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Custom Capture Probes

Custom DNA, RNA and affinity-enhanced oligonucleotide probes for target enrichment, hybrid capture, pull-down assays, nucleic acid isolation, sequencing workflows and molecular diagnostics.

Biotin Dual Biotin DIG Click Handles DNA / RNA / PNA Probe Pools
Choose a Capture Strategy Request a Quote
Overview Affinity Tags Selection Guide Chemistries Design Rules Architectures Design Applications Related Services FAQ Contact
Target Enrichment by Sequence Recognition

Capture Specific DNA or RNA from Complex Samples

Capture probes are sequence-specific oligonucleotides designed to hybridize to a target nucleic acid and enable its selective isolation, enrichment, immobilization or detection. A capture probe typically combines a target-recognition sequence with an affinity tag, surface-reactive group or conjugation handle.

Bio-Synthesis supports capture probes for hybrid capture sequencing, RNA pull-down, microbial detection, biomarker enrichment, sample preparation, bead-based assays, array immobilization and custom molecular workflows.

Probe performance depends on more than sequence complementarity. Target accessibility, GC content, duplex Tm, tag position, spacer length, matrix composition and washing conditions all influence recovery and specificity.

1. Sample mixture
2. Probe hybridization
3. Bead capture
4. Wash and recover
Purified target retained
Affinity Tag Selection Guide

Select the Capture Chemistry That Matches the Support

Affinity tag selection determines how the probe is captured or immobilized on beads, surfaces, antibodies or click-reactive supports. The guide below summarizes common starting configurations.

Biotin Capture Probes

A versatile choice for streptavidin-coated magnetic beads, plates and surfaces. A PEG, HEG or TEG spacer is commonly used to improve accessibility.

Magnetic beads Hybrid capture Pull-down
Typical Spacer

PEG12 / HEG / TEG

Purification

HPLC

Best Support

Streptavidin

Design Note

Keep the tag away from the hybridizing region

Dual-Biotin Capture Probes

Useful when stronger retention or higher surface avidity is desired in demanding pull-down and enrichment workflows.

High-retention capture NGS enrichment Difficult matrices
Typical Spacer

PEG / TEG

Purification

HPLC

Best Support

Streptavidin

Design Note

Evaluate whether very strong binding affects elution

DIG-Labeled Capture Probes

Designed for antibody-mediated capture or detection using anti-DIG reagents.

Immunocapture Hybridization assays Detection workflows
Typical Spacer

TEG / PEG

Purification

HPLC

Best Support

Anti-DIG antibody

Design Note

Match label position to antibody accessibility

Amino-Modified Capture Probes

A practical handle for coupling to NHS-activated surfaces, beads and array substrates.

Microarrays Covalent coupling Activated surfaces
Typical Spacer

C6 / C12 / HEG

Purification

HPLC

Best Support

NHS ester / carboxyl surface

Design Note

Control surface density to avoid crowding

Thiol-Modified Capture Probes

Preferred for gold surfaces and selected maleimide-based coupling chemistries.

Gold sensors SPR Maleimide coupling
Typical Spacer

C6 / HEG / PEG

Purification

HPLC

Best Support

Gold / maleimide

Design Note

Use appropriate reducing and handling conditions

Azide-Modified Capture Probes

Bioorthogonal handle for CuAAC or strain-promoted click immobilization.

Click surfaces Custom beads Orthogonal conjugation
Typical Spacer

PEG

Purification

HPLC

Best Support

Alkyne / DBCO

Design Note

Choose CuAAC or copper-free chemistry by application

Alkyne-Modified Capture Probes

Reactive partner for azide-bearing supports and click-functionalized assay architectures.

CuAAC Surface coupling Custom conjugation
Typical Spacer

PEG

Purification

HPLC

Best Support

Azide-bearing support

Design Note

Confirm copper tolerance for biological samples

Application-First Selection

What Are You Trying to Capture?

Select the closest workflow to review a practical starting design and common chemistry choices.

Biotinylated DNA or RNA Probe

Use a high-purity probe with a terminal biotin separated from the hybridizing region by an appropriate spacer. For difficult targets, consider LNA/BNA or PNA enhancement.

5′ Biotin 3′ Biotin Dual Biotin TEG / PEG Spacer

Key Design Priorities

  • Target accessibility
  • Balanced Tm
  • Low off-target homology
  • Controlled wash stringency

Main Caution

Placing a bulky tag too close to the duplex may reduce hybridization or capture efficiency.

Biotin or Click-Functionalized Pull-Down Probe

Choose a capture tag compatible with the intended support and plan a spacer long enough to reduce steric crowding near the bead or surface.

Biotin Azide Alkyne Amino Thiol

Key Design Priorities

  • Support chemistry
  • Spacer length
  • Target accessibility
  • Elution strategy

Main Caution

Highly hydrophobic or multiply modified probes may show nonspecific bead binding.

