Oligo mass calculator
Mass, ε, GC% and Tm for any sequence, plus the coupling-failure ladder and a match for a mass you measured. Masses come from the Assemblon monomer catalogue; nothing here reads or writes an order.
Use [brackets] for modifications and (parentheses), * or # for backbone linkages. Nothing here is saved, read from, or written to any order.
—nt
—Da
—M⁻¹·cm⁻¹
—%
—°C
Masses are average mass · 5′-OH, 3′-OH free acid, taken from the Assemblon monomer catalogue. If your deconvolution reported a monoisotopic mass, this comparison is not valid.
Coupling-failure ladder
Synthesis runs 3′→5′, so the last couplings sit at the 5′ end and 5′ truncations are the coupling-failure ladder proper. A failed coupling removes the residue together with its backbone linkage — a phosphorothioate truncation loses the * as well as the base. Capped failure sequences carry a 5′-acetyl that ammonia deprotection cleaves, so there is no cap mass to add.
Real n−1 populations come from couplings failing anywhere with imperfect capping, so the ladder also lists one row per distinct residue as “one residue lost, position unknown”. Rows that land on the same mass are shown once — the mass spectrum cannot tell them apart.
Enter a sequence to build the ladder.
Observed mass
±0.01–100 Da. The default ±3 Da is the same absolute window the lab's mass-spec gate uses to confirm an order.
Tm conditions
Defaults match the Assemblon datasheet (1–1000 mM Na⁺, 0.001–100 µM oligo accepted). Nearest-neighbour (SantaLucia 1998) for unmodified DNA of 8 residues or more; salt-adjusted GC% when degenerate residues are present; Wallace below 8. Modified residues carry additive literature ΔTm corrections.