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Photoswitchable Base Modified Oligonucleotides

Custom DNA and RNA oligonucleotides with reversible photoswitches for light-controlled hybridization, aptamer capture/release, optical gating, and dynamic nucleic acid structures.

Azobenzene Arylazopyrazole Diazocine Diarylethene Spiropyran / HTI
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Overview Why Photoswitch? Selection Guide Products Design Notes Applications FAQ Contact
Overview

Optical Control of Oligonucleotide Structure and Binding

Photoswitchable base modified oligonucleotides incorporate light-responsive molecular switches that reversibly alter nucleic acid structure, hybridization behavior, affinity interactions, or conformational state upon exposure to defined wavelengths.

In oligonucleotides, azobenzene and related photoswitch families can stabilize or destabilize duplexes in one state and reverse under another wavelength or by thermal relaxation. These systems enable photo-gated hybridization, switchable toeholds, aptamer capture/release, molecular logic, and dynamic nucleic acid engineering.

Bio-Synthesis manufactures custom photoswitchable DNA and RNA oligonucleotides incorporating azobenzene, visible-light azobenzene, arylazopyrazole, diazocine, diarylethene, spiropyran, hemithioindigo, and custom light-responsive chemistries with HPLC/UPLC purification, LC-MS confirmation, and optional switching characterization.

UV / Visible Switching Internal or Linker Placement HPLC / LC-MS QC Optional Switching Plots Fatigue Cycle Testing

State A

Starting conformation, stacking or binding state.

Light Input

UV, violet, blue or green irradiation drives switching.

State B

Hybridization, capture or structure is modulated.

Reset

Reverse wavelength or thermal relaxation returns the system.

Why Photoswitch?

Why Use Photoswitchable Oligos?

Photoswitchable oligos give researchers non-invasive control over nucleic acid behavior using light instead of added chemical reagents.

ON

Reversible Control

Toggle hybridization, structure or binding state across repeated cycles without reagent addition.

λ

Optical Precision

Control the timing, location and intensity of activation using selected wavelengths and filters.

DYN

Dynamic Systems

Regulate aptamers, toeholds, beacons, duplexes or logic constructs in real time.

KIN

Programmable Kinetics

Choose scaffolds based on half-life, fatigue resistance, contrast and visible-light compatibility.

Photoswitch Selection Guide

Photoswitch Selection Guide

Use this guide to compare photoswitch families by switching mechanism, wavelength, relaxation behavior, fatigue resistance and best-fit application.

Wavelength, Half-Life & Workflow Compatibility

For visible-only setups, consider o-fluoro azobenzene, arylazopyrazole, diazocine or hemithioindigo.

Photoswitch selection guide for light-controlled oligonucleotide design.

Family Switch Type Typical Wavelength cis t1/2 / State Lifetime Fatigue Best-Fit Uses Code
Azobenzene trans ⇄ cis 365 ↔ 450–520 nm / thermal min → h Good Photo-gated hybridization; beacons; toeholds [Azo-dT]
o-Fluoro Azo visible trans ⇄ cis 405–520 nm bidirectional h → days Very good Visible-only instruments and reduced UV exposure [oF-Azo]
Arylazopyrazole high-contrast azo switching 365–405 ⇄ 520–560 nm hours → days Excellent Memory/logic designs and long-lived states [AZP-Link]
Diazocine cis ⇄ trans 405–530 nm min → h Good Dark-favored designs and specialty gating [Diazocine]
Diarylethene open ⇄ closed UV ⇄ visible stable Excellent Binary memory and robust repeated toggling [DTE-Link]
Spiropyran SP ⇄ MC UV ⇄ visible sec → min Good Environment-sensitive sensing and switching [SP-Link]
Hemithioindigo E ⇄ Z 450–560 nm min → h Good Visible-only environments and dynamic regulation [HTI-Link]
Products & Ordering

Products We Support: Photoswitchable Oligos

This table preserves the live-site Products & Ordering content while making the supported photoswitchable formats easier to compare.

