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Biotinylated Oligonucleotides

Custom biotin labeling for DNA and RNA oligos with terminal, internal, desthiobiotin, serinol, TEG, phosphoramidite, and post-conjugation options.

Custom biotinylated oligos for streptavidin capture, immobilization, pull-down assays, purification, surface binding, hybridization detection, and reversible affinity workflows.

5′ / 3′ / Internal biotin Biotin C6 and Biotin TEG Desthiobiotin options Phosphoramidite or post-conjugation DNA & RNA compatible
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Overview Biotin Positions Biotin Modification Table Choosing the Right Biotin Biotin vs Desthiobiotin Linker Design Related Services Contact

Overview

Biotinylated oligonucleotides are DNA or RNA constructs modified with biotin to enable affinity capture, streptavidin binding, immobilization, purification, and molecular detection workflows. Biotin can be installed at the 5′ end, 3′ end, or internally depending on the assay architecture, and different linkers can be selected to control accessibility, spacing, and conjugation behavior.

Common biotinylated oligonucleotide modifications including 5' Biotin, 3' Biotin, Biotin-dT, Dual Biotin, and Biotin-TEG linkers

Representative biotinylated oligonucleotide architectures including 5′ biotin, 3′ biotin, internal biotin-dT, dual biotin, and Biotin-TEG linker designs used for affinity capture, immobilization, and molecular detection assays.

Bio-Synthesis provides a broad range of biotin modification options including Biotin C6, Biotin TEG, Biotin-dT, Biotin phosphoramidite, photocleavable biotin, serinol-linked biotin, desthiobiotin, azide-ready biotin, and post-conjugation NHS biotin formats. These chemistries support capture assays, pull-down workflows, streptavidin-coated surface binding, nucleic acid purification, reversible affinity enrichment, and probe development.

Biotin labeling is widely used because the interaction between biotin and streptavidin is exceptionally strong, making it highly effective for capture, purification, immobilization, and surface-based assay workflows. Desthiobiotin provides a useful reversible alternative when downstream release is required.

Design insight: the optimal biotin chemistry depends on where the biotin must be placed, whether streptavidin access is sterically restricted, whether reversible binding is needed, and whether the biotin is introduced directly during synthesis or after synthesis by conjugation.

Common Biotin Placement Formats

5′ Biotin

Standard terminal biotin used for surface capture, streptavidin immobilization, pull-down assays, and probe formats requiring strong terminal affinity binding.

3′ Biotin

Useful when terminal orientation matters or when capture is needed without leaving the 5′ end available for other modifications or probe architecture. A 3′ biotin can also help block extension while preserving affinity capture capability.

Internal Biotin

Biotin-dT, LC Serinol, and Desthiobiotin TEG internal formats allow capture or affinity labeling within the oligo sequence rather than only at the ends.

Biotin Modifications Available for Oligonucleotides

The table below organizes the biotin chemistries you offer by structure type, placement flexibility, and typical function in assay design. Long linkers can also be incorporated when higher streptavidin accessibility is needed.

