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Affinity Binding & Capture Oligonucleotides

Custom DNA, RNA, aptamer and probe synthesis with affinity tags, capture ligands and immobilization chemistries for purification, target enrichment, biosensors, diagnostics and molecular detection workflows.

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Overview Affinity Technologies Selection Map Modification Table Applications Reading FAQ Contact
Overview

Custom affinity-tagged oligonucleotides for capture, purification and detection

Affinity binding and capture oligonucleotides are designed to connect nucleic acid recognition with a defined binding partner, surface, bead, antibody, protein, metal complex or immobilization platform. These constructs allow researchers to capture targets, enrich nucleic acid or protein complexes, immobilize probes on analytical surfaces, build biosensors, and develop molecular detection workflows.

Bio-Synthesis manufactures custom affinity-modified DNA, RNA, aptamer, probe and specialty oligonucleotide constructs using a broad set of capture tags and ligand chemistries. Common options include biotin, desthiobiotin, digoxigenin (DIG), dinitrophenyl (DNP), FITC/FAM, Ni-NTA/His systems, thiol and amino handles, click-ready groups, chelators, peptide ligands, aptamer constructs, and other custom affinity or immobilization chemistries.

Modification placement can be configured at the 5′ end, 3′ end or internal positions depending on the assay format. Spacer and linker options such as C6, C12, TEG and PEG can be used to improve accessibility on beads, plates, membranes, nanoparticles, gold surfaces, SPR chips, microarrays and other crowded capture environments.

Biotin & Desthiobiotin DIG, DNP & FITC Labels Ni-NTA / His Capture Surface Immobilization HPLC / PAGE / MS QC
Affinity capture workflow animation Three animated lanes showing biotin oligo capture on streptavidin beads, DIG hapten detection with antibodies, and thiol oligo immobilization on a gold surface. Biotin oligo → streptavidin beadHigh-affinity capture, pull-down and target enrichmentCaptured target DIG / DNP / FITC oligo → antibody recognitionHapten labeling, non-radioactive detection and immunoassaysDetection readout Thiol / amino / click oligo → surface immobilizationGold surfaces, SPR chips, microarrays, beads and biosensorsSurface-bound probe

Biotin Systems

Biotin, Biotin-TEG, desthiobiotin and internal biotin.

DIG, DNP & FITC

Hapten and fluorescent labels for antibody recognition.

Ni-NTA / His Capture

Reversible metal-affinity capture and immobilization.

Surface Chemistries

Thiol, amino and activated-surface attachment handles.

Click Handles

Azide, alkyne, DBCO, TCO and tetrazine-ready designs.

Chelator Systems

DOTA, NOTA, DTPA, EDTA and metal-binding ligands.

Aptamer Constructs

Affinity capture reagents for target recognition and biosensing.

Protein & Peptide

Oligo-protein, oligo-peptide and ligand conjugates.

Affinity Capture Technologies

Affinity binding and capture modification platforms

Bio-Synthesis offers a broad portfolio of affinity binding and capture modifications designed for purification, target enrichment, immobilization, biosensing, molecular detection and custom bioconjugation workflows.

BIO

Biotin Capture Systems

Biotin, Biotin-TEG, desthiobiotin and internal biotin modifications for high-affinity streptavidin-mediated capture and enrichment.

  • Pull-down assays
  • Magnetic beads
  • Target enrichment
  • NGS workflows
DIG

DIG Labels

Antibody-recognized digoxigenin modifications for hybridization assays, blotting applications and non-radioactive detection systems.

  • Southern blot
  • Northern blot
  • In situ hybridization
  • Immunodetection
DNP

DNP & Hapten Tags

DNP and related hapten chemistries enabling antibody-mediated recognition, detection and affinity capture.

  • ELISA workflows
  • Capture assays
  • Detection platforms
  • Custom immunoassays
FITC

FITC & Fluorescein Labels

Fluorescent affinity tags supporting detection, tracking and affinity-based recognition applications.

  • Fluorescence assays
  • Cell studies
  • Imaging workflows
  • Hybridization analysis
NTA

Ni-NTA & His Capture

Metal-affinity interaction platforms supporting reversible immobilization, protein capture and purification workflows.

  • Protein capture
  • Surface immobilization
  • Biosensors
  • Purification systems
SUR

Surface Immobilization

Reactive groups for attachment to beads, chips, nanoparticles, electrodes and analytical surfaces.

  • SPR
  • Microarrays
  • Biosensors
  • Gold surfaces
M+

Chelator-Based Systems

DOTA, NOTA, DTPA, EDTA and related ligands for metal coordination and specialized affinity workflows.

  • Metal capture
  • Radiolabeling
  • Imaging probes
  • Research applications
APT

Protein, Peptide & Aptamer Conjugates

Custom affinity constructs combining oligos with proteins, peptides, antibodies, aptamers and other biomolecules.

