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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‑dUInternal pyrene on deoxyuridineExcimer/exciplex sensing; duplex stabilizationExcimer emission with adjacent pyrenes; strong stacking[Py-dU]
Pyrene‑dCInternal pyrene on deoxycytidineSignal enhancement; FRET donor/acceptorPlacement-sensitive; consider spacer to tune PET[Py-dC]
Perylene‑dUInternal perylene intercalatorBright far‑green emission; hybridization probesHigh quantum yield; larger steric footprint[Per-dU]
Anthraquinone‑dUElectron‑acceptor intercalatorPeT studies; photocleavage mappingEfficient charge transfer; verify polymerase tolerance[AQ-dU]
Thiazole Orange‑dT (TO‑dT)Cyanine intercalator tethered to dTLight‑up (bound‑enhanced) probesLow background until intercalated (FI principle)[TO-dT]
Thiazole Orange linkerTO via flexible linker (internal)Signal‑on hybridization probesSpacer length controls brightness and background[TO-linker]
Acridine‑C6Acridine via C6 spacer (terminus)Triplex/footprinting; intercalative probingClassic intercalator; strong stacking; pH‑dependent[Acr-C6]
Ethidium‑C3Ethidium tethered via C3Fluorescent intercalation reporterPotent binder; avoid over‑labeling[Eth-C3]
Daunomycin (Anthracycline)Anthracycline intercalatorRed‑channel reporting; redox studiesLight/oxidation sensitive; protect from light[Dau]
1,10‑Phenanthroline‑dTMetal‑binding intercalator at dTMetallo‑intercalator probes; redox catalysisCoordinate 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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