Available Biotin Modifications for Oligonucleotide Synthesis
Biotin Modification Structure / Linker Type Placement Options Function & Structure Explanation
Biotin C6 Biotin attached through a C6 alkyl linker 5′ or 3′ Standard terminal biotin with a short alkyl spacer. Useful for streptavidin capture, immobilization, pull-down assays, and ELISA-type nucleic acid detection.
Biotin TEG Biotin linked through triethylene glycol spacer 5′, 3′, or internal depending on chemistry Hydrophilic flexible linker improves streptavidin accessibility and reduces steric hindrance relative to shorter alkyl linkers.
Biotin-dT Biotin attached to modified thymidine base 5′, 3′, or internal Supports internal placement of biotin within a probe sequence. Useful when terminal biotin is not ideal or when multiple site-controlled affinity handles are needed.
Biotin Phosphoramidite Direct synthesis phosphoramidite reagent Commonly 5′; selected internal use depending on design Installed during automated solid-phase synthesis for efficient direct biotin incorporation without post-synthetic conjugation.
PC Biotin Phosphoramidite Photocleavable biotin phosphoramidite 5′ or internal Introduces a light-cleavable connection between biotin and the oligo, enabling controlled release after capture or enrichment.
Biotin Serinol Biotin linked through serinol scaffold 5′, 3′, or internal Serinol provides stable attachment and flexible presentation of the biotin group, often improving accessibility in crowded assay formats.
5′ Biotin Terminal biotin modification 5′ Widely used for immobilization, streptavidin-coated bead capture, affinity purification, and hybridization assays requiring terminal orientation.
5′ Biotin II Extended-linker terminal biotin 5′ Longer spacer version of 5′ biotin that helps reduce steric crowding on surfaces or in bead-based capture formats.
3′ Biotin Serinol 3′ terminal serinol-linked biotin 3′ Useful when 3′ capture is needed or when the 5′ end is reserved for another modification or reporter function.
PC Biotin NHS Post-Conjugation Photocleavable NHS biotin reagent for post-synthetic coupling Requires amino handle; often 5′ or internal amino-modified oligo Allows biotin installation after synthesis through an NHS ester reaction. Useful for custom conjugation workflows or sensitive builds.
Biotin TEG Azide Biotin-TEG with azide functionality 5′, 3′, or internal depending on design Combines flexible biotin spacing with an azide click handle, supporting orthogonal bioorthogonal conjugation strategies.
Biotin TEG Phosphoramidite TEG-spaced biotin amidite 5′ and selected internal formats Direct synthesis route for introducing biotin with a flexible PEG-like linker during oligonucleotide assembly.
3′-Biotin LC Serinol Long-chain serinol biotin linker 3′ Longer chain improves streptavidin binding accessibility in immobilized or sterically restricted systems.
3′ Desthiobiotin TEG Desthiobiotin analog with TEG spacer 3′ Provides reversible affinity to streptavidin, allowing gentler elution than permanent biotin capture systems.
Desthiobiotin TEG Reversible affinity analog with TEG linker 3′, 5′, or internal Used when streptavidin-based enrichment is needed but elution under milder conditions is desired.
3′ Biotin TEG 3′ terminal TEG-spaced biotin 3′ Flexible terminal biotin for capture and hybridization workflows with improved accessibility versus shorter linkers.
Desthiobiotin TEG Azide Desthiobiotin with azide click handle and TEG spacer 5′ or internal depending on route Supports reversible affinity capture plus click chemistry compatibility for multifunctional assay designs.
Biotin LC Serinol Long-chain serinol-linked biotin 5′, 3′, and internal Longer flexible linker helps present the biotin away from the oligo backbone for better streptavidin interaction in crowded systems.
3′-Biotin TEG 3′ terminal TEG biotin 3′ Useful for capture probes, streptavidin-coated bead binding, and hybridization systems requiring a flexible 3′ biotin handle.

Choosing the Right Biotin Modification

Different biotin modifications provide different linker lengths, binding strengths, and functional capabilities. Selecting the correct biotin chemistry depends on the assay design, steric accessibility, and whether reversible release is required.

Guide to Selecting the Right Biotin Modification
Application Recommended Biotin Type Reason
Standard streptavidin capture 5′ Biotin / Biotin C6 Direct attachment with a short linker suitable for most purification, pull-down, and immobilization workflows.
Reduced steric hindrance Biotin TEG / Biotin LC Serinol Longer hydrophilic spacers improve accessibility of biotin to streptavidin on crowded surfaces or beads.
Internal labeling Biotin-dT Allows biotin placement within the oligonucleotide sequence for hybridization probes and internal affinity handles.
Strong streptavidin retention Dual Biotin Two biotin groups can improve effective binding strength for more stable immobilization.
Reversible capture Desthiobiotin TEG Supports streptavidin binding with gentler downstream release than permanent biotin capture.
Light-triggered release PC-Biotin Photocleavable linker enables controlled release after capture or enrichment.

