Login / Register Order My Items
Contact Us
800.227.0627
Contact Us Quote Order Login / Register

Bioorthogonal Probes — Oligo Modifications

Build DNA/RNA probes that react only with their intended partners using bioorthogonal chemistries: azide–alkyne CuAAC, copper‑free SPAAC (DBCO/BCN), TCO–tetrazine iEDDA, aldehyde–aminooxy oxime/hydrazone, Staudinger ligation, and SuFEx handles. We design, synthesize, and QC your oligos from research to GMP‑like supply.

Click (CuAAC / SPAAC) TCO–Tetrazine (iEDDA) Oxime / Hydrazone Staudinger SuFEx

Overview

Bio-Synthesis manufactures bioorthogonal oligonucleotides for enzyme-free, chemoselective DNA/RNA labeling and ligation—spanning azide–alkyne click (CuAAC), copper-free SPAAC (DBCO/BCN/DIBAC), TCO–tetrazine (iEDDA), oxime/hydrazone (aldehyde ↔ aminooxy/hydrazide), Staudinger ligation (azide ↔ phosphine), and SuFEx handles, with optional SPANC (nitrone–cyclooctyne) for added orthogonality. Designs are optimized for copper-free live-cell compatibility, site-specific probe assembly, and two-color / dual-route labeling.

Typical use cases include orthogonal dual labeling (e.g., SPAAC + TCO–Tz), templated strand ligation, surface/nanoparticle conjugation, protein/peptide coupling, and in-situ pull-downs. Provide sequences, target chemistry, buffer/pH, and scale; we’ll recommend the best handles, spacers (TEG/PEG), and purification/QC to maximize yield and preserve activity.

Formats
Tubes • 96-well plates
Scale
µmol → multi-gram
QC
UPLC/HPLC • LC-MS
Supply
RUO → GMP-like

Also searched as: bioorthogonal probes, DBCO oligo SPAAC, TCO–tetrazine oligo, azide–alkyne click DNA, oxime/hydrazone DNA ligation, Staudinger ligation oligo, SuFEx oligo, SPANC oligo, copper-free click oligonucleotide.

Products & Notes

Modification Description Typical use Code
5′‑Azide / 3′‑Azide Terminal azide for CuAAC or SPAAC. Head‑to‑tail ligation; label coupling. [5′‑N3], [3′‑N3]
Internal Azide‑dU / Azide‑dC Base or sugar azide placement. Internal crosslinks; branched constructs. [N3‑dU]
5′‑Alkyne (Hexynyl) Terminal alkyne for CuAAC. Labeling; enzyme‑free junctions. [5′‑Alkyne]
DBCO (5′ / internal) Strained cyclooctyne for SPAAC. Copper‑free ligation; live‑cell friendly. [DBCO]
BCN / DIBAC / DIFO Alternative strained alkynes. Fast SPAAC with azides; orthogonality. [BCN]
Technical Notes
  • CuAAC: pH 7–8 with CuSO4/TBTA(or THPTA)+ascorbate; remove copper post‑reaction if needed.
  • SPAAC: DBCO/BCN + azide proceeds rapidly without copper; ideal for peptides/proteins & live systems.

Modification Description Typical use Code
TCO (5′ / internal) Trans‑cyclooctene handle. Ultrafast iEDDA ligation; live‑cell compatible. [TCO]
Tetrazine (5′ / internal) Dienophile partner for TCO. Rapid ligation at low µM concentrations. [Tz]
Cyclopropene Tag Small‑tag partner for tetrazine. Minimal sterics; fast cycloaddition. [CPE]
Technical Notes
  • Pair with hydrophilic linkers to reduce hydrophobic sticking in cells or on beads.
  • Excellent for orthogonal two‑color labeling (e.g., SPAAC + TCO–Tz).

Modification Description Typical use Code
5'Aldehyde C2, Aldehyde-Oligo Electrophilic –CHO handle. Oxime/hydrazone ligation with aminooxy/hydrazide. [–CHO]
5' aminooxy 11, Aminooxy‑Oligo Oxime‑forming nucleophile. Rapid oxime formation to aldehyde partners. [ONH2]
5-Formylindole Aldehyde-functionalized base analog. Site-specific aldehyde introduction for oxime/hydrazone bioconjugation. [Formyl-Ind]
Hydrazide‑Oligo Hydrazone-forming nucleophile. Adaptive linkages; optional post‑reduction. [Hyd]
Technical Notes
  • Typical pH 4.5–6.5 (anilinium catalysts enable near‑neutral conditions).
  • Reduce the oxime/hydrazone post‑ligation for permanence if needed.