Multiplexed Biotinylated Capture Probe Pool

Use individually designed probes or tiled probe sets with uniform Tm, low cross-hybridization and controlled representation across the panel.

Tiled Probes Probe Pools Plate Format Dual Biotin

Key Design Priorities

  • Uniform hybridization behavior
  • Panel-level specificity
  • Coverage redundancy
  • Pooling accuracy

Main Caution

Panel performance must be evaluated as a system, not only probe by probe.

RNA-Compatible Capture Probe with Stabilized Chemistry

DNA probes are often effective, while 2′-OMe, LNA/BNA, PNA or mixed chemistries may improve stability or target recognition in structured RNA.

DNA 2′-OMe LNA/BNA PNA Biotin

Key Design Priorities

  • RNA structure
  • RNase control
  • Probe stability
  • Hybridization temperature

Main Caution

Strong affinity does not compensate for inaccessible or protein-bound RNA regions.

Surface-Immobilized Capture Probe

Select a terminal amino, thiol or other surface-reactive handle with a spacer that preserves probe accessibility after immobilization.

Amino Thiol Biotin PEG Spacer HPLC Purification

Key Design Priorities

  • Surface density
  • Orientation
  • Spacer length
  • Assay reproducibility

Main Caution

Overcrowded surfaces can reduce hybridization kinetics and target recovery.

Representative Architectures

Visual Capture Probe Architectures

Probe orientation, spacer placement and handle position can be customized to match the assay geometry.

5′ Biotin—Spacer—Probe

Common for bead-based capture and enrichment.

Probe—Spacer—3′ Biotin

Alternative orientation when the 5′ end must remain free.

Dual-Biotin Probe

Higher surface avidity for demanding capture workflows.

Internal Amino Handle

Useful for custom surface coupling or branched formats.

Click-Functionalized Probe

Azide or alkyne handle for bioorthogonal immobilization.

PNA or Affinity-Enhanced Probe

For short, structured or difficult targets.

Compatible Chemistries

Combine Recognition Chemistry, Capture Handles and Functional Labels

Capture-probe performance is determined by the complete construct—not only the recognition sequence. Bio-Synthesis can combine the probe backbone, affinity-enhancing residues, capture handle, spacer and optional reporter into a single application-specific design.

NA

Probe Recognition Backbones

Choose the primary hybridization scaffold

DNA RNA 2′-OMe RNA 2′-F RNA PNA
Best used for

DNA for general capture and probe pools; RNA or 2′-modified RNA for RNA-compatible architectures; PNA for short, highly structured targets or workflows that require strong nuclease resistance.

Tm

Affinity & Specificity Enhancers

Tune duplex strength and mismatch discrimination

LNA BNA ENA cEt 2′-OMe Mixed Chemistry
Typical uses

Short targets, structured RNA, difficult GC regions, higher-stringency washes or improved mismatch discrimination. Modified residues should be positioned deliberately rather than distributed uniformly.

●

Capture & Immobilization Handles

Match the probe to beads, surfaces or conjugation chemistry

Biotin Dual Biotin DIG Amino Thiol Azide Alkyne DBCO / BCN
Typical uses

Streptavidin capture, antibody-mediated capture, NHS-activated supports, gold surfaces and bioorthogonal click immobilization.

FX

Spacers, Reporters & Conjugates

Improve access or add downstream functionality

TEG HEG PEG4–PEG24 Fluorophores Quenchers Peptides Cholesterol Custom Conjugates
Typical uses

Reducing surface crowding, enabling assay tracking, adding orthogonal detection, or integrating the probe into a larger molecular construct.

Application Compatibility Matrix

General compatibility guidance; the final design depends on target accessibility, support chemistry, hybridization conditions and wash stringency.

Custom combinations available
Chemistry Family Magnetic Bead Capture RNA Pull-Down NGS Enrichment Surface / Sensor Difficult Target
DNA Common fit Common fit Common fit Common fit Useful
2′-OMe / 2′-F Useful Common fit Application-dependent Useful Common fit
LNA / BNA / ENA / cEt Useful Common fit Application-dependent Useful Common fit
PNA Useful Common fit Specialized use Common fit Common fit
Biotin / Dual Biotin Common fit Common fit Common fit Useful Useful
Amino / Thiol / Click Handles Useful Application-dependent Specialized use Common fit Useful

Chemistry note: Affinity-enhancing residues can improve hybridization, but over-modification may slow dissociation, complicate elution or increase nonspecific interactions. Probe chemistry should be matched to the complete capture and recovery workflow.

Capture Probe Engineering Rules

Core Design Variables

Probe Length

20–120 nt

Selected according to target complexity, fragmentation and capture workflow.

GC Content

Balanced

Avoid long GC tracts and strongly self-complementary regions.

Affinity Tag

5′ / 3′ / Internal

Choose the orientation that preserves target accessibility.

