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Fluorescent Base-Modified Oligonucleotides

Custom DNA and RNA oligos containing built-in fluorescent base analogs for stacking, base-flipping, hybridization, FRET, PET and nucleic acid microenvironment studies.

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Overview Fluorescent Bases Choosing Guide Applications Quality Reading FAQ Contact
Overview

Fluorescence Built Into the Oligonucleotide Sequence

Bio-Synthesis provides fluorescent base-modified oligonucleotides for structure and dynamics studies using internal base reporters such as tC°/tC/tCnitro, 2-Aminopurine, pyrrolo-C/dC, pyrene-/perylene-dU and etheno-dA (εdA).

Unlike terminal dye labels, fluorescent base analogs place the reporter directly inside the duplex. This enables direct readouts of base stacking, base flipping, hybridization kinetics, protein–nucleic acid interactions and local microenvironment changes with lower steric impact than large external dyes.

tC° / tC / tCnitro 2-Aminopurine Pyrrolo-C / Pyrrolo-dC Pyrene / Perylene-dU HPLC / PAGE / ESI-MS

Bio-Synthesis supports placement at 5′, 3′ or internal sites, TEG/PEG spacers when needed, scales from nmol to multi-gram, and fit-for-purpose HPLC/PAGE purification with ESI-MS identity confirmation. Most requested fluorescent base modifications include tC°, 2-Aminopurine, Pyrrolo-dC, tCnitro, Pyrene-dU and Perylene-dU.

Internal Base Reporters vs Terminal Dye Labels

Feature Base Analog Terminal Dye
Base stacking Excellent Limited
Base flipping Excellent No
Local structure Direct Indirect
Multiplexing Moderate Excellent
Steric effect Lower Higher
FRET/PET Supported Supported

Internal Base Reporter vs Terminal Dye

A T tC° G C

Fluorescent base analog embedded inside the sequence.

5′ A T G Dye

Terminal dye placed outside the base stack.

Fluorescent Bases

Fluorescent Base Selection Guide

Compare common fluorescent base analogs by color, spectral range, application and fluorescence behavior. Spectral values are practical planning ranges and can shift with sequence context and assay conditions.

Fluorescent Base Analogs for DNA & RNA

Select internal reporters for stacking, base-flipping, hybridization, FRET, PET and excimer-based assays.

Base Analog Color Spectral Range Typical Use Key Advantages
Ribo-tC° Green
Ex 365–370Em 455–460
 RNA hybridization studies Bright, minimal duplex perturbation
tC° Green
Ex 365–370Em 455–460
 Duplex stability & hybridization High brightness, environment-insensitive
tC Green
Ex ~375Em ~500
 Structural studies Internal fluorescent reporter
2-Aminopurine (DNA) UV
Ex ~305Em ~370
 Base flipping & enzyme kinetics Highly stacking-sensitive
2-Aminopurine (RNA) UV
Ex ~305Em ~370
 RNA base-flipping dynamics Quenched when stacked; bright when unstacked
Pyrrolo-C (RNA) Green
Ex ~350Em ~460
 RNA structure studies Environment-responsive fluorescence
Pyrrolo-dC Green
Ex ~350Em ~455
 Hybridization & mismatch detection Sensitive to local microenvironment
Pyrene-dU Blue-Green
Ex 340–350Em 390–400 / 470–500 excimer
 Excimer & stacking studies Dual-emission behavior
Perylene-dU Green
Ex 430–450Em 470–500
 Bright internal reporter High quantum yield; larger steric footprint
Etheno-dA (εdA) Blue
Ex ~310Em ~410
 Lesion & interaction studies Distinct fluorescent adenine analog
tCnitro Quencher
Ex ~440Em Low fluorescence / quencher
 FRET / PET designs Efficient internal quencher

Wavelength guidance: Ex/Em badges are planning ranges. Actual fluorescence can shift with sequence context, solvent, duplex formation, base stacking and assay buffer.

Choosing a Fluorescent Base

Start with the desired readout, then select the analog and placement based on stacking sensitivity, brightness and assay mechanism.

Stable duplex brightness

tC° for quantitative hybridization readouts.

Base-flipping dynamics

2-Aminopurine or pyrrolo-C/dC for stacking-sensitive changes.

Excimer / exciplex design

Pyrene-dU or perylene-dU with planned spacing.