Representative Photoswitchable Oligonucleotide Formats

Product availability, placement geometry, purification and optional switching validation can be confirmed during quote review.

Representative photoswitchable base and linker-modified oligonucleotide products.

Product / Modification Description Function Application Code
Azobenzene-dT (Azo-dT) Internal base analog with reversible trans↔cis switching. Duplex modulation Hybridization gating; beacons; toeholds [Azo-dT]
Visible-Light Azobenzene (oF-Azo) Ortho-fluoro or push-pull variant operating in visible range. Visible-range switching Live-cell, tissue-friendly or UV-sensitive workflows [oF-Azo]
Arylazopyrazole Linker High photostationary-state contrast and long-lived cis state. Strong contrast Logic, memory and long-state storage designs [AZP-Link]
Diazocine Linker Bridged azo photoswitch with cis favored in the dark. Dark-state control Specialty gating and bidirectional switching [Diazocine]
Diarylethene (DTE) Linker Bistable open/closed switch with high fatigue resistance. Binary memory Robust repeated toggling and long-lived states [DTE-Link]
Spiropyran (SP) Linker SP↔MC switch with environment-sensitive optical behavior. Reporting + switching Sensing/control hybrids and polarity-responsive systems [SP-Link]
Hemithioindigo Linker Visible-light E/Z photoswitch for dynamic regulation. Visible-light control Visible-only environments and optical gating [HTI-Link]
Custom Photoswitch Oligo Sequence-specific placement, purification and validation plan. Turn-key build Assay-ready light-responsive constructs [PS-Custom]

Availability note: Specific photoswitch families, placement geometries, scale and validation options should be confirmed during quote review. Customizations: internal or pendant placement, multiple photoswitch units, PEG/hexa-EG spacers, mixed backbones such as 2′-OMe or LNA, HPLC/UPLC purification, LC-MS identity, switching spectra and fatigue-cycle testing are available on request.

Design Notes

Design Notes for Photoswitchable Oligos

Photoswitch performance depends on wavelength hardware, placement, relaxation kinetics, buffer compatibility and intended cycle count.

λ

Wavelength & Filters

Match switch absorption bands to LEDs, lasers and filters. For UV-sensitive samples, prefer visible-light azo, AZP, diazocine or HTI.

T½

Thermal Relaxation

cis→trans half-life can range from minutes to days depending on scaffold and substituents.

CYC

Photofatigue

DTE and AZP are useful when repeated high-cycle switching or strong fatigue resistance is required.

POS

Placement Strategy

Internal base replacements maximize Tm modulation. Multiple units can amplify switching but should be tested for sequence-specific effects.

Attachment Geometry

Photoswitches can be designed as internal base replacements, pendant labels or backbone/linker elements depending on the desired effect on duplex stability, aptamer structure or toehold behavior.

Buffer Compatibility

Avoid strong reducing agents when azo stability is important. Validate buffer, oxygenation, irradiance and exposure time under final assay conditions.

Applications

Applications for Photoswitchable Oligonucleotides

Photoswitchable oligos are used when light must control binding, structure, proximity, switching state or assay timing.

HYB

Photo-Gated Hybridization

Toggle duplex formation, melting behavior or strand displacement with light-controlled base stacking.

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APT

Switchable Aptamer Capture & Release

Control aptamer binding and elution by changing conformation with light instead of heat or chemical reagents.

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LOG

Molecular Logic & Memory

AZP and DTE switches support high-contrast, bistable or long-lived states for molecular logic designs.

Application Use Case

TOE

Light-Controlled Toehold Systems

Use optical switching to regulate strand displacement, dynamic nucleic acid structures and responsive hybridization systems.

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FRET

FRET & Fluorescence Switching

Combine photoswitchable bases with fluorophores or quenchers to modulate signal, proximity or conformational readout.

