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Aptamer-Modified Oligonucleotides

Custom DNA and RNA aptamers for high-affinity binding, diagnostics, biosensors, targeted delivery and research — from SELEX-ready libraries to stabilized, labeled and conjugated aptamer constructs.

DNA & RNA Aptamers SELEX Libraries 2′-OMe • 2′-F • LNA/BNA Biotin • Dyes • PEG • Click HPLC/UPLC • LC-MS • Binding Support
Start by Application View Aptamer Formats
Overview Application Guide Formats Stabilization Conjugation Design & QC Applications FAQ Contact
Overview

Organize Aptamer Projects Around the Target and Use Case

Aptamers are single-stranded DNA or RNA oligonucleotides that fold into defined three-dimensional structures to bind targets such as proteins, small molecules, cell markers and biomarkers. For most projects, the important question is not just “which aptamer sequence?” but how the aptamer must perform in the final assay, delivery system or research workflow.

Bio-Synthesis supports aptamer programs from library and SELEX support through chemical synthesis, truncation, stabilization, labeling, bioconjugation, purification and analytical QC. Aptamers can be configured as capture ligands, fluorescent probes, biosensor reagents, targeted-delivery ligands, aptamer–siRNA/ASO chimeras, multivalent constructs or payload-conjugated oligos.

SEL
Discovery
Libraries • SELEX • truncation
Fold
Design
DNA/RNA • stem-loop • controls
Stab
Stability
2′ mods • PS • caps • PEG
QC
QC
HPLC/UPLC • LC-MS • Kd support

From Folded Binder to Application-Ready Aptamer

Aptamer performance depends on target binding, folding, modification placement, conjugation chemistry and final assay conditions.

1. Select / Source

Known aptamer sequence, SELEX library or new target-discovery campaign.

2. Optimize

Truncation, stem-loop tuning, counter-selection and affinity maturation.

3. Stabilize

2′-OMe, 2′-F, LNA/BNA/cEt, PS, terminal caps or PEGylation.

4. Functionalize

Biotin, fluorophore, quencher, click handle, peptide, GalNAc or payload.

5. Purify

Desalting, HPLC, PAGE, RNase-free workflows and custom scale support.

6. Verify

UV quantitation, HPLC/UPLC, LC-MS and optional binding assay support.

Application Guide

Choose the Aptamer Format by Application

Aptamers are easier to design when the final application is defined first. Use this guide to select the most practical starting format.

Target Binding

Binder
  • Known DNA/RNA aptamer sequence
  • Truncation and folding review
  • Optional affinity maturation

Best for protein, cell or small-molecule binding

Capture & Pull-Down

Biotin
Biotin
  • 5′ or 3′ biotin aptamer
  • Spacer / linker optimization
  • Streptavidin bead or plate formats

Best for enrichment, ELISA-like and immobilization assays

Targeted Delivery

Ligand
Targeted Cell
  • Receptor-binding aptamer
  • Spacer, PEG or linker design
  • Optional GalNAc, peptide or lipid pairing

Best for receptor-directed delivery research

Aptamer Chimeras

siRNA / ASO
Aptamer siRNA / ASO
  • Aptamer–siRNA or aptamer–ASO
  • Cleavable or non-cleavable linker
  • Duplex and folding compatibility

Best for targeted gene-modulation designs

Payload Conjugates

ODC
Payload Aptamer
  • Small molecule, dye or imaging payload
  • Click, amide, thiol or spacer chemistry
  • Purification and conjugate QC

Best for aptamer-drug, imaging and biosensor probes

Multivalent Aptamers

Multimer
  • Dimeric, multivalent or bispecific design
  • PEG, hexa-EG or branched linkers
  • Avidity and spacing optimization

Best for avidity-driven binding and complex targets

Design Guide by Function

Use this quick reference when the required aptamer property is already known.

