch-point fidelity, prevent mixed-arm products, and tailor purification + QC for high-valency constructs—not just “we can make MAP peptides”.

Not sure which approach fits? Send your sequence(s), desired copy number/valency, and downstream use—we’ll recommend a practical branching strategy and QC plan.

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Design guidance: how to reduce risk for branched peptides

Branched peptides fail most often due to steric crowding at the branch point, uneven arm growth, and on-resin aggregation. A few practical choices can improve yield, purity, and timeline.

Design checklist
  • ✓ Specify architecture: lysine-branched vs MAP-2/4/8 vs custom
  • ✓ State whether arms are identical (homo) or different (hetero)
  • ✓ Identify “must-keep” residues (binding/epitope critical)
  • ✓ Define handles/labels and attachment positions (if any)
  • ✓ Share downstream use: immunization, assay, binding, materials
Common risk factors
  • Hydrophobic/aggregation-prone motifs near the branch point
  • Long arms with high local density (steric congestion)
  • Hetero-branch designs requiring deeper QC
  • Solubility limitations impacting purification/formulation

For challenging sequences, see Difficult Peptide Synthesis.

Biotin / fluorophores Click handles (azide/alkyne) Cleavable linkers PEG/spacers Isotope labels

Synthesis workflow

1) Design review

Confirm branch architecture, protection strategy, arm order (hetero-branch), and success criteria.

2) SPPS assembly

Build arms using orthogonal deprotection and optimized coupling cycles near branch-point congestion.

3) Purify & validate

Purify with a plan aligned to hydrophobicity/charge and verify identity with fit-for-purpose analytics.

What we optimize (practically)
  • Orthogonal protecting groups for clean arm growth
  • Coupling completeness at sterically hindered sites
  • Aggregation control to maintain resin mobility
  • Purification strategy matched to construct complexity
  • Analytical plan to confirm architecture and identity
  • Documentation aligned to screening vs assay-grade needs

Specifications: what to define for a fast quote

Core specs
  • Sequence(s) for each arm (and whether arms are identical)
  • Architecture: lysine-branched, MAP-2/4/8, dendrimeric (or ask us to recommend)
  • Required modifications/handles (biotin, dyes, azide/alkyne, cysteine, linkers)
  • Quantity (mg) and intended application (immunization vs assay vs binding)
  • Purification/QC needs (desalt vs HPLC; MS; HPLC report)
Fastest quote checklist
  • ✓ One construct per line (or attach a spreadsheet)
  • ✓ State “screening” vs “assay-grade”
  • ✓ Note solubility constraints (buffer / co-solvent limits) if known
  • ✓ Indicate required purity threshold (if strict)
  • ✓ Provide timeline and shipping requirements

Branched peptide deliverables are sequence- and architecture-dependent. We recommend fit-for-purpose purity/QC targets and a purification plan aligned to your application.

Parameter Typical options Notes / guidance
Architecture Lysine-branched (Y/star); MAP-2/4/8; dendrimeric Hetero-branch constructs may require deeper characterization.
Branch points Single or multiple Strategy depends on orthogonal protecting groups and arm order.
Arm length Project-dependent Long or hydrophobic arms may require aggregation control or staged approaches.
Purification Desalted or HPLC purified (where feasible) High valency can increase hydrophobicity and broaden peaks; we plan accordingly.
QC MS identity, HPLC profile/purity (when applicable) Additional analyses recommended for complex hetero-branch constructs as needed.
Options Labels, click handles, PEG/spacers, isotope labels Specify handle location and downstream chemistry.
Quantity 1–10 mg typical (more upon request) Yield depends on sequence risk, valency, and purification level.
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QC & deliverables

Standard analytics
  • Mass spectrometry identity confirmation (MALDI-TOF or ESI-MS)
  • HPLC profile / purity assessment (where feasible)
  • Certificate of Analysis (COA)

For high-valency or hydrophobic constructs, we align analytical conditions to solubility and chromatographic behavior.

Fit-for-purpose guidance
  • Immunogens/MAP: prioritize architecture fidelity and consistent epitope presentation
  • Assay-grade: prioritize purity and analytical clarity
  • Screening: prioritize throughput and identity confirmation

For conjugation-ready constructs, see Peptide Bioconjugation.

