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Photo-Regulation & Photocleavable Oligonucleotide Chemistries

Light-controlled hybridization, release, and crosslinking with photocleavable linkers, photocaged nucleotides (NPOM-dT, DEACM-dG), azobenzene photoswitches, and CNVK photo crosslinkers. Custom design, synthesis, purification/QC, and documentation.

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Overview SEO Products Workflow Technical Notes FAQ Speak to a Scientist

Overview

Photoregulation is a property—the ability of an oligonucleotide system to respond to light. Bio-Synthesis provides end-to-end services for photocleavable oligonucleotides, photocaged nucleotides (NPOM-dT, DEACM-dG), azobenzene photoswitch constructs, and CNVK photo crosslinkers—including custom design, sequence optimization, wavelength selection (UV-A / 365–405–450 nm), synthesis at RUO → GMP-like scale, purification (HPLC/PAGE), LC-MS, and ISO-aligned documentation. These light-controlled chemistries enable signal reset for MERFISH/smFISH, capture-and-photorelease from surfaces, time-resolved activation/uncaging, and UV photo-locking of duplexes.

Formats
Tubes • Plates • Kitting
Scale
µmol → multi-gram
QC
UPLC/HPLC • LC-MS •
Binding
Supply
RUO → GMP-like
What we manufacture
  • Photocleavable linkers & spacers: PC-Linker, PC-Amino C6, PC-Biotin, PC-Spacer C3.
  • Photocaged nucleotides: NPOM-dT, DEACM-dG for uncaging/activation.
  • Photoswitches & crosslinkers: Azobenzene (reversible), CNVK (UV snap-lock).
  • Custom panels & barcodes: MERFISH/smFISH readouts, strip-and-rerun cycles.
Services you can expect
  • Application-led design: sequence optimization, spacer geometry, label strategy.
  • Process & purification: desalt/HPLC/PAGE, controlled drying, stabilized storage.
  • Documentation: ISO-aligned CoA, sequence map, exposure/dose guidance.
  • Scale-up & transfer: RUO → GMP-like pathways with phased tech transfer.

Workflow — Uncage/Release → Image → Reset → Rerun

Light enables activation or release, followed by imaging/collection, then signal reset for the next round.

Step 1 Uncage / Release NPOM-dT, DEACM-dG PC-Linker / PC-Biotin / PC-AmC6 Step 2 Image / Collect Acquire signal or elute payload Protect dyes; manage dose Step 3 Reset / Rerun Strip labels or photorelease Prepare for next round
Step 1
Uncage / Release

NPOM-dT, DEACM-dG
PC-Linker / PC-Biotin / PC-AmC6

Step 2
Image / Collect

Acquire signal or elute payload
Protect dyes; manage dose

Step 3
Reset / Rerun

Strip labels or photorelease
Prepare for next round

Active step Process rail

Products

Product Description Function Application Code
CNVK Photo Cross Linker 3-Cyanovinylcarbazole (CNVK) base analog enabling fast UV-induced inter-strand crosslinking to a complementary pyrimidine; “photo-locking” of duplexes. Photo-crosslinking [cnvK]
PC Amino C6 (Photocleavable) Photolabile amino handle on a C6 spacer. Capture by chemistry (e.g., NHS) then light-triggered release to regenerate a free amine. Photocleavage / Release [PCAmC6]
PC Biotin (photocleavable) Biotin tag attached through a photolabile linker for streptavidin capture with gentle, on-demand photorelease of the oligo. Photocleavage / Capture-Release [PCBio]
PC Linker (photocleavable) General-purpose photolabile linker for light-gated bond scission between an oligo and its payload, surface, or partner. Photocleavage [PCL]
PC Spacer C3 (photocleavable) Short photolabile spacer that introduces separation while permitting UV-induced release for strip-and-rerun imaging or elution workflows. Photocleavage / Spacer [PC-Sp-C3]
Azobenzene Reversible trans↔cis photoswitch embedded in the strand; toggles duplex stability with light for photoregulated hybridization. Photoswitch / Affinity Control —
DEACM Cage-dG Coumarin (DEACM)-caged deoxyguanosine; base pairing is blocked until visible/near-UV irradiation uncages the base. Uncaging / Activation [DEACM-dG]
NPOM Caged-dT NPOM-protected deoxythymidine; light removes the NPOM cage to restore hybridization competence for timed activation. Uncaging / Activation [NPOM-dT]
Technical notes
Wavelengths, Dose & Instrument Fit
Photogroup Recommended λ (nm) Typical Power Density* Notes
NPOM-dT 350–370 (best ~365) 3–15 mW·cm⁻² Fast uncaging; watch UV dose on dyes/tissue.
DEACM-dG 400–420 (405 friendly) 5–30 mW·cm⁻² Gentler on samples; compatible with 405 nm lasers/LEDs.
Azobenzene 365–405 (trans→cis); 440–460 (cis→trans) 1–10 mW·cm⁻² Reversible photoswitch; thermal back-switch possible.
CNVK (crosslink) ~365 3–15 mW·cm⁻² Rapid “photo-lock”; avoid overexposure to limit off-target effects.

