Post‑synthetic functionalization, reactive handles, and lesion mimics for assay development. Popular options include 5‑F‑dC (TMP‑5‑F‑dU), O6‑Phenyl‑dI, 2‑F‑dI, O4‑Triazolyl‑dU, and m6A—plus halogenated and thio/oxo variants for crosslinking, mutagenesis, and epigenetics.
Convertible base oligonucleotides incorporate bases engineered to be transformed or to provide a reactive leaving group after synthesis. These scaffold bases are used to install probes, form crosslinks, mimic DNA/RNA lesions, or introduce epigenetic marks at defined sites.
O4‑triazolyl‑dU and activated 5‑position pyrimidines undergo substitution with amines, thiols, or azides to install labels or linkers after synthesis.
5‑Br/5‑I pyrimidines and 8‑Br purines support photo/radical crosslinking/footprinting to probe nucleic acid–protein contacts.
Defined modifications such as m6A or oxidized bases serve as standards for reader/writer assays and sequencing controls.
Install dyes, quenchers, biotin, or click handles at a single locus for FRET, hybridization probes, and pull‑down.
Map protein–nucleic acid interfaces using photo/radical‑activated bases (e.g., 5‑Br‑dU).
Introduce convertible lesions or epigenetic marks (m6A) to study repair fidelity and reader proteins.
Send sequence, placement, conversion goal, and purification level—We’ll return a tuned design and QC plan.
A base with a reactive/convertible position that can be transformed after oligo synthesis—useful for on‑demand labeling or crosslinking.
Usually minimal effects; we compensate via length/composition or by adding LNA/2′‑OMe nearby.
Yes. We can convert, purify (HPLC/UPLC), confirm by LC‑MS, and supply a CoA.
Selected chemistries are available for RNA—share your target and we’ll confirm feasibility.
O4‑triazolyl‑dU supports nucleophilic substitution (amines/thiols/azides) for post‑synthetic labeling. 5‑Br/5‑I dU are favored for photo/radical crosslinking and footprinting. Select by intended mechanism and buffer constraints.
Yields depend on sequence context, reagent, and work‑up. Typical crude‑to‑purified conversion recoveries can range from ~50–90%. We recommend a short pilot conversion to tune conditions before scaling.
Yes—common partners are NHS esters (amines), maleimides (thiols), and azide/alkyne pairs for click chemistry. Spacers (PEG/hexa‑EG) can reduce quenching and steric effects.
Generally yes. LNA/2′‑OMe can flank a convertible base to maintain Tm. Consider sterics for bulky substituents and confirm with a short Tm check.
HPLC/UPLC is recommended for clean separation of converted vs. unconverted species. Desalting alone may leave mixed populations.
We can evaluate feasibility. 4‑Thio‑dT and psoralen require UVA and light controls; we’ll advise on placement and handling.
We confirm by LC‑MS; for chromophores, we can also provide UV/Vis data. PAGE or CE can assist with size/charge shifts.
Synthesis from µmol → multi‑gram with CoA, method summaries, and optional RUO→GMP‑like documentation.
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We can align specific literature protocols to your design upon request.
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