  • Aptamer development
  • Target recognition
  • Oligo-peptide conjugates
  • Custom affinity reagents
Affinity Modification Selection Map

Match the affinity modification to the capture partner and workflow

A compact decision map for comparing affinity systems by binding partner, best-use case, capture strength, reversibility and design constraints.

Affinity Modification Compatibility Guide

Use the table as a starting point. Final selection should consider target accessibility, background binding, reversibility, surface capacity, buffer compatibility and downstream readout.

Affinity Technology Binding Partner / Surface Best For Binding Profile Design Notes
Biotin Streptavidin, avidin, NeutrAvidin beads, plates or membranes Pull-down assays, target enrichment, immobilization, magnetic separation Very high affinity Excellent default for strong capture. Use spacers to improve access on crowded surfaces.
Desthiobiotin Streptavidin capture matrices Reversible capture, gentle elution, enrichment workflows Reversible high affinity Useful when recovery of captured material is required under milder conditions.
DIG Anti-digoxigenin antibodies Hybridization assays, blotting, non-radioactive detection, immunodetection High antibody recognition Widely used for nucleic acid probe detection and antibody-mediated capture.
DNP Anti-DNP antibodies ELISA-style workflows, immunoassays, antibody capture and detection High antibody recognition Useful hapten tag for custom immunodetection systems.
FITC / FAM Anti-FITC antibodies, fluorescence readers, imaging systems Fluorescence detection, tracking, flow and hybridization workflows Moderate affinity + signal Combines direct fluorescence readout with antibody recognition potential.
Ni-NTA / His Ni2+ or Co2+ NTA surfaces, His-tag proteins Reversible immobilization, protein capture, biosensors, purification workflows Reversible metal affinity Avoid EDTA and strong chelators during binding. Elute with imidazole or EDTA.
Thiol Gold surfaces, maleimide partners, disulfide-exchange systems Gold nanoparticle attachment, electrodes, SPR, self-assembled monolayers Covalent / surface affinity Protect thiols before use and reduce/deprotect immediately before conjugation when needed.
Amino NHS-activated surfaces, aldehyde surfaces, carboxylated materials via EDC/NHS Slides, beads, microarrays, activated polymers and carrier conjugation Covalent attachment Flexible and broadly compatible, but linker length and surface density matter.
Azide / Alkyne / DBCO Click-ready particles, surfaces, biomolecules and polymers Orthogonal immobilization, nanoparticles, biomaterial conjugation Bioorthogonal covalent Useful when selective chemistry is required in complex biomolecular mixtures.
DOTA / NOTA / DTPA / EDTA Metal ions and chelator-compatible imaging or capture systems Metal capture, radiolabeling-compatible probes, imaging and specialty workflows Metal coordination Choose chelator based on metal identity, stability requirements and downstream conditions.
Modification Table

Available affinity tags & capture modifications

Bio-Synthesis supports a broad set of affinity binding, detection, chelation, immobilization and custom conjugation handles for DNA, RNA, aptamer and specialty oligonucleotide constructs.

System Function Common Modifications Applications
Biotin / Avidin Systems Very strong noncovalent capture on streptavidin, avidin and NeutrAvidin supports. 5′ Biotin, 3′ Biotin, Biotin-TEG, internal Biotin-dT, dual biotin, desthiobiotin. Magnetic beads, pull-down assays, target enrichment, purification, immobilized probes.
Hapten Tags Antibody-recognized labels for detection and capture workflows. DIG, DIG-dT, DNP, fluorescein/FITC, FAM, hapten-linker formats. Hybridization assays, blotting, ELISA-style detection, non-radioactive probes.
Metal Affinity Systems Reversible metal-mediated capture or immobilization. His6 peptide, NTA, NTA-TEG, Ni-NTA compatible formats. Protein capture, biosensors, reversible immobilization, purification workflows.
Thiol / Gold Surface Handles Attachment to gold, maleimide partners and disulfide-compatible systems. 5′ Thiol C6, 3′ Thiol, disulfide-protected thiol, thioctic acid, dithiolane, lipoic acid. Gold nanoparticles, electrodes, SPR, self-assembled monolayers, surface probes.
Amino / Activated Surface Handles Covalent attachment to NHS, aldehyde, carboxylated or activated surfaces. 5′ Amino C6/C12, 3′ Amino, internal amino-dT, amino-TEG, hydrazide, aminooxy. Microarrays, glass slides, beads, polymers, hydrogels, activated carriers.
Click-Ready Handles Bioorthogonal attachment to compatible particles, surfaces and biomolecules. Azide, alkyne, DBCO, BCN, TCO, tetrazine, norbornene. Nanoparticle conjugation, orthogonal labeling, biomaterial attachment, custom assemblies.
Chelator Tags Metal coordination for capture, imaging and specialty workflows. DOTA, NOTA, DTPA, EDTA, NTA, chelator-linker formats. Metal binding, radiolabeling-compatible probes, imaging, specialty purification.
Aptamer & Protein-Binding Constructs Affinity recognition through sequence-defined aptamers or ligand conjugates. Aptamer constructs, peptide tags, RGD, Strep-tag, FLAG, HA, oligo-protein conjugates. Aptamer development, target recognition, protein binding, custom affinity reagents.
Applications

Where affinity-modified oligos are used

Affinity-modified oligonucleotides serve as capture probes, immobilized reagents, detection tags, biosensor interfaces and custom bioconjugation intermediates.

