Long probes cannot distinguish a single mismatch
Supplied working report; original verdicts not validated.
Review status: Held for correction. This is an archival source note, not a passed proof.
README.md
# Long probes cannot distinguish a single mismatch **XXII, Theory 03 / Molecular / DNA duplexes** · verdict: **supported** Claim (verbatim): > Hybridisation specificity is set by the ratio of mismatch destabilisation to duplex length, so long probes cannot distinguish a single mismatch. ## Result Discrimination falls from 1.9 C at 6 nt to 0.1 C at 60 nt as the fixed mismatch penalty is spread over more base pairs. ## Headline Single-mismatch discrimination falls from 1.9C to 0.1C between 6 and 60 nt. ## Design Melting temperatures of perfect and single-mismatch duplexes were computed from a two-state nearest-neighbour model with a fixed mismatch penalty, varying probe length from 6 to 60 nt. ## Key statistics - dTm_at_6nt_C = 1.92145 C - dTm_at_60nt_C = 0.0670605 C ## Predictions - **P1** (supported): dTm falls from 1.9C to 0.1C with length ## Limitations - A fixed mean mismatch penalty is an approximation; real penalties depend on the mismatch and its neighbours. - Specificity in practice also depends on washing stringency, which can recover some discrimination. - The two-state model ignores secondary structure and probe-surface effects. Provenance: Two-state nearest-neighbour melting model (Marky-Breslauer / SantaLucia convention, mean parameters). *Working paper — not peer reviewed. AI-assisted. Not medical, clinical, financial or safety advice.*