*Guidance only. Optimize for your optics, sample, and footprint. Use energy budgeting (dose = mW·cm⁻² × s) and validate on controls.

Design & Technology Considerations
  • Branch factor: co-use with bDNA amplifiers; choose label density judiciously.
  • Probe tiling/stringency: balance kinetics vs background.
  • Label strategy: enzyme vs direct dyes vs cleavable readouts.
  • Compatibility: MERFISH barcoding & imaging rounds.
Placement Guidelines
  • Spacer first, then function: Insert TEG/PEG spacers around PC linkers and cages to minimize steric hindrance and dye quenching.
  • Keep reactive sites apart: Separate PC linkers from fluorophores/quencher pairs; avoid direct adjacency to G-rich motifs.
  • Surface workflows: Validate capture → photorelease efficiency (PC-Biotin / PC-Amino C6) under your illumination geometry.
  • MERFISH/smFISH: Coordinate formamide/salt stringency with dye photostability and round count; prefer lower-dose, longer exposures when possible.
Buffers, Materials & Compatibility
  • Use low-autofluorescence, neutral pH buffers; rinse residual primary amines prior to PC-cleavage steps.
  • Confirm plastics/adhesives and mounting media tolerate UV/405 nm exposure (no yellowing or cracking).
  • Maintain oxygen and temperature conditions consistently across rounds for reproducible kinetics.
QC & Safety
  • Purification: HPLC/PAGE; identity by LC-MS when applicable; confirm dye/cage loading.
  • Record illumination dose and irradiance map for each setup to aid reproducibility.
  • Wear UV/blue PPE; minimize stray reflections; interlock enclosures for high-power sources.
Quick Recipes (Starting Points)
  1. MERFISH signal reset (NPOM-dT): 365 nm LED at 5–10 mW·cm⁻² for 15–60 s → rinse → next round. Validate minimal dye loss on controls.
  2. Gentle uncaging (DEACM-dG): 405 nm at 10–20 mW·cm⁻² for 10–45 s; preferable for sensitive samples and live-cell–adjacent preps.
  3. Surface capture & photorelease (PC-Biotin): Bind → wash → 365–405 nm at 5–15 mW·cm⁻² for 15–60 s while collecting eluate; verify recovery by OD260/fluorescence.

FAQ

Is photoregulation a property, a function, or an application?

Property. Photoregulation describes light-responsive behavior. It enables functions like photocleavage, uncaging, and photoswitching, which support applications such as MERFISH signal reset, ISH probe stripping, and light-gated assays.

What’s the difference between photocleavable linkers and photocaged bases?

Photocleavable linkers split a bond to release the oligo/payload. Photocaged bases block pairing or activity until light uncages them, restoring function without strand scission.

When should I use azobenzene vs CNVK?

Azobenzene provides reversible affinity control (no bond breakage). CNVK performs irreversible UV crosslinking to lock duplexes or capture interactions.

Can these be used for MERFISH strip-and-rerun imaging?

Yes. Photocleavable linkers and caged readouts support multi-round imaging by enabling signal reset or on-demand release with minimal chemical perturbation.

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References — Photoregulation & Photocleavable (Caged) Oligonucleotides

Core siRNA Photoregulation
  1. Mikat V, Heckel A. Light-dependent RNA interference with nucleobase-caged siRNAs. Nucleic Acids Res. 2007. Article • PubMed
  2. Govan JM, Lively MO, Deiters A. Optochemical control of RNA interference in mammalian cells. Nucleic Acids Res. 2013. Article • PubMed
  3. Shah S, Rangarajan S, Friedman SH. Light-activated RNA interference using double-stranded RNA. Nucleic Acids Res. 2009. Article
Antisense / Morpholino (MO) Light Control
  1. Deiters A. Photocaged Morpholino Oligomers for the Light-Regulation of Gene Function. J. Am. Chem. Soc. 2010. PMC • PubMed • ACS
Photocaged Bases & Photocleavable Linkers (for Oligo Synthesis)
  1. Glen Research. Glen Report 23.25 — New Product: NPOM-Caged-dT. Article
  2. Glen Research. NPOM Caged-dT-CE Phosphoramidite (Cat# 10-1534) — product page with usage notes. Product
  3. Berry & Associates / LGC. NPOM-Caged-dT CEP — Product Information Sheet (BA0317) (structure, 365-nm uncaging). PDF
  4. Glen Research. Photocaged Phosphoramidites (overview & ordering). Catalog
  5. Glen Research. Products for DNA Research — 2024/2025 Catalog (NPOM-dT, DEACM-caged dG listed). PDF
Additional / Related Optochemical Control
  1. Hemphill J, Deiters A. Site-Specific Promoter Caging Enables Optochemical Gene Activation. J. Am. Chem. Soc. 2014. ACS
  2. Ankenbruck N, et al. Optochemical Control of Biological Processes in Cells and Animals. Angew. Chem. Int. Ed. 2018 (review). Europe PMC
  3. Bollu A, et al. 2′-caged-tethered siRNA shows light-dependent RNAi. Bioorg. Med. Chem. 2021. Article

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