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Modified Bases

Intercalators Modified Oligonucleotide

Pyrene, perylene, anthraquinone, thiazole orange, acridine and other intercalator labels for signal enhancement, excimer/exciplex sensing, duplex stabilization, and photoinduced electron transfer—custom DNA/RNA synthesis with HPLC/PAGE and ESI‑MS QC, scalable to ISO 13485.

Overview

Bio‑Synthesis designs and manufactures intercalator‑modified oligonucleotides— DNA and RNA labeled with pyrene, perylene, anthraquinone, thiazole orange (TO), acridine, and related scaffolds. Intercalators stack between base pairs to boost fluorescence signal, enable excimer/exciplex readouts, drive photoinduced electron transfer (PeT), or tune duplex stability (Tm) for probes, sensors, and mechanistic studies.

We offer site‑specific placement at the 5′, 3′, or internal position with spacer engineering (e.g., TEG/PEG) to control sterics and signal geometry. Production spans nmol → multi‑gram with HPLC/PAGE purification, ESI‑MS identity, and optional endotoxin testing—supported by documentation for ISO 9001/13485 programs. For assay development, our team can recommend the optimal intercalator, placement, and buffer conditions for your instrument and readout.

  • Keywords (SEO): intercalator modified oligonucleotide, pyrene‑dU, perylene‑dU, thiazole orange oligo, acridine oligo, anthraquinone oligo, excimer probes, PeT quencher/donor, duplex stabilization, custom DNA/RNA synthesis, ISO 13485 oligos.
  • Highlights: 5′/3′/internal placement • TEG/PEG spacers • HPLC/PAGE • ESI‑MS • nmol→multi‑gram • RUO→ISO 9001/13485.

Intercalators

Select from popular intercalators for excimer/exciplex readouts, FI light‑up probes, PeT studies, and duplex stabilization. Placement and spacer length are key to performance.

Hide Table and Notes
Product / Modification Description Typical Use Notes Code
Pyrene‑dU Internal pyrene on deoxyuridine Excimer/exciplex sensing; duplex stabilization Excimer emission with adjacent pyrenes; strong stacking [Py-dU]
Pyrene‑dC Internal pyrene on deoxycytidine Signal enhancement; FRET donor/acceptor Placement-sensitive; consider spacer to tune PET [Py-dC]
Perylene‑dU Internal perylene intercalator Bright far‑green emission; hybridization probes High quantum yield; larger steric footprint [Per-dU]
Anthraquinone‑dU Electron‑acceptor intercalator PeT studies; photocleavage mapping Efficient charge transfer; verify polymerase tolerance [AQ-dU]
Thiazole Orange‑dT (TO‑dT) Cyanine intercalator tethered to dT Light‑up (bound‑enhanced) probes Low background until intercalated (FI principle) [TO-dT]
Thiazole Orange linker TO via flexible linker (internal) Signal‑on hybridization probes Spacer length controls brightness and background [TO-linker]
Acridine‑C6 Acridine via C6 spacer (terminus) Triplex/footprinting; intercalative probing Classic intercalator; strong stacking; pH‑dependent [Acr-C6]
Ethidium‑C3 Ethidium tethered via C3 Fluorescent intercalation reporter Potent binder; avoid over‑labeling [Eth-C3]
Daunomycin (Anthracycline) Anthracycline intercalator Red‑channel reporting; redox studies Light/oxidation sensitive; protect from light [Dau]
1,10‑Phenanthroline‑dT Metal‑binding intercalator at dT Metallo‑intercalator probes; redox catalysis Coordinate metals (e.g., Cu/Fe); control conditions [Phen-dT]
5′-Psoralen C6 Psoralen crosslinker via C6 spacer (5′ terminus) UVA photo‑crosslinking; interstrand crosslinks Activates ~320–365 nm; bias for 5′‑TA steps; protect from light [5‑Pso‑C6]
3′-Psoralen C6 Psoralen crosslinker via C6 spacer (3′ terminus) UVA photo‑crosslinking; interstrand crosslinks Activates ~320–365 nm; bias for 5′‑TA steps; protect from light [3‑Pso‑C6]
Psoralen‑TEG Psoralen via TEG spacer (internal/terminal) UVA photo‑crosslinking; flexible placement Longer spacer improves accessibility; light‑sensitive [Pso‑TEG]
YO linker (Oxazole Yellow) Light‑up intercalator (YO) via flexible linker (internal) Signal‑on hybridization probes; low background Emission increases on binding; choose spacer to minimize quenching [YO‑linker]
YOYO dimer linker Dimeric intercalator (YOYO) via flexible linker High‑brightness intercalative probes Strong binding; may over‑stabilize duplex; adjust length/salt [YOYO‑linker]
Acridinium Ester‑C6 Chemiluminescent acridinium tethered via C6 Chemiluminescent readouts; intercalative binding Light‑sensitive; avoid strong base; plan trigger chemistry [Acrid‑Ester‑C6]
Naphthalimide‑C6 Naphthalimide intercalator via C6 Green emission; environment‑sensitive probes Photostable; stacking dependent; verify Tm [Naph‑C6]
Rhodamine‑C6 (intercalator) Rhodamine‑based intercalator via C6 Red‑channel probes; FRET donor/acceptor May partially bind externally; pilot background and brightness [Rh‑C6]
Show Technical Notes
  • Tm shift & stacking: Intercalators can increase duplex stability; re‑optimize probe length and salt.
  • Excimer/exciplex formation: Pyrene pairs produce excimer emission when proximal; design spacing accordingly.
  • PeT effects: Electron donor/acceptor combinations (e.g., anthraquinone) can quench or enhance signal—pilot at working ionic strength.
  • Polymerase compatibility: Bulky intercalators may impede enzymes; position internally with spacers and validate amplification/extension.
  • Handling & QC: Protect from light; use HPLC purification and confirm by MS; consider additional SEC/desalting for conjugates.

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FAQ

How do intercalators differ from standard fluorophores?

Intercalators stack between base pairs and often show signal‑on behavior upon binding (e.g., TO), or enable excimer/exciplex or PeT readouts not accessible with standard terminal dyes.

Where should I place the intercalator—5′, 3′, or internal?

Internal placements maximize stacking effects; 5′/3′ placements are simpler but may show weaker intercalation. Spacers (TEG/PEG) help control sterics and background.

Will intercalators affect amplification or ligation?

They can. Bulky labels may hinder polymerases/ligases near the modification. We recommend internal placement away from the active junction and empirical validation.

Need help selecting the right intercalator?

We’ll recommend label, placement, spacer, and QC to match your instrument and assay.

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