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DYN

Dynamic Nucleic Acid Engineering

Build responsive oligo systems for optical gating, nanotechnology, capture/release and advanced assay engineering.

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Frequently Asked Questions

FAQ

What is a photoswitchable oligonucleotide?
A photoswitchable oligonucleotide contains a light-responsive base, linker or pendant group that changes structure or conformation after illumination. This can alter duplex stability, aptamer binding, fluorescence readout or strand-displacement behavior.
Which photoswitch is best for visible-light applications?
Visible-light azobenzene, arylazopyrazole, diazocine and hemithioindigo are often preferred for visible-light systems because they reduce UV exposure while maintaining reversible switching performance.
How many photoswitch units should be included?
One photoswitch may be sufficient for small changes, while two or three units can increase Tm shift or switching amplitude. Placement and clustering should be evaluated against the target structure and assay window.
Can Bio-Synthesis provide switching validation?
Yes. Depending on the project, optional UV/Vis switching plots, photostationary state comparison, fatigue-cycle testing and LC-MS identity confirmation can be included.
Can photoswitchable oligos be used in biological samples?
 Yes, but wavelength, light dose, buffer compatibility and phototoxicity should be considered. Visible-light photoswitches are usually preferred for sensitive samples.
Can photoswitchable oligos be combined with fluorophores or quenchers?
 Yes. Photoswitchable bases can often be combined with fluorophores, quenchers, spacers or affinity tags when the placement strategy avoids unwanted quenching, steric interference or spectral overlap with the switching wavelengths.
What information is needed for a quote?
 Provide sequence, desired photoswitch family, switch placement, wavelength hardware, intended application, scale, purification target and whether switching spectra or fatigue testing are needed.
More FAQ'sAll FAQ's
Before Requesting a Quote

Information Helpful for Photoswitchable Oligo Design

Sequence DNA/RNA sequence and target length
Switch Family Azo, oF-Azo, AZP, DTE, SP or custom
Placement Internal base, pendant or linker position
Wavelengths LED/laser/filter setup and exposure plan
QC Needs HPLC/UPLC, LC-MS, spectra or fatigue tests
Contact & Quote Request

Need help selecting a photoswitch?

Share your sequence, desired photoswitch family, placement position, wavelength hardware, intended application, scale, purification target and switching-validation needs. Bio-Synthesis can recommend an appropriate photoswitch, spacer architecture, purification workflow and QC plan.
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)
λ

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Fast Quote Checklist

Include sequence, switch, position, wavelengths, scale and QC.

Sequence Switch Position λ QC
Scientific Background & Recommended Reading

Scientific Background & Recommended Reading

Selected references covering azobenzene photoswitches, photoregulated nucleic acids, visible-light photoswitches and dynamic molecular switching systems. These citations provide scientific background rather than product-performance claims.

  1. Asanuma H, Liang X, Nishioka H, et al. Synthesis of azobenzene-tethered DNA for reversible photoregulation of DNA duplex formation. Foundational literature for azobenzene-modified oligonucleotide design and photo-controlled hybridization.
  2. Beharry AA, Woolley GA. Azobenzene photoswitches for biomolecules. Chemical Society Reviews. 2011;40:4422-4437. DOI
  3. HĂĽll K, Morstein J, Trauner D. In vivo photopharmacology. Chemical Reviews. 2018;118(21):10710-10747. DOI
  4. Crespi S, Simeth NA, König B. Heteroaryl azo dyes as molecular photoswitches. Nature Reviews Chemistry. 2019;3:133-146. DOI
  5. Irie M, Fukaminato T, Matsuda K, Kobatake S. Photochromism of diarylethene molecules and crystals: memories, switches, and actuators. Chemical Reviews. 2014;114(24):12174-12277. DOI

Note: Photoswitch selection should be aligned with the final wavelength hardware, desired state lifetime, sample sensitivity, cycle count and downstream assay readout. Bio-Synthesis can help align literature-style switching conditions to your oligonucleotide design.

Why Choose Bio-Synthesis

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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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