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Light-Activated Caged Oligonucleotides

Custom caged DNA, RNA, antisense oligonucleotides, siRNA, aptamers, guide RNAs and molecular probes activated by light for spatial and temporal control of hybridization, gene regulation, enzymatic activity and cellular signaling.

NPOM Bases DEACM Coumarin Cages Nitrobenzyl Modifications Photocleavable Linkers Caged siRNA / sgRNA Light-Controlled Imaging
Discuss a Caged Oligo Design Explore Caging Options
Overview Light-Gated Workflow Design & Technology Modification Guide Applications Related Services FAQ Reading Contact
Overview

What Are Caged Oligonucleotides?

Caged oligonucleotides contain photolabile protecting groups that temporarily block hybridization, enzymatic activity or molecular recognition. Upon exposure to a selected wavelength of light, the caging group is removed and native oligonucleotide function is restored.

Bio-Synthesis supports custom photocaged DNA and RNA designs for light-controlled gene expression, RNAi, CRISPR guide control, aptamer binding, molecular imaging, strand release and optochemical biology studies.

This page organizes product formats by caging strategy: photocaged bases, photocleavable linkers, terminal caging groups and complete light-activated oligo constructs.

CAGE
Active
oligo
light-triggered activation
Light-Gated Oligo Workflow

From Inactive Caged Oligo to Active Probe

Caged oligos are designed around a simple experimental sequence: mask function, deliver or position the oligo, illuminate, then measure activation.

🔒

Caged Oligo

Photolabile groups block hybridization, cleavage, binding or enzymatic recognition.

🧬

Inactive State

The oligo remains silent during delivery, setup or localization.

💡

Light Exposure

Illumination triggers uncaging at the selected wavelength and dose.

✂

Photocleavage

The protecting group or linker is removed from the oligo.

🟢

Active Oligo

Hybridization, gene regulation, imaging or catalytic function is restored.

Why Use Caged Oligos?

Optical Control of Oligonucleotide Function

Time

Temporal Control

Activate oligos only when needed, making it easier to study fast or staged biological processes.

Space

Spatial Precision

Use local illumination to control activity in selected wells, cells, tissues or regions.

Bg

Reduced Background

Prevent premature hybridization, gene regulation, fluorescence or enzymatic activity before activation.

Dyn

Dynamic Biology

Investigate signaling, development, RNA regulation, CRISPR timing and light-controlled molecular events.

Caging Strategy Selector

Choose a Light-Activated Design for Your Experiment

Select the biological function you want to control. The guide will show a practical starting chemistry, design focus and recommended readout.

Select your experimental goal
Recommended approach

Trigger Strand or Payload Release

Photocleavable o-nitrobenzyl, DEACM/coumarin or PEG linker

Design focus

Position the cleavable linker between the oligo and a blocker, payload, surface or complementary segment.

Typical evaluation

HPLC/UPLC cleavage profile, release efficiency, fluorescence change or restored target binding.

Recommended approach

Activate RNA Interference

Caged siRNA, Dicer-substrate siRNA or photocleavable blocker design

Design focus

Suppress guide-strand loading or target recognition until light exposure while preserving duplex stability.

Typical evaluation

Target RNA knockdown, protein reduction, reporter response or cellular phenotype.

Recommended approach

Control CRISPR Activity

Caged sgRNA, crRNA, tracrRNA or pegRNA

Design focus

Block guide-target recognition, Cas loading or a critical guide-RNA region before illumination.

Typical evaluation

Editing efficiency, cleavage, CRISPRi/CRISPRa response or reporter activation.

Recommended approach

Activate Imaging or Sensing

Caged molecular beacon, aptamer, FRET probe or photocleavable quencher design

Design focus

Balance low pre-activation background with efficient uncaging and strong post-activation target recognition.

Typical evaluation

Fluorescence intensity, localization, kinetic response or target-dependent signal change.

Recommended approach

Control Hybridization

NPOM-, nitrobenzyl- or DEACM-caged nucleobases

Design focus

Place the cage within a critical target-binding region to suppress duplex formation before illumination.

Typical evaluation

Melting analysis, hybridization signal, gene-expression change or functional recovery after uncaging.

λ

Light Source

Match caging chemistry to wavelength, dose, exposure time and phototoxicity limits.

Site

Cage Placement

Choose base, backbone, terminal or linker placement based on the masked function.

Multi

Activation Efficiency

Multiple cage sites can improve suppression before light exposure but increase design complexity.

Cell

Cell Compatibility

Consider wavelength, illumination dose, cellular uptake, nuclease stability and assay timing.

Modification Guide

Caged Oligo Product & Modification Selector

Browse complete caged oligo product coverage by chemistry and construct type.

Photocaged Nucleobases — block base pairing or recognition until light exposure.

