Peptide–Oligonucleotide Conjugation

POCs for delivery, targeting, and functional studies—built with site-specific chemistry, linker strategy selection, and fit-for-purpose QC.

Integrated peptide–oligonucleotide conjugation—designed, synthesized, and validated under one roof by Bio‑Synthesis.

Overview

Integrated peptide and oligonucleotide biosynthesis with site‑defined conjugation
Peptide–siRNA / ASO / aptamer Flexible Chemistries Bench to Kilo Scale ISO 9001:2015/ISO 13485:2016 45+ Years of Expertise U.S. Facilities – Texas

Peptide–oligonucleotide conjugation at Bio‑Synthesis uniquely integrates in‑house peptide synthesis and oligonucleotide manufacturing into a single, tightly controlled workflow. Unlike providers that focus only on oligonucleotides or outsource peptide components, we design, synthesize, conjugate, purify, and analyze both molecules internally.

This unified biosynthesis approach reduces hand‑off risk, shortens timelines, and ensures that linker chemistry, attachment site, purification strategy, and QC are aligned from the start. It is particularly important for peptide–DNA, peptide–RNA, peptide–ASO, and peptide–siRNA conjugates, where small deviations in purity, stoichiometry, or handle placement can significantly affect biological performance.

By combining expert peptide chemistry, automated oligonucleotide synthesis, and site‑specific bioconjugation, we deliver reproducible peptide–oligonucleotide conjugates supported by fit‑for‑purpose analytical confirmation.

Peptide–oligonucleotide conjugation is the covalent attachment of a peptide to an oligonucleotide (DNA or RNA) to add functionality that nucleic acids alone often lack. Common goals include enhanced cellular uptake (CPPs), targeted delivery (receptor-binding peptides), endosomal escape, improved serum stability, or controlled presentation on surfaces.

Because peptides and oligonucleotides behave very differently (charge, solubility, stability), successful POC synthesis depends on a practical plan: choose a site of attachment, select a linker chemistry compatible with both components, and define a QC strategy that confirms identity, purity, and conjugation ratio.

Peptide–oligonucleotide conjugation schematic showing optional linking chemistries (thiol–maleimide, click, disulfide) for DNA/RNA/ASO/siRNA.
Figure: Optional linking chemistry for peptide–oligonucleotide conjugates (thiol–maleimide, click, disulfide) compatible with DNA/RNA/ASO/siRNA.

Related services: Click Chemistry Peptides, Cysteine-Specific Chemistry, Cleavable Linker Peptides, Peptide Conjugates.

What is a peptide–oligonucleotide conjugate?

A peptide–oligonucleotide conjugate (POC) is a hybrid biomolecule made by covalently linking a peptide (typically 5–50 aa, but broader is possible) to an oligonucleotide (DNA or RNA, including ASOs, aptamers, guide RNAs, or siRNA strands). The peptide provides a functional domain (e.g., targeting, uptake, endosomal escape) while the oligonucleotide provides sequence-specific hybridization or gene regulation.

When POCs help most

When delivery is limiting: uptake, biodistribution, or endosomal escape.

What defines “site-specific”

A single planned attachment point that avoids heterogeneous mixtures and improves reproducibility.

What to decide early

Peptide role + oligo chemistry + linker type + QC success criteria.

Why conjugate a peptide to an oligonucleotide?

Cellular uptake

CPPs and uptake-enhancing peptides reduce reliance on transfection reagents for many workflows (sequence and cargo dependent).

Targeting

Receptor-binding peptides can bias distribution to cell types or tissues—useful for in vitro targeting studies and translational programs.

Endosomal escape

Endosomolytic or pH-responsive peptides can increase effective cytosolic availability for RNAi/ASO mechanisms.

Serum stability

Linker choice and steric shielding can improve stability—often used alongside backbone/sugar modifications on the oligo.

Modularity

Peptide and oligo can be optimized independently, then combined via a defined conjugation handle set.

Assay compatibility

Add tags (biotin/fluorophores) or immobilization handles while keeping nucleic-acid recognition intact.

