Twelve two-base-pair helices: an exact designability bound for a fixed family in the maxStacks model

Article draft v1.1 and certificate package for a fixed RNA target family in the maxStacks model. A 71-base sequence uniquely designs T12; all D>=13 are excluded. The model allows GU pairs, forbids isolated pairs and requires j-i>=2 (one unpaired hairpin base, not the usual three). The package supplies standard-library DP, rival and CNF checks, word-case coverage and U14 LRAT proofs. Large D13 DRAT/LRAT proofs are separate companions. The question comes from Boury, Bulteau and Ponty. No claim is made for arbitrary RNA trees, every D<=12, Turner energies, priority or human peer review. Code: Apache 2.0; original prose, data and proof certificates: CC BY 4.0.

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Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2026-10-27
DOI
https://doi.org/10.5281/zenodo.23679267
Primary Topic
RNA and protein synthesis mechanisms
Type
preprint
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preprint

Twelve two-base-pair helices: an exact designability bound for a fixed family in the maxStacks model

竜彦 滝本
Zenodo (CERN European Organization for Nuclear Research)
RNA and protein synthesis mechanisms
preprint

Twelve two-base-pair helices: an exact designability bound for a fixed family in the maxStacks model

竜彦 滝本
preprint en

Abstract

Article draft v1.1 and certificate package for a fixed RNA target family in the maxStacks model. A 71-base sequence uniquely designs T12; all D>=13 are excluded. The model allows GU pairs, forbids isolated pairs and requires j-i>=2 (one unpaired hairpin base, not the usual three). The package supplies standard-library DP, rival and CNF checks, word-case coverage and U14 LRAT proofs. Large D13 DRAT/LRAT proofs are separate companions. The question comes from Boury, Bulteau and Ponty. No claim is made for arbitrary RNA trees, every D<=12, Turner energies, priority or human peer review. Code: Apache 2.0; original prose, data and proof certificates: CC BY 4.0.

Zenodo (CERN European Organization for Nuclear Research)
RNA and protein synthesis mechanisms
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Twelve two-base-pair helices: an exact designability bound for a fixed family in the maxStacks model — 竜彦 滝本 · Zenodo (CERN European Organization for Nuclear Research) (2026) | TGRS Research Map | TGRS