CAP

Pull-Down Assays

Affinity-tagged oligos for isolating nucleic acid, protein or molecular complexes from mixed samples.

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BIO

Biotin-Based Capture & Enrichment

Biotinylated oligonucleotides enable high-affinity streptavidin-mediated capture, purification, target enrichment, pull-down assays, hybridization workflows and bead-based isolation.

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DX

Molecular Diagnostics

Affinity-modified probes and capture reagents for molecular diagnostics, hybridization assays, target detection, pathogen identification and assay development workflows.

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APT

Aptamer Development

Aptamer constructs with capture tags, fluorophores, linkers and immobilization chemistries.

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SPR

Biosensors & SPR

Surface-ready oligos for SPR, electrochemical biosensors and analytical detection surfaces.

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SUR

Surface Immobilization

Thiol, amino, click and chelator handles for slides, beads, chips and polymer supports.

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NP

Nanoparticle Conjugation

Affinity handles for gold nanoparticles, magnetic beads, polymer particles and nanomaterial assemblies.

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PRO

Protein–Nucleic Acid Studies

Oligo-protein, oligo-peptide and affinity-tagged constructs for interaction and capture studies.

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FAQ

What linker length should be used for bead-based capture?
C6 is a common starting spacer. C12, TEG, PEG or longer linkers may improve accessibility on crowded beads, nanoparticles, surfaces or protein-rich systems.
Which affinity tag is best for pull-down assays?
Biotin is usually the most common starting point because streptavidin beads and plates are widely available and provide strong capture. Desthiobiotin or cleavable linkers may be preferred when target recovery is required.
What is the difference between biotin and desthiobiotin?
Biotin provides extremely strong streptavidin binding and is a common default for pull-down and immobilization workflows. Desthiobiotin is useful when reversible capture and milder elution are desired.
Can affinity tags be placed internally within an oligonucleotide?
Yes. Many affinity tags can be incorporated internally through modified bases such as dT linkers. However, 5′ or 3′ placement is often preferred when maximum accessibility is needed.
Can Bio-Synthesis synthesize affinity-tagged aptamers?
Yes. Aptamers can be synthesized with affinity tags, fluorophores, quenchers, PEG spacers, biotin, thiol, amino, click handles and other functional modifications.
Are affinity-modified oligonucleotides available with HPLC purification?
 Yes. Depending on the sequence, modification and application, purification may include desalting, HPLC, PAGE or other fit-for-purpose workflows with analytical QC documentation.
More FAQ'sAll FAQ's
Contact & Quote Request

Need help selecting the right affinity capture strategy?

Share your sequence, desired affinity tag, capture target, surface type, purification requirements and downstream application. Bio-Synthesis can help identify the optimal affinity modification, linker architecture, purification workflow and analytical characterization package.
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)

Related Product

Affinity-tagged and conjugation-ready oligo options.

Biotinylated Oligos Aptamer Development Oligo Bioconjugation

Fast Quote Checklist

Include sequence, tag, position, purification target and QC needs.

Sequence Affinity Tag Position Purification QC
Scientific Background & Recommended Reading

Recommended reading & literature references

Selected references covering avidin-biotin systems, affinity conjugation, oligonucleotide functionalization and aptamer-based capture. These citations are provided for scientific background and design context rather than product-performance claims.

  1. Green NM. Avidin and streptavidin. Methods in Enzymology. 1990;184:51-67.
  2. Wilchek M, Bayer EA. The avidin-biotin complex in bioanalytical applications. Analytical Biochemistry. 1988;171(1):1-32.
  3. Hermanson GT. Bioconjugate Techniques. 3rd Edition. Academic Press; 2013.
  4. Niemeyer CM. Functional devices from DNA and proteins. Nano Today. 2007;2(3):42-52.
  5. Bunka DHJ, Stockley PG. Aptamers come of age - at last. Nature Reviews Microbiology. 2006;4:588-596.

Note: Affinity tag selection should be based on binding partner, surface type, reversibility, linker accessibility, purification strategy, background signal and downstream readout. Literature references provide general scientific context and should be evaluated within the specific assay workflow.

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Greetings Researchers,

Please be advised that any information, guidelines, writeups, and oral/video/graphic content on our website are intended solely as general guidelines.
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their designs to Biosynthesis for review of production feasibility.
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