Best for
hybridization control
Readout
binding / gene regulation
Design focus
base position
QC focus
LC-MS
Category Product / Modification Code / Format Function Typical Application
Photocaged Base NPOM-dT [NPOM-dT] Photocaged thymidine that suppresses base pairing until uncaging Light-controlled hybridization, antisense and gene regulation
Photocaged Base NPOM-dC [NPOM-dC] Photocaged cytidine for sequence-specific activation Transcription, hybridization and regulatory studies
Photocaged Base NPOM-dA [NPOM-dA] Caged adenine analog for duplex or enzyme control Hybridization control and light-gated probe activation
Photocaged Base NPOM-dG [NPOM-dG] Caged guanine analog for base-pair disruption Duplex activation and gene regulation studies
Coumarin-Caged Base DEACM-Caged dG [DEACM-dG] Coumarin-caged deoxyguanosine that suppresses guanine base pairing or molecular recognition until illumination removes the photolabile group. Longer-wavelength light-controlled hybridization, antisense, CRISPR and optochemical biology studies
Nitrobenzyl Base Nitrobenzyl-dU [NB-dU] Photolabile uridine/thymidine-style base blocking Photocontrolled hybridization and light activation
Nitrobenzyl Base Nitrobenzyl-dC [NB-dC] Photolabile cytidine base protection Gene expression and transcription control
Photocaged Base DMNPE-Protected Bases [DMNPE] Photolabile protecting group for optochemical biology Light-controlled oligo function and mechanistic studies
Photocaged Base CNV-dT / Cyanovinyl-Caged Thymidine [CNV-dT] Photocaged thymidine family for photoregulated duplex and gene-control studies Photoresponsive hybridization, antisense and optochemical biology
Photocaged Base Bhcmoc-Caged Bases [Bhcmoc] Photolabile caging group used to suppress nucleobase recognition Light-gated base pairing and functional activation studies
Photocaged RNA Base NPOM-Caged RNA Bases [NPOM-rA/rC/rG/rU] Photocaged RNA nucleosides designed to block RNA base pairing or protein recognition before illumination. Caged siRNA, sgRNA, crRNA, aptamers and RNA imaging studies
Coumarin-Caged RNA Base DEACM-Caged RNA Bases [DEACM-rA/rG] Longer-wavelength coumarin-caged RNA nucleosides for light-controlled RNA folding, hybridization and protein interaction. Guide RNA, RNAi, aptamer and live-cell optochemical studies
Photocaged Base Photocaged 2′-OMe RNA Bases [PC-2′OMe-RNA] Caged ribose-modified RNA bases for nuclease-resistant light-controlled RNA designs Caged antisense, RNAi controls and RNA-binding studies

Photocleavable Linkers & Spacers — trigger release, strand separation or linker cleavage with light.

Best for
release
Readout
cleavage conversion
Design focus
linker placement
QC focus
photocleavage
Category Product / Modification Code / Format Function Typical Application
Photocleavable Linker o-Nitrobenzyl Linker [oNB] Light-triggered cleavage of oligo conjugates or blockers Antisense activation, controlled release and strand release
Photocleavable Linker Nitrobenzyl Linker [NB-Linker] General photolabile linker for UV-triggered release Caged probes, bead release and light-controlled constructs
Photocleavable Spacer Photocleavable Spacer [PC-Spacer] Spacer that separates oligo segments until light exposure Controlled strand release and caged hybridization
Coumarin Linker Coumarin Photolabile Linker [PC-Coumarin] Photolabile linker option for longer-wavelength activation Cell-sensitive light activation and imaging workflows
PEG Linker Photocleavable PEG Spacer [PC-PEG] Hydrophilic photocleavable spacer Controlled delivery systems, surfaces and conjugates
Coumarin Linker DEACM Photocleavable Linker [DEACM-Linker] Coumarin-based photocleavable linker for longer-wavelength triggered release or strand activation. Cell-compatible release, caged probes, affinity capture and light-triggered conjugate cleavage
Backbone Caging Photocaged Phosphate / Backbone Linker [PC-Backbone] Photolabile backbone or phosphate modification that suppresses hybridization, enzymatic recognition or strand processing until uncaging. Antisense, RNAi, CRISPR and mechanistic nucleic-acid studies
Photolabile Linker DMNB Photolabile Linker [DMNB-Linker] Dimethoxy nitrobenzyl-style photocleavable linker Light-triggered release, caged conjugates and controlled strand separation
Photocleavable Blocker Photocleavable Hairpin Blocker [PC-Hairpin] Light-cleavable blocking segment used to keep a probe or target-binding region inactive Caged molecular beacons, aptamers and split-probe activation
Surface Release Photocleavable Biotin / Capture Linker [PC-Biotin] Photoreleasable affinity handle for streptavidin or surface workflows Light-triggered bead release, pull-down and capture assays

Terminal Caging — mask terminal activity, ligation, extension or conjugation until illumination.