Need serum stability
2′-OMe / 2′-F + terminal cap
Need immobilization
Biotin + TEG/PEG spacer
Need fluorescence
FAM, Cy5, ATTO or quencher pair
Need conjugation
Azide, alkyne, DBCO, TCO or amino handle
Need higher affinity
Truncation, LNA/BNA or multivalent design
Need delivery
Aptamer-ligand or aptamer-siRNA/ASO construct
Need lower background
Spacer tuning, purification and control oligos
Need scale-up
HPLC/UPLC, LC-MS and CoA documentation
Formats & Products

Aptamer Product Formats and Ordering Options

This table turns aptamer options into practical ordering categories so users do not have to sort through discovery, modification and conjugation terms separately.

Common Aptamer Oligonucleotide Formats

Choose the format based on whether the aptamer is being used for discovery, binding, detection, capture, delivery or conjugation.

Representative aptamer formats supported by Bio-Synthesis.

Format Typical Design Best Use Code
Selection & Libraries Random DNA/RNA library, fixed primer regions, counter-selection planning SELEX campaigns and new binder discovery [SELEX]
Synthetic Aptamer Known aptamer sequence with standard or custom purification Research binding studies and assay development [Apt]
Biotinylated Aptamer 5′ or 3′ biotin with TEG, PEG or custom spacer Capture, pull-down, bead, plate and lateral-flow systems [Bio-Apt]
Fluorescent Aptamer FAM, Cy3, Cy5, ATTO, NIR dye, quencher or dual label Flow, microscopy, biosensors and binding readouts [Fl-Apt]
Clickable Aptamer Azide, alkyne, DBCO, BCN, TCO, tetrazine or amino/thiol handle Post-synthetic conjugation, surfaces and modular assembly [Click-Apt]
Aptamer Chimeras Aptamer linked to siRNA, ASO, payload, peptide, protein or polymer Targeted delivery, gene modulation and functional constructs [Apt-Chim]
PEGylated / Multivalent PEG, hexa-EG, branched, dimeric or bispecific aptamer architectures Half-life, spacing, avidity and multivalent binding [PEG-Apt]
Controls & Standards Scrambled controls, mutant aptamers, unlabeled references and standards Assay validation and binding specificity controls [Apt-Ctrl]
Stabilization

Aptamer Stabilization Strategy

Stabilization must protect the aptamer without disrupting the folded binding structure. Modification placement should be reviewed against the aptamer motif, target interface and final buffer.

Choose Stability Without Breaking Binding

Protect vulnerable ends and nuclease-sensitive positions first, then add affinity or scaffold changes only where folding is preserved.

Common aptamer stabilization approaches.

Strategy Primary Benefit Placement Guidance Common Applications
3′ inverted dT / terminal caps Blocks exonuclease attack Usually outside the binding core Serum-stable aptamers, capture probes
2′-O-Methyl Improves RNA stability with moderate affinity support Use where folding and binding are tolerated RNA aptamers, binding assays
2′-Fluoro Strong RNA resistance and duplex/fold stabilization Common in selected RNA aptamers; validate target binding Serum-stable aptamers, therapeutic research
LNA / BNA / cEt High affinity and nuclease resistance Use selectively; excessive locking can disrupt folding Short aptamers, high-affinity constructs
Partial phosphorothioate Backbone nuclease resistance Terminal or selected linkages; monitor protein binding Serum exposure and in vivo research
PEGylation Improves spacing, solubility or apparent persistence Use linker length to separate aptamer fold from payload/surface Delivery, surfaces, multivalent formats
Conjugation & Labeling

Aptamer Conjugation and Functional Labels

Functional aptamers often need labels, handles, surfaces or payloads. The key is to select a position and linker that preserves folding and target recognition.

Bio
Biotin-Streptavidin

Biotinylated aptamers for capture, immobilization, pull-down, lateral-flow and plate-based assays.

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Dye
Fluorescent Labels

FAM, Cy dyes, ATTO dyes, NIR dyes and quenchers for imaging, biosensors and binding readouts.

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Click
Click Handles

Azide, alkyne, DBCO, TCO, tetrazine, amino or thiol handles for modular post-synthetic conjugation.