Biotin vs Desthiobiotin

Biotin
  • Very strong streptavidin affinity
  • Best for stable immobilization and persistent capture
  • Common for pull-down, bead capture, and coated-surface assays
  • Preferred when permanent binding is acceptable
Desthiobiotin
  • Reversible streptavidin interaction
  • Useful for affinity enrichment followed by gentle elution
  • Supports purification workflows where recovery matters
  • Helpful in reversible capture or analytical enrichment methods

Biotin Linker Design Considerations

Why use longer linkers?

Spacer length can significantly influence biotin accessibility. Short linkers such as C6 biotin are suitable for many standard assays, while longer linkers such as TEG and LC serinol increase the distance between the oligonucleotide backbone and the biotin group, improving streptavidin access when steric hindrance may occur on surfaces, beads, or dense probe architectures.

Reduced steric hindrance Improved capture efficiency Better surface presentation
Direct synthesis vs post-conjugation

Biotin can be introduced directly during oligonucleotide synthesis using phosphoramidite reagents, or after synthesis through NHS post-conjugation routes when an amino-modified oligo is available.

Direct phosphoramidite build Photocleavable options Custom post-labeling
Dual Biotin Configurations

Dual biotin designs can be useful when enhanced retention on streptavidin-coated supports is desired, particularly in workflows that require very stable immobilization, repeated wash steps, or stronger effective surface anchoring.

Common Applications

Affinity Capture

Streptavidin-coated beads or surfaces for capture, pull-down, enrichment, and purification workflows.

Immobilized Probes

Surface-bound DNA or RNA probes for hybridization assays, biosensors, microarrays, and assay development.

Reversible Enrichment

Desthiobiotin-based systems for capture followed by gentle release and downstream recovery.

Magnetic Bead Workflows

Biotinylated oligos for streptavidin magnetic bead capture, washing, enrichment, and purification workflows.

Surface Immobilization

Attachment to streptavidin-coated plates, chips, and sensor surfaces for molecular detection platforms.

Nanoparticle and NGS Enrichment

Compatible with nanoparticle conjugation concepts, pull-down, and enrichment-based sequencing support workflows.

FAQ

What types of biotin modifications are available for oligonucleotides?

Available options can include terminal biotin, internal Biotin-dT, Biotin C6, Biotin TEG, serinol-linked biotin, photocleavable biotin, desthiobiotin, and post-conjugation NHS biotin formats.

Can biotin be placed internally in an oligonucleotide?

Yes. Internal insertion can be achieved using chemistries such as Biotin-dT, Biotin LC Serinol, or Desthiobiotin TEG depending on the sequence design and assay requirements.

Why use a TEG or long-chain linker?

Longer linkers improve streptavidin accessibility and reduce steric hindrance, especially in surface-bound or bead-based capture systems.

What is the difference between biotin and desthiobiotin?

Biotin is preferred for strong stable capture, while desthiobiotin is used when reversible affinity binding and gentler recovery are important.

More FAQ'sAll FAQ's

Contact & Quote Request

For the fastest quote, share your sequence, DNA or RNA type, desired biotin modification, placement position, synthesis scale, and required purity.

Quote checklist
  • Sequence(s) and format
  • Biotin type and position
  • Single, dual, or internal placement
  • Scale and purity target
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Recommended Reading

  1. Green NM. Avidin and streptavidin. Methods Enzymol. 1990.
  2. Wilson DS, Szostak JW. In vitro selection of functional nucleic acids. Annu Rev Biochem. 1999.
  3. Holmberg A et al. The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures. Electrophoresis. 2005.
  4. Fairhead M, Howarth M. Site-specific biotinylation of purified proteins using BirA. Methods Mol Biol. 2015.
  5. Hermanson GT. Bioconjugate Techniques. Academic Press.

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