3-Methylthymidine

Technical Specifications

Product Description & Scientific Applications

3-Methylthymidine is 2′-deoxythymidine carrying a methyl group on N3 — the Watson-Crick hydrogen-bond donor that forms the thymine N3–H···N1 contact in A·T pairing. The methyl sits on the base-pairing face, abolishing the donor interaction and making the residue a defined N3-alkylation lesion inside DNA; this is the key distinction from C5- or sugar-modified thymidine analogues. The N3-methyl is reversed by Fe(II)/α-ketoglutarate-dependent dioxygenases of the AlkB family, which hydroxylate the methyl to a hydroxymethyl intermediate that loses formaldehyde, restoring the unmodified thymidine.

AlkB-family demethylase substrate. 3-Methylthymine in DNA is repaired by bacterial AlkB and the human homologues ABH2 and ABH3 — ABH2 biased toward duplex DNA, AlkB and ABH3 active in single- and double-stranded formats. FTO is reported with 3-meT in ssDNA, 3-meU in ssRNA, and a mononucleotide complex, disfavouring duplex, and is treated separately. Use the nucleoside for analytical assignment and substrate preparation, and 3-meT oligonucleotides for kinetic profiling, AlkB/ABH2/ABH3 comparison, and enzyme–substrate structural work.

Defined replication-blocking lesion. Loss of the adenine-pairing donor blocks template reading. Use the nucleoside to place a single 3-methylthymine lesion at a chosen oligonucleotide position — a clean context for polymerase stalling, primer-extension blockage, AlkB-mediated reversal, and the consequences of unrepaired N3-alkylation, without the noise of mixed chemically methylated DNA.

Analytical reference standard. Authentic 3-methylthymidine supports retention-time assignment and mass-spectral confirmation of methylated nucleosides released from digested DNA, where low-abundance peaks cannot be assigned by mass alone; isotope-labelled material enables absolute quantification. For damage-spectrum calibration it distinguishes methylating agents — SN2-like MMS favouring ring-nitrogen methylation (N7-methylguanine, N3-methyladenine), SN1-like MNU raising oxygen adducts (O6-methylguanine, O4-methylthymine) — with 3-methylthymine a minor product tracked against the dominant N7 and N3 lesions.

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