Typical peptide roles in POCs
  • CPP / uptake enhancer: increase internalization and reduce formulation complexity
  • Targeting ligand: receptor-binding peptides for cell-type bias
  • Endosomal escape: pH-responsive or membrane-active segments
  • Stability / half-life: albumin-binding motifs, PEG spacers (project-dependent)
  • Assembly / display: multivalent scaffolds for surfaces and nanostructures
  • Controls: scrambled peptide or non-binding variants for mechanistic interpretation

Conjugation chemistry and linker strategies

Thiol–maleimide (Cys)

Fast, efficient coupling when the peptide contains a single planned cysteine (or engineered thiol handle).

  • Best for: single-site attachment + defined stoichiometry
  • Design tip: avoid competing thiols; control thiol state
  • Linker options: stable or cleavable variants (project-dependent)
Click chemistry (SPAAC / CuAAC)

Bioorthogonal azide–alkyne ligation. SPAAC avoids copper; CuAAC can be higher-yield for some systems.

  • Best for: harsh-condition avoidance + modular assembly
  • Design tip: choose handle placement to avoid disrupting hybridization
  • Great for: multi-component build strategies
Amide coupling (NHS/EDC)

Carboxyl-to-amine coupling for straightforward attachment when selectivity is controlled by design.

  • Best for: single, unique amine or carboxyl handle constructs
  • Watch-outs: multiple amines can cause heterogeneity
  • Often paired with: protected/orthogonal handle planning
Disulfide (reducible)

Reversible linkage for intracellular release concepts (redox environment dependent).

  • Best for: triggered release designs
  • Watch-outs: scrambling if multiple cysteines exist
  • Requires: clear handling conditions for storage/use
Cleavable linkers

Disulfide, enzyme-cleavable, or pH-labile linkers (project-dependent) to release peptide or oligo in cells.

  • Best for: mechanism-driven delivery hypotheses
  • Design tip: define cleavage trigger and assay readout
  • QC: confirm intact + expected cleavage products (if required)
Handle planning

Where you attach matters as much as how you attach. We support N-term, C-term, or side-chain handles with orthogonal protection.

  • Attachment sites: N-terminus, C-terminus, Lys, Cys, internal modifier
  • Spacer tuning: PEG units, alkyl linkers, aromatic linkers
  • Goal: minimize impact on binding/hybridization
How we reduce common POC risks
  • Heterogeneity control: single planned reactive handle; orthogonal protection strategies
  • Oligo integrity: mild conditions, salt/pH control, avoid unnecessary heat/metal exposure
  • Solubility planning: spacer choices and buffer-compatible handling to avoid aggregation
  • Purification realism: choose methods aligned to charge + hydrophobicity + expected byproducts
  • QC alignment: LC–MS where feasible + orthogonal confirmation (gel/UV) for oligo components
  • Interpretability: define “success” (ratio/purity) based on application, not a generic number

Design considerations (how to choose a practical POC strategy)

1) Define the peptide’s job

Targeting ligand, CPP/uptake enhancer, endosomal escape, immobilization tag, or control. The role determines whether you need a stable or cleavable linker.

2) Choose the attachment site

N-terminus, C-terminus, Lys side-chain, or a single engineered Cys. One planned site = fewer mixtures and cleaner analytics.

3) Pick the linker by biology

Stable (tracking/assays) vs cleavable (release concepts). Match trigger (redox, enzyme, pH) to where the conjugate needs to activate.

4) Manage charge & solubility

POCs combine highly charged oligos with peptide hydrophobicity. Spacer choice (PEG/alkyl) and buffer planning reduces aggregation and broad chromatography.

5) Plan purification realistically

Expect peak broadening and construct-dependent retention. We select purification methods that match charge/hydrophobicity and likely byproducts—not a template method.

6) Align QC to what you need

Confirm identity + ratio with orthogonal evidence (LC–MS where feasible, HPLC/UPLC profile, UV/Vis, gel). Define success criteria for your assay, not a generic number.

