Login / Register Order My Items
Contact Us
800.227.0627
Contact Us Quote Order Login / Register
Intercalator Bases

Intercalator Base Modified Oligonucleotides

Build signal‑on probes, photo‑crosslinkable constructs, and redox readouts by integrating intercalators— TO/YO/YOYO, acridine, naphthalimide, anthraquinone, pyrene/perylene, psoralen, and CNVK. Delivered assay‑ready with full QC.

Overview Selection Guide Chemistries & Placement Products Technical Notes Applications Workflow FAQ References Speak

Overview

Intercalators are planar aromatic units that insert between base pairs to alter stacking, modulate local Tm, and yield strong optical or redox signals. We install them as internal base analogs (e.g., pyrene‑dU, CNVK) or via pendant linkers at 5′/3′/internal sites—keeping probes compact and responsive.

Applications span signal‑on hybridization (TO/YO), UVA crosslinking (psoralen, CNVK), and electron‑transfer readouts (anthraquinone). Manufacturing covers µmol→multi‑gram with HPLC/UPLC purification, LC‑MS identity, and optional spectral sheets.

Thiazole Orange (TO)
Oxazole Yellow (YO/YOYO)
Acridine/Acridinium
Naphthalimide
Psoralen • CNVK
Formats
Internal base •
5′/3′/internal linker
Readouts
Fluor • Crosslink •
Redox/ET
QC
UPLC/HPLC • LC‑MS •
Spectra
Supply
RUO → GMP‑like

Selection Guide

Family Key effect Exc/Em (typical) Specialty Best‑fit uses Code
Thiazole Orange (TO) Huge fluorescence turn‑on ~510/530–560 nm Signal‑on hybridization Beacons; binding readouts [TO‑Link‑5′/int]
Oxazole Yellow (YO/YOYO) Very bright mono/bis‑intercalators ~491/509 nm (YO) YOYO as bis‑intercalator High‑SNR sensors [YO‑Link] [YOYO‑Link]
Acridine/Acridinium Intercalator; acridinium is chemiluminescent Abs ~360–430 nm CL labels (acridinium esters) CL assays [Acr‑Base] [Acri‑Ester]
Naphthalimide Blue‑green emissive; polarity‑sensitive ~420–470/500–540 nm Environment reporting Structural probes [Naph‑Base]
Anthraquinone Redox/photo ET intercalator UV/blue Photoinduced ET Electrochemical probes [AQ‑Link]
Pyrene / Perylene Excimer/exciplex; strong stacking Py: ~340/376&396; Ex ~470 nm Excimer distance reporter Conformation sensors [Py‑dU] [Per‑dU]
Psoralen (C2/C6/TEG) Intercalates; UVA crosslinking (T/A) ~365 nm Permanent crosslinks Footprinting; capture [Pso‑C2] [Pso‑C6‑5′/3′] [Pso‑TEG]
3‑Cyanovinylcarbazole (CNVK) Base analog; UV‑induced crosslink ~365 nm Fast photo‑crosslinking Transient duplex mapping [CNVK‑dN]
Tip: For visible‑only instruments, pick TO/YO, naphthalimide, or pyrene/perylene; psoralen/CNVK need near‑UV for activation.

Chemistries & Placement

Internal base analogs

Pyrene‑dU, perylene‑dU, CNVK replace a natural base at a chosen site to maximize stacking and local reporting or crosslinking.

Pendant linkers

Attach TO/YO, acridinium, naphthalimide, or anthraquinone via 5′/3′ or internal handles for flexible geometry and minimal mismatch impact.

Bis‑intercalators

YOYO‑type constructs can bridge adjacent sites for very bright signals; space linkers to avoid over‑stabilization.

