Modified Bases

Halogenated Bases

5‑fluoro, 5‑bromo, and 5‑iodo analogs of U/C (DNA & RNA) for UV photo‑crosslinking, heavy‑atom phasing, duplex tuning, and enzyme/kinetic studies — synthesized, purified, and QC’d to your specs, scalable to ISO 13485.

Overview

Bio‑Synthesis provides custom halogenated oligonucleotides—DNA and RNA modified with 5‑bromo, 5‑iodo, or 5‑fluoro pyrimidines (U/C)—for UV photo‑crosslinking, X‑ray crystallography heavy‑atom phasing (MAD/SAD), duplex Tm tuning, and enzyme/kinetic studies. These halogenated bases preserve native pairing while adding photochemical or heavy‑atom functionality, making them ideal for crosslink mapping, structural biology, and biophysics workflows.

We deliver site‑specific placement at the 5′, 3′, or internal position (including spacer/PEG options), with scales from nmol to multi‑gram. Every lot is purified (HPLC/PAGE) and identity‑confirmed by ESI‑MS, with optional endotoxin and documentation for ISO 9001/13485 programs. Related services include custom probe design for photo‑crosslinking assays, biotin/ enzyme conjugation, and diagnostic oligos—all supported by experienced scientists. Ready to plan your construct? Use Speak to a Scientist for fast, expert guidance.

  • Keywords (SEO): halogenated bases, 5‑bromouracil, 5‑iodouracil, 5‑fluorouracil analogs, halogenated DNA/RNA, photo‑crosslinking oligos, heavy‑atom phasing, custom oligonucleotide synthesis, ISO 13485 oligo manufacturing.
  • Highlights: Site‑specific installation • HPLC/PAGE purification • ESI‑MS QC • nmol→multi‑gram scale • RUO→ISO 9001/13485 support.

Halogenated Bases

Ideal for crosslink mapping, structural biology, and tuning duplex energetics, these 5‑position halogenated pyrimidines are available at desired sites and scales with HPLC/MS QC and optional functional testing.

Hide Products & Notes
Product / Modification Description Typical Use Notes Code
5-Bromo-dU 5-Br substitution at uracil (deoxy) UV photo-crosslinking; structure probing Slight Tm↑; strong photoreactivity [5-Br-dU]
5-Iodo-dU 5-I substitution at uracil (deoxy) UV crosslinking; heavy atom for X-ray phasing Heavier atom; strong absorber [5-I-dU]
5-Fluoro-dU 5-F substitution at uracil (deoxy) Duplex tuning; enzymology / kinetics Minimal steric change; small Tm effect [5-F-dU]
5-Bromo-dC 5-Br substitution at cytidine (deoxy) Photoreactive probes; structure mapping May increase hydrophobicity [5-Br-dC]
5-Iodo-dC 5-I substitution at cytidine (deoxy) Heavy-atom labeling; crystallography aids Check stability; monitor for side reactions [5-I-dC]
5-Fluoro-dC 5-F substitution at cytidine (deoxy) Subtle affinity modulation; enzyme studies Low perturbation analog [5-F-dC]
5-Bromo-rU (RNA) 5-Br substitution at uridine (ribo) RNA UV crosslinking; structural biology Photoreactive; protect from light [5-Br-rU]
5-Bromo-rC (RNA) 5-Br substitution at cytidine (ribo) RNA interaction mapping; crosslink assays Useful for RNP studies [5-Br-rC]
5-Iodo-rU (RNA) 5-I substitution at uridine (ribo) Heavy-atom aids; crosslinking workflows Heavier atom; strong UV sensitivity [5-I-rU]
5-Fluoro-rU (RNA) 5-F substitution at uridine (ribo) NMR labeling; subtle energetic tuning Low perturbation; polymerase selectivity varies [5-F-rU]
Technical Notes
  • Photochemistry: 5‑Br/5‑I bases are efficient for UV crosslinking (typ. 312–365 nm); balance exposure to limit damage.
  • Heavy atoms: Br/I facilitate MAD/SAD phasing; confirm incorporation by MS and absorbance before crystallography.
  • Duplex effects: Halogens can shift Tm slightly; adjust probe length/salt to maintain assay windows.
  • Enzyme tolerance: Polymerase/RT preferences vary; pilot short templates and controls around the modified site.
  • QC & handling: HPLC purification and MS identity recommended; protect photoreactive oligos from strong light.

Speak to Scientist

FAQ

Will halogenation change Tm?

Usually small shifts. Verify your probe length/salt to maintain desired Tm and specificity.

When should I choose 5‑Br vs 5‑I?

5‑I provides stronger absorption/heavy‑atom effects but can be less stable; 5‑Br is a good balance for UV crosslinking. Pilot both when possible.

Any special storage?

Store dry and protected from light; avoid prolonged UV exposure prior to use. Standard –20 °C recommended.

Need help selecting the right halogenated base?

We’ll recommend base/position, purification, and assay conditions to match your workflow.

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Tell us about your project

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Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 40+ years of delivering high quality, fast and scalable synthetic biology solutions.