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Caged Oligonucleotides

Light-trigger the function of DNA/RNA with photocaged bases and linkers: o-nitrobenzyl/DMNB, coumarin (DEACM/Bhc), photocleavable (PC) spacers, and photoreleasable biotin. Enable spatiotemporal control of hybridization, ligation/extension, capture, and release—delivered with full QC.

oNB / DMNB) DEACM / Bhc PC Spacers Photoreleasable Biotin 365–405 nm • 740–800 nm
Overview Products Design Highlights Related Chemistry FAQ Speak to Scientist

Overview

Bio-Synthesis designs and manufactures custom caged oligonucleotides (photocaged DNA and RNA) for light-controlled molecular biology and synthetic biology applications. These modified oligos remain biologically inert until illuminated, enabling precise spatiotemporal control of hybridization, extension, ligation, capture, and release. We offer base-caged nucleotides and photocleavable (PC) linkers/spacers built on o-nitrobenzyl (oNB/DMNB), coumarin (DEACM/Bhc), and NPOM families, along with photoreleasable biotin for one-way uncaging in capture workflows. Researchers can use 365–405 nm UV or two-photon 740–800 nm excitation for deep, localized activation.

Applications include antisense oligos, RNAi/siRNA, gene editing, optogenetics, nucleic acid diagnostics, and synthetic biology, with scales from research-grade to GMP-like manufacturing. All products are delivered with comprehensive QC (UPLC/HPLC, LC-MS) and available in tube or plate formats.

Formats
Tubes • 96-well plates
Scale
µmol → multi-gram
QC
UPLC/HPLC • LC-MS
Supply
RUO → GMP-like
What you get with Bio-Synthesis
  • Assay-driven design: cage family/wavelength selection, placement (base vs linker), spacer length, uncaging buffer and dose.
  • Manufacturing breadth: desalting → HPLC/UPLC; plate/kitting and barcoding; light-protected packaging.
  • Analytical package: LC-MS, purity traces, UV260, COA; optional endotoxin/residual copper (if used in other steps).
  • Supply pathway: RUO → GMP-like with change control and documentation.

Products & Notes

Modification Description Typical use Code
o-Nitrobenzyl-dT (oNB-dT) oNB caging group on thymidine. Light-unlock hybridization/extension. [oNB-dT]
DMNB-dC / dG / dA Dimethoxy-oNB variants on bases. Photocontrol base pairing; general assays. [DMNB-dN]
NPOM-caged dT (NPOM-dT) 6-nitropiperonyloxymethyl (NPOM) cage on thymidine; light removes the cage to restore pairing/extension. 365–405 nm uncaging for on/off hybridization or extension control. [NPOM-dT]
DEACM-caged dG (DEACM-dG) (7-Diethylaminocoumarin-4-yl)methyl cage on guanosine; blue-shifted absorption, bright readouts. 405 nm (optionally 2-photon ~740–800 nm) for lower-energy uncaging and live-cell friendly setups. [DEACM-dG]
Technical Notes
  • Start at 365–405 nm (oNB/DMNB) or explore 740–800 nm two-photon for DEACM/Bhc where available.
  • Validate uncaging by LC-MS and functional gain (ΔTm, ligation/extension restored).
  • Use light-safe handling (foil, amber tubes) to prevent premature activation.

Modification Description Typical use Code
PC Spacer (oNB-PC) oNB-based PC linkage. Time-controlled hybridization/ligase access. [PC-Sp]
PC-TEG Photocleavable TEG spacer. Release cargo or de-mask capture regions. [PC-TEG]
Technical Notes
  • Optimize spacer length (TEG/PEG) for post-uncage sterics and access.
  • Confirm clean cleavage by LC-MS; consider scavengers to quench reactive by-products.

Modification Description Typical use Code
PC-Biotin (5′/3′) Biotin linked via PC linker. Captures on SA; light elutes on-demand. [PC-Bio]
Technical Notes
  • Match cage λ to instrument; minimize photodamage to targets during elution.
  • Use compatible SA supports (plates, beads) and validate release efficiency.

Modification Description Typical use Code
Abberior CAGE 500 Photoactivatable dye; 405 nm activation, green channel emission (~500 nm). Light-gated fluorescence of labeled oligos; localization/patterning. [Abberior-CAGE-500]
Abberior CAGE 532 Photoactivatable dye; 405 nm activation, ~532 nm emission. Dual-color/orthogonal uncaging sets with base/linker cages. [Abberior-CAGE-532]
Abberior CAGE 552 Photoactivatable dye; 405 nm activation, ~552 nm emission. Light-gated signal turn-on for tracking/release assays. [Abberior-CAGE-552]
Abberior CAGE 590 Photoactivatable dye; 405 nm activation, ~590 nm emission. Red-shifted channel for multiplex with 500/532 dyes. [Abberior-CAGE-590]
Abberior CAGE 635 Photoactivatable dye; 405 nm activation, ~635 nm emission. Far-red channel; minimized background in complex matrices. [Abberior-CAGE-635]
Technical Notes
  • Order dyes as NHS-ester/azide/maleimide/DBCO and couple via 5′/3′-NH2 or click handles.
  • Validate activation at 405 nm; confirm turn-on and signal stability in your buffer/matrix.
  • Use short PEG/TEG spacers to mitigate quenching and sterics near the hybridization site.

Technology • Design • Application

Technology
  • oNB/DMNB: widely used 365–405 nm cages; efficient and affordable (photolabile nitrobenzyl ether).
  • Coumarin (DEACM) / Bhc: brighter reporters, blue-shifted absorption; some support two-photon uncaging (740–800 nm).
  • PC spacers/linkers: photocleavable tethers that gate hybridization, ligation, release or capture (e.g., PC-biotin).
  • Base-caged vs linker-caged: base cages suppress pairing/extension; linker cages modulate geometry or tethering.
Design
  • Place base cages near the key contact to suppress function; use short PEG/TEG spacers to relieve sterics post-uncage.
  • Define wavelength, dose, and time; validate uncaging by LC-MS and functional gain (ΔTm, ligation/extension).
  • For live cells, prefer lower-energy cages and minimal UV exposure; consider two-photon setups.
  • Shield from ambient light; work in foil or red light as needed.
Application
  • Light-controlled hybridization/strand displacement and polymerase extension.
  • Templated ligation gating; photorelease of targets or capture probes (PC-biotin).
  • Spatial patterning in tissues/cells; optochemical control in microfluidics.

Tip: report uncaging conditions (λ, dose, buffer, temp) alongside functional metrics to ensure reproducibility.

FAQ

Which cage should I pick for live-cell work?

Prefer coumarin/Bhc families or lower-energy uncaging; minimize UV dose/time. Two-photon setups (740–800 nm) can localize activation in thicker samples.

How do I verify successful uncaging?

Confirm by LC-MS and function (e.g., ΔTm shift; ligation/extension restored; capture/release enabled). Include light/dark controls and dose series.

Will uncaging damage my oligo or cargo?

Use minimal fluence that achieves function; keep samples cool, use scavengers, and test lower-energy cages where possible.

Can I combine cages with click handles or dyes?

Yes—place click handles/dyes away from the cage to limit quenching/sterics, and add a short PEG/TEG spacer if needed.

More FAQ'sAll FAQ's

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Tell us about your caged-oligo project. We’ll recommend cage family, placement, spacers, and uncaging conditions with the right QC.

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