How to compare branched peptide synthesis providers

Many branched peptide pages on the market focus on keywords like “MAP peptide synthesis” but skip the details that actually determine whether you receive the intended architecture (and whether it will behave in your assay). Use the checklist below when evaluating providers—including large catalog-style suppliers and specialty peptide labs.

Questions that predict success
  • ✓ How do you prevent mixed-arm products in hetero-branched designs?
  • ✓ What orthogonal protecting group strategy do you use at the branch point?
  • ✓ How do you manage aggregation / steric congestion for MAP-8 or high-valency constructs?
  • ✓ Will you recommend spacers/PEG/linkers to improve presentation and solubility?
  • ✓ What is your plan for purification when peaks broaden for multivalent constructs?
QC that matters for branched peptides
  • ✓ MS identity aligned to architecture complexity (not only linear mass)
  • ✓ HPLC profile/purity where feasible, with conditions compatible with your solubility constraints
  • ✓ Clear COA + documentation level: screening vs assay-grade
  • ✓ Option to add handles and confirm labeling readiness
  • ✓ Consistency approach for repeat orders / scale-up

Our approach emphasizes branch-point control, practical purification planning, and fit-for-purpose analytics so you receive a construct that matches the intended multivalent design.

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Applications

Vaccines & immunology

MAP peptides and branched epitopes are used to increase epitope density for immune studies and antibody generation.

Multivalent binding

Multivalent formats can increase avidity and enable receptor clustering or enhanced assay signal.

Diagnostics & assays

Branched constructs can improve capture/detection performance and surface presentation (design-dependent).

Also explore: Peptide Libraries and Peptide Arrays.

FAQ

What is branch (branched) peptide synthesis?

Branch peptide synthesis produces peptides with two or more peptide arms connected to a single branching core (often lysine α/ε amino groups). It’s used to increase valency and epitope density for immunology and multivalent binding applications.

Are branched peptides limited to lysine MAP peptides?

No. Lysine-based MAP peptides are common, but branched peptides can also be designed using alternative diamino acid branch points (Dap/Dab/Orn), dendrimeric or small-molecule cores, and post-synthetic branching chemistries (e.g., cysteine/thioether or click chemistry). The best strategy depends on the required spacing/geometry, steric congestion risk, solubility, stability, and your downstream application.

What are MAP peptides (MAP-2, MAP-4, MAP-8)?

MAP peptides are Multiple Antigen Peptide constructs that present multiple copies of an epitope on a lysine-based dendrimer core. MAP-2/4/8 refers to the number of epitope copies displayed (commonly 2, 4, or 8).

Can each branch have a different sequence?

Yes. Hetero-branched peptides can be made using orthogonal protecting groups so each arm is elongated independently, enabling distinct motifs on different branches.

Why do branched peptides fail in standard SPPS?

Common issues include steric crowding at the branch point, uneven arm growth, and on-resin aggregation due to high local sequence density. We mitigate these risks through coupling optimization, aggregation control, and orthogonal deprotection strategies.

What QC is recommended for branched peptides?

Most projects use MS identity and HPLC profile/purity where feasible. For complex hetero-branch constructs, additional characterization may be recommended depending on your application and required confidence in architecture fidelity.

What QC is recommended for branched peptides?

Most projects use MS identity and HPLC profile/purity where feasible. For complex hetero-branch constructs, additional characterization may be recommended depending on your application and required confidence in architecture fidelity.

Do branched peptides replace carrier-protein conjugation for immunogens?

Sometimes. MAP/branched formats can increase epitope density without a carrier protein, which may be useful in certain immunology workflows. The best choice depends on your epitope and desired immune response.

More FAQ'sAll FAQ's
CONTACT

Speak to a Peptide Scientist

Share your sequence(s), target architecture (lysine-branched, MAP-2/4/8, or “recommend”), any modifications/handles, quantity, and intended application. We’ll propose practical specifications and a synthesis/purification/QC plan aligned to your goals.

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Tip: For MAP designs, specify epitope copy number (2/4/8), spacing/linker preferences, and whether you want carrier-free presentation.

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