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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

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.

Explore related chemistries
Services at a glance
  • Design consult (λ, dose, placement)
  • RUO → GMP-like manufacturing
  • QC: UPLC/HPLC, LC-MS (COA)
Need help choosing the best cage?

We’ll recommend cage family, placement, spacers, and uncaging conditions for your matrix.

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.

Speak to a Scientist

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

Please avoid confidential details; we can arrange an NDA if needed.

You’ll receive a confirmation by email.
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Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 40+ 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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