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Modified Bases

Fluorescent Base Analogs (DNA & RNA)

Built‑in fluorescent bases—tC°, tCnitro, 2‑Aminopurine, pyrrolo‑C/dC, pyrene/perylene‑dU, εdA—to monitor stacking, base flipping, hybridization, and microenvironments with minimal structural perturbation. Custom synthesis, purification, and QC, scalable to ISO 13485.

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Overview

Bio‑Synthesis provides fluorescent base–modified oligonucleotides for structure and dynamics studies—covering tC°/tC/tCnitro, 2‑Aminopurine (2‑AP), pyrrolo‑C/dC, pyrene‑/perylene‑dU, and etheno‑dA (εdA). These analogs place the reporter inside the duplex, enabling direct readouts of base stacking, pairing, and conformational change with lower impact than external dyes.

We support placement at 5′, 3′, or internal sites (with TEG/PEG spacers as needed), scales from nmol → multi‑gram, and full HPLC/PAGE purification with ESI‑MS identity. Optional endotoxin and ISO‑aligned documentation (ISO 9001/13485) are available. Our scientists can recommend the right analog(s), spacing, and buffer conditions for your instrument and assay.

  • Keywords (SEO): fluorescent base analog, tC°, tCnitro, 2‑aminopurine, pyrrolo‑C, pyrene‑dU, perylene‑dU, εdA, base‑flipping, stacking, hybridization kinetics, custom oligo synthesis, ISO 13485.
  • Highlights: Minimal perturbation • Internal reporters • HPLC/PAGE • ESI‑MS • nmol→multi‑gram • RUO→ISO 9001/13485.

Fluorescent Bases

Select internal reporters for base‑flipping, stacking, hybridization, excimer, and PET assays.

Hide Products & Notes
Product / Modifications Description Typical Use Notes Code
Ribo‑tC° RNA version of tC° cytosine analog (pairs with G) RNA folding & hybridization readouts; FRET donor/acceptor Bright, environment‑insensitive; minimal structural impact [ribo‑tC°]
2‑Aminopurine (RNA) Fluorescent adenine analog (ribo) RNA base‑flipping & stacking dynamics Quenched when stacked; bright when unstacked [r2‑AP]
Pyrrolo‑C (RNA) Fluorescent cytosine analog (ribo) Microenvironment sensing; mismatch detection Emission sensitive to local stacking/solvent [Pyr‑C]
Perylene‑dU Large polycyclic base analog in dU Bright reporter; duplex stabilization; excimer studies High quantum yield; larger steric footprint [Per‑dU]
Pyrene‑dU Polycyclic pyrene on dU (internal) Excimer/exciplex probes; stacking readouts Excimer emission for adjacent pyrenes; tune spacing [Py‑dU]
tCnitro Electron‑acceptor analog; quencher partner to tC° FRET/PET pairs with tC°; proximity sensing Low intrinsic fluorescence; strong quenching [tCnitro]
tC° Bright cytosine analog (pairs with G) Hybridization monitoring; steady‑state/TCSPC studies Environment‑insensitive; excellent brightness [tC°]
tC Early cytosine analog; predecessor to tC° Duplex reporting; historical comparator to tC° Lower brightness vs tC°; still useful for controls [tC]
2‑Aminopurine (DNA) Fluorescent adenine analog (deoxy) Base‑flipping, polymerase kinetics, mismatch probing Stacking quenches; unstacking brightens [2‑AP]
Pyrrolo‑dC Fluorescent cytosine analog (deoxy) Local environment probe; mismatch/lesion studies Emission shift with microenvironment [Pyr‑dC]
Etheno‑dA (εdA) Etheno‑adenine fluorescent analog Lesion mimic; protein–DNA interaction mapping Distinct emission; confirm polymerase tolerance [εdA]
Technical Notes
  • Stacking sensitivity: 2‑AP and pyrrolo‑C/dC respond strongly to stacking; useful for base‑flipping and enzyme pathways.
  • Environment‑insensitive option: tC° offers stable brightness across contexts—great for quantitative hybridization readouts.
  • Excimer/exciplex: Pyrene/perylene pairs can form excimers; plan spacing (adjacent or with short spacer) for desired signal.
  • Assay setup: Validate polymerase/ligase compatibility when placing analogs near active junctions; adjust probe length/salt to maintain Tm.
  • QC: HPLC purification and MS identity are recommended; protect polycyclic labels from strong light.

Speak to a Scientist

Need help choosing a fluorescent base?

We’ll recommend the analog, placement, and QC to match your instrument and readout.

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FAQ

Which analog should I start with?

tC° for stable brightness in duplex; 2‑AP or pyrrolo‑C/dC for stacking‑sensitive readouts; pyrene/perylene‑dU for excimer designs.

Will fluorescent bases affect Tm?

Often slightly. Re‑optimize probe length/salt to hit the same Tm window you use with unmodified controls.

Can I combine a base analog with terminal dyes?

<p>Yes&mdash;use spacers (TEG/PEG) and orthogonal chemistries to control distance/geometry for FRET or PET.</p>

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