Common build patterns we support
  • Oligonucleotide peptide conjugation via SPAAC (azide–DBCO) for copper-free conditions
  • Peptide–siRNA: strand-specific attachment (sense vs antisense) to preserve RNAi activity
  • Peptide–ASO: attachment planned to avoid steric blocks near functional regions
  • Cys–maleimide for fast, defined 1:1 coupling (single planned thiol)
  • Cleavable designs: disulfide or other triggers (project-dependent) with optional cleavage verification
  • POC controls: unconjugated components + scrambled peptide variants (recommended)

Internal resources: Click Chemistry Peptides, Cysteine-Selective Conjugation, Cleavable Linker Peptides.

Supported oligonucleotide and peptide formats

Oligonucleotide types
  • siRNA (single strand or duplex strategies; strand-specific attachment)
  • ASO (gapmer and related formats; attachment position planned to preserve activity)
  • DNA (ssDNA/dsDNA probes; barcodes; nanostructure components)
  • RNA (ssRNA; guide/handle RNAs; project-dependent)
  • Aptamers (targeted binding + peptide-enabled features)

We can work with modified backbones/sugars/bases when compatible with the chosen conjugation chemistry. Related: Peptide–DNA conjugation and Peptide–RNA conjugation.

Peptide options
  • CPPs and uptake-enhancing peptides
  • Targeting ligands (receptor-binding motifs)
  • Endosomal escape / pH-responsive segments
  • Spacer + handle engineering (Lys/Cys/azide/alkyne)
  • Controls (scrambled or non-binding variants)

We can also add optional functional tags (biotin/fluorophores) when they do not interfere with conjugation/QC requirements.

Service menu: common POC builds
Peptide–siRNA conjugation

Targeting/uptake peptides linked to one strand (or handle) with ratio control and gel/LC confirmation.

Peptide–ASO conjugation

Peptide-enabled delivery with attachment planned to minimize impact on RNase H or steric accessibility.

Peptide–probe conjugation

DNA/RNA probes or barcodes with peptide tags for immobilization, capture, or assay workflows.

Need a different bioconjugate? See Peptide Bioconjugation for polymer/protein/small-molecule and imaging conjugation options.

Workflow: from concept to conjugate

1) Strategy & design review

Define peptide role, oligo format/chemistry, attachment site, linker type, and success criteria (ratio/purity/analytics).

2) Build components

Synthesize peptide (SPPS) and oligo with planned reactive handles (azide/alkyne, thiol, amine, carboxyl, internal modifier).

3) Conjugate, purify, QC

Run conjugation under oligo-compatible conditions, purify with a practical method, and confirm identity using orthogonal analytics.

Fit-for-purpose deliverables
  • Research-grade: MS + HPLC/UPLC profile (where feasible) + UV/gel confirmation as appropriate
  • Assay-grade: optimized purification + clear ratio reporting + documentation for reproducibility
  • Controls: unconjugated peptide/oligo, scrambled peptide, or alternative linkage site (project-dependent)
  • Scale: mg-scale common; higher quantities available depending on components and purity requirements

Specifications: what to define for a fast quote

Core specs
  • Oligo: type (DNA/RNA/ASO/siRNA), sequence, length, chemistry/modifications, strand/duplex requirements
  • Peptide: sequence, modifications, role (CPP/targeting/escape), desired attachment site (N/C/side-chain)
  • Linker: preferred chemistry (click, maleimide, amide, disulfide, cleavable) or “recommend”
  • Stoichiometry: 1:1 (common) or multivalent (project-dependent)
  • Quantity/purity: mg amount + intended use (screening vs assay-grade)
Fastest quote checklist
  • One construct per line (or attach a spreadsheet)
  • State your intended mechanism (delivery / targeting / probe)
  • Indicate buffer/solvent constraints for your assays
  • Specify whether you need strand-specific attachment (siRNA)
  • List required QC outputs (LC–MS, HPLC, gel, UV)

Practical planning matters because peptides and oligos can change each other’s chromatography and solubility. We recommend specifications that match your application and analytics goals.