Modification Description Typical use Code
Azide‑Oligo Partner for ligation with aryl‑phosphines. Labeling and conjugation without metal catalysts. [N3‑Oligo]
Phosphine‑Oligo Staudinger ligation handle. Selective coupling to azide‑functional partners. [PPh3‑Oligo]
Technical Notes
  • Use degassed buffers and protect phosphines from oxidation; prepare fresh.

Modification Description Typical use Code
Aryl Sulfonyl Fluoride Oligo –SO2F electrophile. Click‑like conjugation via SuFEx partners. [Ar‑SO2F]
Fluorosulfate Oligo –OSO2F handle. Link to amines/phenols via SuFEx chemistry. [OSO2F]
Technical Notes
  • Optimize pH and nucleophile (amine/phenol) for clean conversion; avoid competing nucleophiles.

Modification Description Typical use Code
Nitrone‑Oligo Spin‑trapping nitrone handle. SPANC to DBCO/BCN analogs; orthogonal routes. [Nitrone]
DBCO/BCN Partner Strained alkyne counterpart. Copper‑free cycloaddition with nitrone. [DBCO], [BCN]
Explore related chemistries
Services at a glance
  • Custom design review
  • RUO → GMP‑like manufacturing
  • QC: UPLC/HPLC, LC‑MS
Need help choosing the best bioorthogonal route?

We’ll recommend handles, spacers, and buffers to maximize yield and preserve activity.

Technology • Design • Application

Technology
  • CuAAC (azide ↔ alkyne); SPAAC (DBCO/BCN—copper‑free).
  • TCO–Tetrazine iEDDA — ultrafast ligation at low µM; excellent for live‑cell compatible workflows.
  • Oxime/Hydrazone (aldehyde ↔ aminooxy/hydrazide) — tunable, reducible to permanence.
  • Staudinger ligation (azide ↔ phosphine) — mild, chemoselective labeling.
  • SuFEx (–SO2F) — sulfur(VI) fluoride exchange for robust conjugation in water‑compatible media.
Design
  • Place complementary pairs on opposite strands/termini (e.g., 5′‑azide × 3′‑DBCO).
  • Use short PEG/TEG spacers near junctions for yield and accessibility.
  • For live cells or sensitive cargos, prefer SPAAC or TCO–Tz (no copper).
  • For oxime/hydrazone, consider anilinium catalysts at neutral pH; optionally reduce after ligation.
  • Include 3′ end blockers where needed to prevent unwanted extension.
Application
  • Enzyme‑free strand joining, circularization, templated reactions.
  • Conjugation to peptides, proteins, nanoparticles, and surfaces.
  • Live‑cell labeling, pull‑downs, and proximity assays (copper‑free routes).
  • Dual/orthogonal labeling using CuAAC + TCO–Tz in one construct.

Tip: provide sequences, target chemistry, and environment (buffer, pH, additives) for best design.

FAQ

Which chemistry is best for live‑cell or protein‑sensitive systems?

Use copper‑free routes: SPAAC (DBCO/BCN) or TCO–Tetrazine. Both are fast and biocompatible in aqueous buffers.

Can I combine two orthogonal reactions on one oligo?

Yes. Common pairs are SPAAC + TCO–Tz or CuAAC + Oxime/Hydrazone to enable multiplex labeling or staged assembly.

How should I handle phosphine or TCO reagents?

Phosphines oxidize—prepare fresh and use degassed buffers. TCO can isomerize—store protected from light and avoid prolonged high temperatures.

What purification/QC do you recommend?

We recommend HPLC/UPLC purification and LC‑MS confirmation; additional testing (endotoxin, residual copper) is available on request.

Speak to a Scientist

Tell us about your bioorthogonal project. We’ll recommend the most suitable chemistry (CuAAC, SPAAC/DBCO, TCO–Tetrazine, Oxime/Hydrazone, Staudinger, SuFEx), spacers, and purification/QC.

Please avoid confidential details; we can arrange an NDA if needed.

Email Instead

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 40+ years of delivering high quality, fast and scalable synthetic biology solutions.

Greetings Researchers,

Please be advised that any information, guidelines, writeups, and oral/video/graphic content on our website are intended solely as general guidelines.
It is the researcher's sole responsibility to conduct thorough research on the designs of the products intended for their experiments before submitting
their designs to Biosynthesis for review of production feasibility.
Thank you for your understanding.

Quick Links