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PEG
PEG / Spacer Design

TEG, PEG, hexa-EG and custom spacers reduce steric conflict between target, surface and payload.

Lig
Targeting Ligands

GalNAc, peptides, lipids or other ligands can be paired with aptamers for delivery-oriented designs.

Drug
Payload Conjugates

Small molecules, dyes, imaging agents or research payloads can be attached through tuned linkers.

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Surf
Surface Attachment

Chip, bead, nanoparticle and polymer-compatible aptamer formats for biosensor and capture systems.

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Chim
Aptamer Chimeras

Aptamer–siRNA, aptamer–ASO and multivalent constructs for targeted delivery and mechanism studies.

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Design & QC

Design, Purification and QC Considerations

Aptamer QC is not only identity and purity. For functional constructs, folding, binding, linker placement and application conditions matter.

Fold
Structure Preservation

Review modification placement against the binding motif, stem-loop structure and known truncation data.

Kd
Binding Assay Support

Optional Kd, EC50 or method-specific binding support can be discussed for qualifying aptamer performance.

LC
Identity Confirmation

LC-MS, MALDI-TOF or ESI-MS can support identity confirmation depending on sequence and modification complexity.

HPLC
Purification Strategy

HPLC, PAGE, desalting or RNase-free purification can be selected by length, label, conjugate and assay requirement.

Ctrl
Controls & Standards

Scrambled, mutant, unlabeled and reference aptamers help confirm specificity and assay background.

Scale
Scale-Up Support

Bench to larger-scale synthesis, conjugation, CoA and phase-appropriate documentation are available on request.

Related Applications

Where Aptamer Oligonucleotides Are Used

Aptamers are useful wherever a programmable nucleic acid binder needs capture, detection, targeting, delivery or molecular recognition.

App
Modification by Application

Explore application-driven oligo modification strategies for targeting, delivery, detection and capture.

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Bind
Affinity Binding

Biotin, affinity tags, capture ligands and immobilized oligo systems for pull-down and detection.

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Fl
Fluorescent Oligos

Fluorescent aptamers and labeled probes for imaging, binding, biosensing and diagnostic assays.

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Bio
Biotinylated Oligos

Biotin aptamers for streptavidin capture, bead immobilization, microarrays and lateral-flow systems.

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Click
Click-Ready Oligos

Azide, alkyne, DBCO, TCO and tetrazine handles for modular aptamer conjugation.

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PEG
PEGylated Oligos

PEGylated aptamers and spacer-modified constructs for distance, solubility and multivalency.

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BioC
Oligo Bioconjugation

Custom aptamer conjugation to payloads, peptides, proteins, polymers, surfaces or nanoparticles.

Explore →

Tx
Therapeutic Research

Aptamer, siRNA, ASO and chimera support for research and translational oligonucleotide programs.

Explore →

Frequently Asked Questions

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.
More FAQ'sAll FAQ's
Before Requesting a Quote

Information Helpful for Aptamer Design

Sequence
DNA/RNA aptamer or library design
Target
Protein, cell, small molecule, biomarker
Application
Binding, capture, delivery, sensor
Modification
2′ mods, biotin, dye, PEG, click
Format
Single aptamer, chimera, multivalent
QC
HPLC/UPLC, LC-MS, binding assay
Contact & Quote Request

Need help turning an aptamer sequence into an assay-ready construct?

Share your aptamer sequence or discovery goal, target, application, desired modification, conjugation strategy, scale, purification level and QC needs. Bio-Synthesis can help recommend a practical synthesis, stabilization, labeling and verification plan.
Request a Quote Speak to a Scientist

Need help before quoting?

Email: info@biosyn.com
Phone: 800-227-0627 (US/CAN)
Phone: +001-972-420-8505 (INT)
Apt

Related Services

Related aptamer, capture, fluorescent, click and bioconjugation services.

Biotin Aptamers Fluorescent Aptamers Click-Ready Oligos Oligo Bioconjugation
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Greetings Researchers,

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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.

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