Best for
end control
Readout
extension / ligation
Design focus
5′ or 3′ end
QC focus
end identity
Category Product / Modification Code / Format Function Typical Application
5′ Caging 5′ Photocaged Phosphate [5′-PC-PO4] Blocks 5′ phosphate-dependent ligation or recognition until uncaging Light-controlled ligation, PCR activation and kinase/ligase studies
5′ Caging 5′ Photocaged Amine [5′-PC-NH2] Masks amine reactivity until light exposure Conjugation control and staged probe assembly
3′ Caging 3′ Photocaged Hydroxyl [3′-PC-OH] Temporarily blocks 3′-OH extension potential Light-gated primer extension and caged PCR workflows
End Cap Photocleavable End Cap [PC-Cap] Terminal cap removed by light Activation-on-demand probes and extension blockers
3′ Caging 3′ Photocleavable Spacer / Blocker [3′-PC-Spacer] Light-removable terminal spacer that keeps an oligo non-extendable or inactive before uncaging Caged primers, extension blocking and light-gated polymerase assays
5′ Caging 5′ Photocleavable Spacer / Blocker [5′-PC-Spacer] Light-cleavable 5′ end blocker or spacer Light-controlled ligation, capture and surface-release workflows
Duplex Caging Photocleavable Complementary Blocker Strand [PC-Blocker] Blocking strand or segment removed by light to expose the functional oligo Caged aptamers, beacons, antisense and split-oligo activation

Light-Activated Functional Constructs — complete caged oligo formats for RNAi, CRISPR, aptamers and imaging.

Best for
biological control
Readout
phenotype / signal
Design focus
activity suppression
QC focus
function + identity
Category Product / Modification Code / Format Function Typical Application
Antisense Caged Antisense Oligo Caged ASO Temporarily inactive ASO activated by light Light-controlled gene silencing or splice modulation
RNAi Caged siRNA Duplex Caged siRNA RNAi duplex with light-gated activity Spatiotemporal RNAi activation
RNAi Caged Dicer-Substrate siRNA Caged DsiRNA Longer RNAi construct with photocaged regulation Light-controlled RNAi with Dicer processing
miRNA Caged miRNA Inhibitor / Mimic Caged miRNA Light-controlled miRNA pathway reagent Regulatory network and developmental biology studies
CRISPR Caged sgRNA / Guide RNA Caged sgRNA Guide RNA activity controlled by light Photoactivatable CRISPR and genome editing control
Guide RNA Caged crRNA / tracrRNA Caged crRNA / tracrRNA Separate guide components designed for light-controlled CRISPR function Photoactivatable CRISPR-Cas9 or Cas12 workflows
Prime Editing Caged pegRNA Caged pegRNA Prime-editing guide RNA with light-gated target recognition or extension-domain accessibility. Spatiotemporal control of prime-editing experiments
Template Caged PCR Primer / Primer Extension Probe Caged Primer Primer function blocked until photocleavage Light-controlled PCR, primer extension and polymerase studies
Therapeutic Model Caged ASO Gapmer / Splice-Switching Oligo Caged Gapmer / SSO Antisense or splice-switching construct with light-gated target recognition Temporal gene knockdown, splice modulation and pathway studies
Aptamer Caged Aptamer Caged Aptamer Target recognition blocked until uncaging Light-gated binding, capture and sensing
Probe Caged Molecular Beacon Caged Beacon Reporter probe activated by light Live-cell imaging and spatial detection
Reporter Caged FRET / Quencher Probe Caged FRET Probe Fluorescence or quenching state controlled by photocleavage or uncaging Imaging, proximity assays and kinetics
Catalytic RNA/DNA Caged DNAzyme / Ribozyme Caged Dz / Rz Catalytic oligo function blocked until illumination Light-controlled catalytic assays and signaling studies

Wavelength guidance: Many nitrobenzyl and NPOM chemistries are activated with near-UV light, while DEACM and related coumarin systems are often selected when longer-wavelength violet-light activation is preferred. Exact wavelength, dose and exposure time depend on the specific cage structure, sequence, sample geometry and biological system.

Need a format not listed? Additional base-caged, linker-caged and light-activated oligonucleotide designs may be evaluated based on sequence, synthesis compatibility, illumination conditions and intended assay.

Application-Centered Design

Match the Caged Construct to the Experiment

Caged oligos can be tuned for gene expression, RNAi, CRISPR regulation and imaging.

Recommended Formats

Caged antisense, caged splice-switching oligos, base-caged DNA/RNA.

Design Focus

Place cages in the seed, binding or recognition region.

Readout

qPCR, reporter assay, protein output, splice shift or phenotype.

Recommended Formats

Caged siRNA, caged DsiRNA, caged miRNA inhibitor or mimic.

