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

Aptamer-Modified Oligonucleotides

Engineer high-affinity aptamer ligands and aptamer-conjugated oligos for diagnostics, targeted delivery, and research. From SELEX discovery to stabilization and conjugation (biotin, dyes, PEG, GalNAc, click), we deliver assay-ready materials with full QC.

SELEX Discovery 2′-OMe / 2′-F / LNA / PS Biotin • Dyes • Click Aptamer–siRNA/ASO PEG / Multivalent RUO → GMP-like
Selection Stabilization Conjugations Diagnostics Therapeutics

Overview

Aptamers are single-stranded DNA/RNA that fold into 3D structures to bind proteins, small molecules, and cells with antibody-like specificity. Bio-Synthesis supports custom aptamer programs end-to-end—library design & SELEX, sequence optimization and truncation, stabilization chemistries (2′-OMe, 2′-F, LNA/BNA, cEt, partial PS), and conjugations (biotin, fluorophores, PEG, GalNAc, peptides/antibodies, click handles).

We manufacture at scales from µmol to multi-gram with HPLC/UPLC purification, LC-MS confirmation, and optional binding/functional assays. Deliverables include documentation/COA and RUO → GMP-like pathways.

Formats
Tubes • Plates • Kitting
Scale
µmol → multi-gram
QC
UPLC/HPLC • LC-MS • Bind
Supply
RUO → GMP-like
What you get with Bio-Synthesis
  • Design/SELEX: library strategy, selection, counter-selection, truncation, and affinity maturation.
  • Stabilization: 2′-OMe/2′-F; LNA/BNA/cEt blocks; partial PS; end-caps; PEGylation.
  • Conjugation: biotin/streptavidin, dyes (FAM/Cy5/ATTO), GalNAc, PEG, click (azide/DBCO/TCO), peptide/antibody.
  • Chimeras: aptamer–siRNA/ASO fusions; multivalent and bispecific designs.
  • Analytics: HPLC/UPLC, LC-MS, optional Kd/EC50 binding assays.

Also searched as: aptamer oligonucleotide, aptamer conjugate, aptamer-siRNA chimera, biotinylated aptamer, fluorescent aptamer, PEGylated aptamer, GalNAc aptamer.

Quick chooser — pick the right aptamer format

Goal Best pick Why / notes
Surface capture Biotinylated aptamer High-affinity SA/biotin interface; plates, beads, and sensor chips.
Fluorescent readout Fluorescent aptamer (± quencher) Direct detection, FRET/turn-on designs, imaging.
Targeted RNAi Aptamer–siRNA/ASO chimera Cell-type binding + payload knockdown; stabilize with 2′-OMe/2′-F/LNA, PS.
In vivo half-life PEGylated aptamer Improves PK/PD; reduces renal clearance and aggregation.
Modular assembly Clickable aptamer (azide/DBCO/TCO) Bioorthogonal attachment to surfaces, particles, or payloads.
Browse Products & Notes Read FAQs

Products & Notes

Service / Modification Description Typical use Code
SELEX Campaign (DNA/RNA) Random library (1013–15 diversity); positive/negative selection; sequencing analysis. Discovery of novel binders to proteins, cells, or small molecules. [SELEX]
Truncation & Optimization Minimal binding motif; stem-loop tuning; affinity maturation. Shorter, cheaper, and more stable binders. [Apt-Opt]
Stabilized Library 2′-OMe/2′-F substitutions; LNA/BNA/cEt blocks; partial PS; end-caps. Resistance to nucleases; improved Kd in serum. [Lib-Stab]
Technical Notes
  • Counter-SELEX: include close homologs/surface materials to suppress off-target binders.
  • Early truncation: map minimal motifs before conjugation to reduce sterics and cost.
  • RNA routes: prefer 2′-F pyrimidines + terminal PS; validate Mg2+/Na+ for folding.

Modification Description Typical use Code
5′-Biotin-TEG Biotin via flexible spacer for reduced sterics. ELONA/ELASA, pull-downs, immobilization. [5′-Bio-TEG]
3′-Biotin-TEG Terminal biotin with capture + blocking of 3′ end. Capture with non-extendable end. [3′-Bio-TEG]
Dual-Biotin Biotin at 5′ and internal/3′ for strong anchoring. High-strength immobilization; flow cells. [Apt-2xBio]
Technical Notes
  • Use TEG/short PEG between biotin and the binding domain to preserve Kd.
  • For polymerase exposure, pair with a 3′ terminator (e.g., 3′-inv-dT or 3′-PO4).
  • Dual-biotin improves anchoring on flow cells and high-shear sensors.