FRET / PET proximity

tC° with tCnitro or terminal dye combinations.

Lesion / interaction mapping

εdA for etheno-adenine lesion-mimic studies.

Applications

Applications for Fluorescent Base-Modified Oligonucleotides

Fluorescent base analogs are selected when the fluorescence response must report on local nucleic acid structure rather than simply label the end of an oligo.

HYB

Hybridization Studies

Monitor duplex formation, melting behavior and base-pairing changes with internal fluorescence readouts.

STR

Nucleic Acid Structure

Study folding, stacking, conformational change and local microenvironment differences.

FRET

FRET & PET Designs

Combine donor/acceptor base analogs, quenchers or terminal dyes for proximity-based assays.

ENZ

Enzyme & Polymerase Kinetics

Use stacking-sensitive analogs to monitor base flipping, incorporation, recognition and repair pathways.

PNA

Protein–Nucleic Acid Interactions

Track binding-induced conformational shifts and local structural changes during complex formation.

DX

Probe & Diagnostic Research

Develop internally fluorescent probes for mismatch, microenvironment and hybridization readouts.

Quality & Deliverables

Purification, QC and Delivery

PUR

Purification

  • RP-HPLC or PAGE purification
  • Purity target aligned to assay
  • Light-protected handling when needed
MS

Analytical QC

  • Analytical HPLC/UPLC profile
  • ESI-MS identity when applicable
  • Optional endotoxin and ISO-aligned documentation
DEL

Delivery

  • Tubes, plates or normalized formats
  • Custom concentration or buffer
  • CoA and project documentation

Frequently Asked Questions

FAQ

Which fluorescent base analog should I start with?
tC° is a good starting point for stable brightness in duplex studies. 2-Aminopurine or pyrrolo-C/dC are useful for stacking-sensitive readouts. Pyrene/perylene-dU are useful for excimer-style designs.
How are fluorescent base analogs different from terminal dye-labeled oligos?
Fluorescent base analogs place the reporter directly inside the oligonucleotide sequence, while terminal dyes attach fluorophores at the 5′ or 3′ end. Internal base analogs are often better for local stacking, base-flipping and conformational readouts.
Will fluorescent bases affect Tm?
Often slightly. Probe length, salt conditions and analog position should be re-optimized to match the desired Tm window and assay background.
Can I combine a fluorescent base analog with terminal dyes?
 Yes. Fluorescent base analogs can be combined with terminal dyes, quenchers or spacers for FRET, PET and proximity readout designs. Spacing should be planned carefully.
What purification and QC are recommended?
 HPLC or PAGE purification and MS identity confirmation are recommended for most fluorescent base-modified oligos. Light-sensitive or polycyclic labels should be handled with appropriate light protection.
What information is needed for a quote?
 Provide sequence, DNA/RNA type, fluorescent base analog, placement, scale, purification target, QC requirements, instrument/readout and any terminal dye or quencher needs.
More FAQ'sAll FAQ's
Contact & Quote Request

Need help selecting a fluorescent base modification?

Share your sequence, DNA/RNA format, target fluorescent base analog, placement, desired readout, scale, purification target and QC requirements. Bio-Synthesis can help align analog choice, position and purification with your instrument and assay.
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Need help before quoting?
Email: info@biosyn.com
Phone: 800-227-0627 (US/CAN)
Phone: +001-972-420-8505 (INT)

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Fast Quote Checklist

Include sequence, analog, position, scale, purification and QC needs.

Sequence Analog Position Scale QC
Scientific Background & Recommended Reading

Recommended Reading & Literature References

Selected references covering fluorescent nucleobase analogs, 2-aminopurine, pteridine analogs and fluorescent base readouts for nucleic acid dynamics.

  1. Ward DC, Reich E, Stryer L. Fluorescence studies of nucleotides and polynucleotides. Journal of Biological Chemistry. 1969.
  2. Hawkins ME. Fluorescent pteridine nucleoside analogs. Cell Biochemistry and Biophysics. 2001.
  3. Wilhelmsson LM. Fluorescent nucleic acid base analogues. Quarterly Reviews of Biophysics. 2010.
  4. Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks. Chemical Reviews. 2010.

Note: Literature references provide general design context. Analog selection should be evaluated within the sequence, structural readout, instrument configuration and assay buffer conditions.

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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