Spacer

PEG / HEG / TEG

Separate the hybridizing region from the bead or surface.

Purification

HPLC / PAGE

Match purification rigor to length and modification complexity.

Quality Control

Identity + Purity

OD, chromatography, mass confirmation where compatible and COA.

Capture Probe Design Matrix

Common Starting Configurations

Workflow Recommended Tag Spacer Purification Starting Chemistry
Magnetic bead capture Biotin PEG12 / HEG HPLC DNA; optional LNA/BNA
Stringent bead-based pull-down Dual Biotin PEG / TEG HPLC DNA or 2′-OMe
NGS target enrichment Biotin or Dual Biotin PEG12 HPLC Tiled DNA probe pool
RNA capture Biotin PEG12 HPLC DNA, 2′-OMe, LNA/BNA or PNA
Microarray / activated surface Amino HEG HPLC DNA or PNA
Gold biosensor Thiol HEG / PEG HPLC DNA or PNA
Bioorthogonal immobilization Azide or Alkyne PEG HPLC DNA, RNA or PNA

Design note: The highest-melting probe is not always the most effective capture probe. Productive capture requires a balance of target accessibility, specificity, hybridization kinetics, surface geometry and wash tolerance.

Application Gallery

Capture Probe Applications

From single-target pull-down to multiplexed enrichment panels, the probe architecture can be adapted to the sample, support and downstream readout.

NGS

Hybrid Capture Sequencing

Enrich genes, exons, variants or genomic regions before next-generation sequencing.

Tiled DNA probe pools
RNA

RNA Pull-Down

Isolate selected transcripts or RNA-associated complexes for downstream analysis.

Biotin + PEG spacer
cf

Cell-Free DNA Enrichment

Recover low-abundance circulating targets from fragmented and complex specimens.

Short target optimization
Dx

Diagnostic Capture

Immobilized probes for sandwich hybridization, biosensors and molecular assay platforms.

Surface-oriented design
µ

Microbial & Pathogen Capture

Concentrate bacterial, viral, fungal or environmental nucleic-acid targets before detection.

Single or multiplex
Bio

Biomarker Isolation

Capture tissue-derived, cellular or circulating DNA and RNA biomarkers.

High-specificity probes
Au

Arrays & Surface Sensors

Use amino-, thiol- or click-functionalized probes on arrays, gold sensors and activated supports.

Covalent immobilization
R&D

Custom Molecular Workflows

Develop specialized capture architectures for synthetic biology, assay development and research.

Custom conjugation

FAQ

What is the most common capture probe format?
A terminally biotinylated DNA probe used with streptavidin-coated magnetic beads is one of the most common formats.
Should I use single biotin or dual biotin?
Single biotin is sufficient for many workflows. Dual biotin can increase the probability of bead retention in selected assays, particularly during stringent washes. The benefit depends on tag spacing, support density and assay geometry.
Where should the affinity tag be placed?
The tag may be placed at the 5′ or 3′ end depending on target accessibility, probe orientation and assay design. A spacer is often beneficial.
Can capture probes include LNA, PNA or 2′-OMe?
Yes. These chemistries can be used to tune affinity, stability or mismatch discrimination when standard DNA is not sufficient.
Can you manufacture probe pools?
Yes. Bio-Synthesis can support pooled capture probes, tiled designs, plate-formatted sets and custom panel layouts.
What purification is recommended?
HPLC purification is commonly recommended for modified capture probes. PAGE may be considered for longer or particularly demanding constructs.
More FAQ'sAll FAQ's
Contact & Quote Request

Need help designing a capture probe?

Send the target sequence, sample type, intended capture support, desired affinity tag, probe format, scale, purification target and analytical requirements. Bio-Synthesis can review the requested sequence, chemistry combination and manufacturing approach before quotation.
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)

What to Send

  • Target sequence and organism
  • DNA or RNA target
  • Capture support or bead type
  • Affinity tag and spacer
  • Scale, purification and QC
Quality Systems

Quality Systems & Manufacturing Support

Quality-Managed Oligonucleotide Manufacturing

Custom capture probes, probe pools and affinity-tagged oligonucleotides with controlled production, purification, analytical QC, documentation and packaging.

ISO 9001:2015 Quality management
ISO 13485:2016 Medical-device framework
ISO 14001 Environmental management
Analytical QC HPLC/UPLC, MS where compatible, OD and COA
Recommended Reading

Selected References for Hybrid Capture and Target Enrichment

  1. Gnirke A, et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009.
  2. Albert TJ, et al. Direct selection of human genomic loci by microarray hybridization. Nat Methods. 2007.
  3. Mercer TR, et al. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol. 2012.
  4. Mamanova L, et al. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010.
  5. Bio-Synthesis technical resources for biotinylated oligonucleotides, hybridization probe design, click chemistry and affinity-tagged oligonucleotides.

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 45+ 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.

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