Modification Description Typical use Code
5′-FAM / 3′-FAM Green dye labeling; internal options available. Fluorescence detection, imaging. [FAM-Apt]
Cy5 / ATTO 647N Far-red labels for low background. Imaging, flow cytometry, FRET acceptors. [Cy5-Apt]
Dye + Quencher (BHQ) Turn-on probe designs with stem/loop quenching. Real-time binding assays & sensors. [DQ-Apt]
Technical Notes
  • Place dyes on stems/termini away from the binding pocket; add TEG if bulky.
  • For turn-on probes, tune stem length and pick BHQ/Iowa Black to match emission.
  • Re-check Tm and folding after labeling (buffer/ionic strength dependent).

Format Description Typical use Code
Aptamer–siRNA (duplex) Ligand fused to guide/passenger; 2′-OMe/2′-F/LNA + partial PS. Cell-type specific gene silencing. [Apt-siRNA]
Aptamer–ASO (single) Ligand joined to antisense with stabilizing blocks. Targeted ASO delivery and uptake. [Apt-ASO]
Bispecific / Multivalent Two ligands or ligand+payload on one scaffold. Enhanced avidity or dual targeting. [Apt-Multi]
Technical Notes
  • Stabilization balance: use 2′-OMe/2′-F + partial PS; avoid over-LNA near RISC/target motifs.
  • Junction design: add short PEG/TEG spacers to reduce steric clash.
  • Confirm uptake and knockdown in the final buffer/matrix; include scrambled/non-binding controls.

Format Description Typical use Code
Non-cleavable linker Stable attachment for durable binding or blocking. Receptor antagonism, imaging probes. [Apt-Drug-NC]
Cleavable (disulfide) Reductive release in cytosol (GSH). Intracellular drug delivery. [Apt-Drug-SS]
Cleavable (hydrazone) Acid-labile release (endosomal). Endosomal release strategies. [Apt-Drug-HZ]
Technical Notes
  • Pick cleavable linkers (SS/hydrazone) for intracellular release; non-cleavable for blocking/imaging.
  • Tune linker length/hydrophilicity (PEG) to maintain folding and binding.
  • Site-map attachments away from the pocket; verify Kd post-conjugation.

Modification Description Typical use Code
5′-Azide / 3′-Azide CuAAC/SPAAC-ready handles. Surface coupling, modular probe building. [N3-Apt]
DBCO (SPAAC) Copper-free click partner to azide. Live-cell compatible conjugations. [DBCO-Apt]
TCO IEDDA partner to tetrazine for ultrafast ligation. Rapid labeling; particle assembly. [TCO-Apt]
Technical Notes
  • Insert internal spacers near handles to preserve structure.
  • For CuAAC, ensure nuclease compatibility; prefer SPAAC/IEDDA for live cells.
  • Re-test folding/binding after the click step (salt and solvent history matter).

Format Description Typical use Code
PEGylated (various MW) Linear/branched PEG at 5′/3′ or internal. PK/PD improvement; reduced aggregation. [Apt-PEG]
Multimer (dimer/trimer) Two or more aptamer units on scaffold. Avidity enhancement; multi-epitope binding. [Apt-MultiVal]
Technical Notes
  • Select PEG MW to balance solubility vs. epitope access; avoid masking the pocket.
  • For dimers, match spacer length to receptor spacing to maximize avidity.
  • Confirm activity across relevant shear/flow if used on sensors or particles.

