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Custom DNA, RNA and affinity-enhanced oligonucleotide probes for target enrichment, hybrid capture, pull-down assays, nucleic acid isolation, sequencing workflows and molecular diagnostics.
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.
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
Dual Biotin
DIG
Amino
Thiol
Azide
Alkyne
A versatile choice for streptavidin-coated magnetic beads, plates and surfaces. A PEG, HEG or TEG spacer is commonly used to improve accessibility.
PEG12 / HEG / TEG
HPLC
Streptavidin
Keep the tag away from the hybridizing region
Useful when stronger retention or higher surface avidity is desired in demanding pull-down and enrichment workflows.
PEG / TEG
Evaluate whether very strong binding affects elution
Designed for antibody-mediated capture or detection using anti-DIG reagents.
TEG / PEG
Anti-DIG antibody
Match label position to antibody accessibility
A practical handle for coupling to NHS-activated surfaces, beads and array substrates.
C6 / C12 / HEG
NHS ester / carboxyl surface
Control surface density to avoid crowding
Preferred for gold surfaces and selected maleimide-based coupling chemistries.
C6 / HEG / PEG
Gold / maleimide
Use appropriate reducing and handling conditions
Bioorthogonal handle for CuAAC or strain-promoted click immobilization.
PEG
Alkyne / DBCO
Choose CuAAC or copper-free chemistry by application
Reactive partner for azide-bearing supports and click-functionalized assay architectures.
Azide-bearing support
Confirm copper tolerance for biological samples
Select the closest workflow to review a practical starting design and common chemistry choices.
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.
Key Design Priorities
Main Caution
Placing a bulky tag too close to the duplex may reduce hybridization or capture efficiency.
Choose a capture tag compatible with the intended support and plan a spacer long enough to reduce steric crowding near the bead or surface.
Highly hydrophobic or multiply modified probes may show nonspecific bead binding.
Use individually designed probes or tiled probe sets with uniform Tm, low cross-hybridization and controlled representation across the panel.
Panel performance must be evaluated as a system, not only probe by probe.
DNA probes are often effective, while 2′-OMe, LNA/BNA, PNA or mixed chemistries may improve stability or target recognition in structured RNA.
Strong affinity does not compensate for inaccessible or protein-bound RNA regions.
Select a terminal amino, thiol or other surface-reactive handle with a spacer that preserves probe accessibility after immobilization.
Overcrowded surfaces can reduce hybridization kinetics and target recovery.
Probe orientation, spacer placement and handle position can be customized to match the assay geometry.
Common for bead-based capture and enrichment.
Alternative orientation when the 5′ end must remain free.
Higher surface avidity for demanding capture workflows.
Useful for custom surface coupling or branched formats.
Azide or alkyne handle for bioorthogonal immobilization.
For short, structured or difficult targets.
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.
Choose the primary hybridization scaffold
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.
Tune duplex strength and mismatch discrimination
Short targets, structured RNA, difficult GC regions, higher-stringency washes or improved mismatch discrimination. Modified residues should be positioned deliberately rather than distributed uniformly.
Match the probe to beads, surfaces or conjugation chemistry
Streptavidin capture, antibody-mediated capture, NHS-activated supports, gold surfaces and bioorthogonal click immobilization.
Improve access or add downstream functionality
Reducing surface crowding, enabling assay tracking, adding orthogonal detection, or integrating the probe into a larger molecular construct.
General compatibility guidance; the final design depends on target accessibility, support chemistry, hybridization conditions and wash stringency.
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.
Selected according to target complexity, fragmentation and capture workflow.
Avoid long GC tracts and strongly self-complementary regions.
Choose the orientation that preserves target accessibility.
Separate the hybridizing region from the bead or surface.
Match purification rigor to length and modification complexity.
OD, chromatography, mass confirmation where compatible and COA.
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.
From single-target pull-down to multiplexed enrichment panels, the probe architecture can be adapted to the sample, support and downstream readout.
Enrich genes, exons, variants or genomic regions before next-generation sequencing.
Isolate selected transcripts or RNA-associated complexes for downstream analysis.
Recover low-abundance circulating targets from fragmented and complex specimens.
Immobilized probes for sandwich hybridization, biosensors and molecular assay platforms.
Concentrate bacterial, viral, fungal or environmental nucleic-acid targets before detection.
Capture tissue-derived, cellular or circulating DNA and RNA biomarkers.
Use amino-, thiol- or click-functionalized probes on arrays, gold sensors and activated supports.
Develop specialized capture architectures for synthetic biology, assay development and research.
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Custom capture probes, probe pools and affinity-tagged oligonucleotides with controlled production, purification, analytical QC, documentation and packaging.
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