Design Focus

Suppress guide-strand loading or target recognition until illumination.

Readout

Knockdown, RNA level, protein expression or cell phenotype.

Recommended Formats

Caged sgRNA, caged guide RNA, caged crRNA or tracrRNA designs.

Design Focus

Block guide-target recognition or Cas complex function before light exposure.

Readout

Editing, CRISPRi/CRISPRa, cleavage or reporter activation.

Recommended Formats

Caged molecular beacons, caged aptamers and light-activated probes.

Design Focus

Balance fluorescence suppression, uncaging speed and target binding.

Readout

Fluorescence imaging, live-cell signal, localization or kinetic readout.
Analytical QC & Manufacturing

QC Strategy for Caged Oligos

Caged oligos require confirmation of identity, purity, light response and functional recovery after uncaging.

Analytical Control Matrix

QC packages may include HPLC/UPLC purity, LC-MS identity, OD260 concentration, photocleavage verification, CoA, plate maps and custom documentation.

HPLC / UPLC

Purity assessment for modified, uncaged and photocleaved species.

LC-MS

Identity confirmation of cage incorporation and uncaging product where compatible.

Photocleavage Test

Light-exposure condition testing with before/after analytical profile.

Functional Controls

Uncaged, caged, no-light and light-exposed controls for interpretation.

Light Handling

Amber handling and light-protective storage may be required for sensitive cages.

Cell Studies

Define wavelength, dose, exposure time and phototoxicity limits before scale-up.

Supply Paths

Research-scale, plate and scale-up production options are available with project-appropriate analytical documentation.

FAQ

Can caged oligos regulate CRISPR systems?
Yes. Caged sgRNA, crRNA, tracrRNA or guide RNA constructs can be designed to suppress guide activity until illumination.
How many cage groups can be incorporated?
Single or multiple cage groups can be used. Multiple sites may improve suppression before light exposure but can increase synthesis complexity.
What is a caged oligonucleotide?
A caged oligonucleotide contains a photolabile group that temporarily blocks hybridization, enzymatic activity or molecular recognition until light exposure removes the cage.
What wavelengths are commonly used?
Many nitrobenzyl and NPOM systems use near-UV activation, while coumarin-style linkers may support longer wavelength activation.
How are caged oligos activated?
They are activated by illumination at a wavelength matched to the caging group, commonly near UV or longer-wavelength photolabile systems depending on chemistry.
Can caged oligos be used with siRNA?
Yes. Caged siRNA, Dicer-substrate siRNA and caged miRNA inhibitor designs can control RNAi timing with light.
How is photocleavage verified?
 Photocleavage can be checked by HPLC/UPLC, LC-MS, gel shift, fluorescence readout or a functional assay depending on the construct.
Can caged oligos be combined with fluorescent labels, quenchers or biotin?
 Yes. Caged oligos can often be combined with dyes, quenchers, biotin, amino modifiers, thiol modifiers or bioorthogonal handles. Compatibility depends on cage placement, purification method, light sensitivity and the final assay workflow.
More FAQ'sAll FAQ's
Before Requesting a Quote

Information Helpful for Caged Oligos

Goal
hybridization, RNAi, CRISPR
Sequence
DNA, RNA, ASO, guide
Cage
NPOM, NB, PC linker
Light
wavelength and dose
Format
tube, duplex, plate
QC
HPLC, LC-MS, photocleavage
Contact & Quote Request

Need help designing a caged oligonucleotide?

Share your sequence, biological function to mask, desired activation wavelength, assay readout, cell or in-vitro conditions, scale, purification and QC requirements.
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)

Cage Strategy Review

Compare NPOM bases, DEACM coumarin cages, nitrobenzyl groups, photocleavable linkers and terminal caging options.

NPOM DEACM oNB PC linker

Photocleavage & QC Package

Plan no-light controls, light-exposed controls, HPLC/UPLC, LC-MS and functional recovery tests.

No-light HPLC LC-MS
Recommended Reading

Recommended Reading & Literature References

  1. Mayer G, Heckel A. Biologically active molecules with a light switch. Angewandte Chemie International Edition. 2006.
  2. Young DD, Deiters A. Photochemical control of biological processes. Organic & Biomolecular Chemistry. 2007.
  3. Deiters A. Light activation as a method of regulating and studying gene expression. Current Opinion in Chemical Biology. 2009.
  4. Ellis-Davies GCR. Caged compounds: photorelease technology for control of cellular chemistry and physiology. Nature Methods. 2007.
  5. Shah S, Rangarajan S, Friedman SH. Light-activated RNA interference. Angewandte Chemie International Edition. 2005.

Design consideration: Published examples provide useful starting points, but final performance depends on sequence, cage placement, wavelength, light dose, sample conditions, purification and the selected analytical or functional assay.

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their designs to Biosynthesis for production feasibility review.
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