Modification Description Typical use Code
L-DNA (mirror-image) Enantiomer of D-DNA; nuclease-proof; requires mirror-selection strategy (Spiegelmer concept). Extreme serum stability; resistant matrices. [L-DNA]
L-RNA (mirror-image) L-configured ribonucleotides; highly nuclease-resistant; specialized selection routes. In vivo aptamers with extended half-life. [L-RNA]
LNA / BNA Locked ribose (C3′-endo bias) increases Tm and nuclease resistance. Truncation with Kd retention; serum stability. [LNA]
2′-Fluoro (2′-F) 2′-F pyrimidines (± purines) stabilize C3′-endo; strong nuclease resistance for RNA aptamers. RNA aptamers in serum/cell assays. [2F]
2′-O-Methyl (2′-OMe) Bulky 2′-O-Me increases stability; can improve folding robustness. Serum stability with minimal structural perturbation. [2OMe]
2′-O-Methoxyethyl (2′-MOE) Hydrophilic 2′-O substituent; strong nuclease resistance and improved PK. Therapeutic-leaning designs; reduced nonspecific binding. [2MOE]
Partial PS backbone Phosphorothioate at termini/selected positions slows exonuclease attack. Terminal protection; in vivo exposure. [PS]
Technical Notes
  • L-DNA/L-RNA: require mirror-selection strategies; deliver exceptional nuclease resistance.
  • LNA/BNA: place in stems/non-critical regions; over-locking loops can reduce affinity.
  • 2′-F vs 2′-OMe vs 2′-MOE: 2′-F = compact/high stability; 2′-OMe = balanced; 2′-MOE = PK & low nonspecific binding.
  • Combinatorial: mix 2′-F/2′-OMe with LNA blocks + terminal PS; re-validate folding and Kd.

Item Description Typical use Code
Scrambled Aptamer Sequence-shuffled control preserving base composition. Specificity control in binding assays. [Apt-Scr]
Non-binding Mutant Point mutations to disrupt binding loop. Negative control for signal attribution. [Apt-NB]
Positive Control Aptamer Validated binder for benchmark target. Platform qualification, calibration. [Apt-PC]
Explore related chemistries
Services at a glance
  • SELEX & sequence optimization
  • RUO → GMP-like manufacturing
  • QC: UPLC/HPLC, LC-MS, binding assays
Need help picking an aptamer format?

We’ll recommend stabilization, linker strategy, and labels to meet your Kd and assay goals.

Technology • Design • Application

Technology
  • Folding & binding: stem-loops and bulges create pockets for high-affinity recognition.
  • Stabilization: 2′-OMe/2′-F, LNA/BNA/cEt blocks, end-caps, partial PS; PEGylation for PK.
  • Conjugation: biotin/SA, dyes/quencher pairs, click handles, GalNAc, peptides/antibodies.
Design
  • Map labels/linkers away from the binding pocket; add TEG/PEG spacers to limit sterics.
  • For chimeras, keep junction flexible and protect the payload with 2′-mods + PS.
  • Validate folding (CD/fluorescence) and binding (SPR/ELONA/flow) post-modification.
Application
  • Diagnostics: ELONA/ELASA, lateral flow, electrochemical/optical sensors, imaging.
  • Therapeutics: targeted delivery (aptamer–siRNA/ASO), aptamer–drug conjugates.
  • Research: affinity capture, receptor mapping, live-cell labeling without antibodies.

Tip: include scrambled/non-binding controls to track specificity drift across lots and buffers.

FAQ

Do you run SELEX or only synthesize provided sequences?

We offer both. We can execute end-to-end SELEX campaigns or synthesize and optimize your provided aptamer sequences (including truncation and conjugations).

How do you improve serum stability?

Introduce 2′-OMe/2′-F substitutions, LNA/BNA/cEt blocks, partial PS backbones, and consider PEGylation/end-caps. We tune placement to retain binding while resisting nucleases.

What QC data are provided?

Standard packages include HPLC/UPLC traces and LC-MS confirmation; optional binding/functional data (e.g., Kd by SPR/ELONA) are available.

Which labels and linkers do you support?

Biotin, dyes (FAM/Cy3/Cy5/ATTO), quenchers (BHQ/Iowa Black), PEG (various MW), GalNAc, peptide/antibody, and bioorthogonal handles (azide/DBCO/TCO) with cleavable or non-cleavable linkers.

Typical inputs to start a project?

Target identity and matrix, desired application, known sequences (if any), affinity goals, required conjugations/labels, scale, purification, and QC expectations.

Speak to a Scientist

Tell us about your aptamer target and application. We’ll recommend selection strategy, stabilization, and conjugation to meet your performance goals.

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