Parameter Typical options Notes / guidance
Attachment site N-terminus, C-terminus, Lys side-chain, Cys handle, internal modifier Prefer a single planned site to avoid mixtures.
Linker chemistry SPAAC/CuAAC, maleimide-thiol, amide coupling, disulfide, cleavable Choose based on stability vs release, and oligo compatibility.
Oligo chemistry DNA/RNA; ASO variants; modified bases/sugars (project-dependent) Some modifications improve stability but can affect conjugation conditions.
Purification HPLC/UPLC, SEC, desalting (case-dependent) POCs can broaden peaks; method choice is construct-specific.
QC package LC–MS (where feasible), HPLC profile, UV/Vis, gel confirmation Orthogonal QC is often recommended for oligo-containing products.
Quantity 1–10 mg typical; higher on request Yield depends on components, linker, and purification level.

QC & deliverables

Typical QC outputs
  • LC–MS intact mass (where feasible for the construct)
  • Analytical HPLC/UPLC profile and purity reporting (method depends on construct)
  • UV/Vis quantitation (nucleic acid absorbance) and labeling checks
  • Gel-based confirmation (common for oligo verification; project-dependent)
  • COA + supporting documentation

POCs can be analytically challenging: chromatography may reflect both charge and hydrophobicity. We align methods to your construct rather than forcing a one-size-fits-all purity number.

What “good” looks like (practically)
  • Identity confirmed by MS (or a justified alternative) plus orthogonal evidence
  • Conjugation ratio known (e.g., 1:1) with clear reporting
  • Purity appropriate to the intended use (screening vs assay-grade)
  • Stability handling guidance (buffers, storage, redox considerations)

If you need additional confirmation (e.g., cleavage verification for a cleavable linker), include that requirement up front.

Applications

Delivery research

Test targeting peptides, CPPs, and escape motifs for improved uptake and functional knockdown/readouts.

Diagnostics & biosensors

Peptide tags for immobilization, capture, or signal generation while maintaining oligo recognition.

Nanostructures & assembly

DNA/RNA structures functionalized with peptides to add binding, localization, or catalytic features.

Also exploring imaging or radiochemistry? See Peptide Bioconjugation for imaging-agent and radiolabeling options.

FAQ

Which linker chemistry is best?

It depends on (1) whether you need a stable or cleavable connection, (2) handle availability (Cys vs azide/alkyne), and (3) oligo compatibility. If you provide sequences and goals, we recommend a practical route.

What is the difference between peptide–oligo and peptide–siRNA conjugation?

Peptide–oligo conjugation is the umbrella category. siRNA conjugation often requires strand-specific attachment decisions and duplex handling to preserve RNAi activity.

Can you do site-specific conjugation?

Yes. We prioritize a single planned reactive handle (e.g., one cysteine or a single azide/alkyne) to reduce heterogeneous mixtures and improve reproducibility.

How do you confirm the conjugate?

We typically combine LC–MS (where feasible) with HPLC/UPLC profiling plus orthogonal confirmation such as UV/Vis quantitation or gel-based methods (construct dependent).

Do modified oligos change the conjugation?

They can. Backbone/sugar/base modifications can affect stability, solubility, and compatibility with certain conditions. We factor this into linker selection and reaction planning.

What information do you need to quote?

Oligo type/sequence/chemistry, peptide sequence and desired attachment site, preferred linker or “recommend,” required quantity, and QC expectations.

Can you provide controls?

Common controls include unconjugated peptide/oligo, scrambled peptide variants, or alternate attachment sites (project-dependent). Controls help interpret delivery and mechanism.

Do you support scale-up?

We commonly deliver mg-scale research quantities. Larger quantities are possible depending on component synthesis, linker strategy, and purification requirements.

CONTACT US

Speak to a Peptide Scientist

Share your oligo type/sequence/chemistry, peptide sequence and role (CPP/targeting/escape), desired attachment site, preferred linker chemistry (or “recommend”), and your QC needs. We’ll propose practical specifications and a synthesis/conjugation/purification/QC plan aligned to your application.

Tip: For siRNA projects, tell us which strand should carry the peptide and whether you need a cleavable linker.

Why Choose Bio-Synthesis

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