Products & Ordering

Product / Modification Description Function Application Code
TO Intercalator (5′/3′/internal) Thiazole orange via linker Signal‑on binding Beacons; hybridization sensors [TO‑Link‑5′/3′/int]
YO / YOYO Intercalators Oxazole yellow mono/bis intercalators Bright duplex reporting High‑SNR probes [YO‑Link] [YOYO‑Link]
Acridine / Acridinium Ester Planar intercalator or CL label Fluorescent/chemiluminescent Hybridization CL assays [Acr‑Base] [Acri‑Ester]
Naphthalimide Intercalator Environment‑sensitive reporter Polarity/stacking sensing Conformation probes [Naph‑Base]
Anthraquinone Linker Redox/photo ET intercalator Quenching/electron transfer Electrochemical probes [AQ‑Link]
Pyrene‑dU / Perylene‑dU Internal base analogs (dU) Excimer/exciplex readouts Distance/conformation sensors [Py‑dU] [Per‑dU]
Psoralen C2 / C6 (5′/3′) / Pso‑TEG Intercalating UVA crosslinkers Permanent crosslink Footprinting; capture [Pso‑C2] [Pso‑C6‑5′/3′] [Pso‑TEG]
3‑Cyanovinylcarbazole (CNVK‑dN) Photo‑crosslinkable base analog Fast UV crosslinking Transient duplex trapping [CNVK‑dN]
Customizations: dual reporters (e.g., TO + quencher), PEG/hexa‑EG spacers, mixed backbones (LNA/2′‑OMe), HPLC/UPLC, spectra sheet, and fatigue/cycling tests.

Technical Notes

Design Guides
Intercalator Design Guides
  • Placement & Tm effects. Internal intercalators can raise local Tm and slow off‑rates. Space 3–6 nt apart when using multiple units; avoid tight clustering at termini.
  • Signal‑on designs. TO/YO are weakly emissive free but brighten on intercalation. Pair with a quencher or hairpin to maximize Δsignal and minimize background.
  • Photo‑crosslinking. Psoralen and CNVK require ~365 nm activation. Validate exposure to avoid sample damage; include dark/light controls.
  • Electrochemical probes. Anthraquinone and related systems can report via ET/EC. Provide electrode and buffer details to tune redox windows.
  • Compatibility. Intercalators can interact with nearby dyes/quencher pairs; verify crosstalk/FRET. Add PEG/hexa‑EG spacers to limit unwanted quenching.

Applications

Signal‑On Hybridization Probes

TO/YO intercalator beacons for sensitive detection without wash steps.

Photo‑Footprinting & Capture

Psoralen/CNVK crosslinking for mapping duplex contacts and capturing targets.

Conformation & Distance Sensing

Pyrene excimer pairs report local distance/stacking; naphthalimide senses polarity.

Workflow

1
2
3
Design

Pick intercalator family; choose placement (internal base vs linker); define readout (fluor / redox / crosslink) & target Tm.

Build

Synthesize → Purify (Desalt→HPLC/UPLC) → LC‑MS confirm → (Optional) spectra & extinction coefficients.

Validate

Match filters/λ; set irradiation for psoralen/CNVK; finalize buffers & controls; pilot test signal/ET.

Ready to spec your intercalator‑modified oligos?

Share sequence, placement, intended readout (fluor/redox/crosslink), and instrument filters/irradiance—we’ll return a tuned design and QC plan.

Start a design consult

FAQ

Do intercalators always increase Tm?

Often locally yes, but effects depend on sequence and placement. We can model and test to hit your target Tm. Internal intercalators may slow off‑rates and strengthen clamps.

Can I use visible light only?

Yes for TO/YO, naphthalimide, and pyrene/perylene. Psoralen and CNVK require near‑UV (~365 nm) for crosslink activation.

Will YOYO over‑stabilize duplexes?

Bis‑intercalators can strongly stabilize duplexes and trap kinetics. Use single units or increase spacing (3–6 nt) to avoid over‑stabilization.

Can you provide spectral/validation data?

On request we provide absorption/emission spectra, extinction coefficients, and switching/fatigue cycles. LC‑MS QC is standard for identity.

Speak to a Scientist

Email Instead

References

  1. Intercalating dyes and base analogs in nucleic acid probes (reviews).
  2. Psoralen and CNVK for photo‑crosslinking of nucleic acids.
  3. Excimer/exciplex reporting with pyrene/perylene in DNA/RNA.

On request, we’ll align placement, spectral, and irradiation parameters to your instrument.

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.

Quick Links