Four-Strand Pairing Beyond Watson–Crick: Interaction Hypergraphs, Controlled Degeneracy, and Sequence Constraints
| dc.contributor.author | Barack Ndenga | |
| dc.date.accessioned | 2025-12-23T22:25:29Z | |
| dc.date.issued | 2025-12-23 | |
| dc.description | This work introduces a formal framework for multi-strand molecular recognition in a canonical tetra-stranded genome (Q-DNA), extending genetic pairing principles beyond classical Watson–Crick base pairing. Rather than relying on pairwise interactions, the manuscript defines four-strand recognition units modeled as interaction hypergraphs, capturing cooperative hydrogen-bonding networks that cannot be reduced to independent base pairs. The study classifies families of four-strand pairing motifs, analyzes their energetic and informational degeneracy, and derives sequence–structure compatibility rules required for genome-scale coherence. These rules constrain which sequences can tile consistently across a tetra-stranded genome without inducing geometric or topological frustration. The resulting framework yields a dictionary of Q-recognition units and a set of design principles for constructing tetra-stranded genetic systems with controlled robustness and specificity. By providing a precise language for multi-body recognition, this contribution establishes the molecular basis for information encoding, error tolerance, and replication logic in tetra-stranded hereditary polymers. The framework has direct implications for synthetic genetics, alternative genetic alphabets, and the exploration of non-canonical genome architectures in origins-of-life and astrobiology research. Resource type: theoretical manuscript / molecular recognition framework Intended audience: molecular biophysics, synthetic genetics, theoretical biology, and genome architecture communities | |
| dc.description.abstract | Canonical DNA heredity relies on pairwise Watson–Crick base pairing, a remarkably simple recognition rule that underlies duplex stability and faithful replication. However, a canonical tetra-stranded hereditary polymer such as Q-DNA cannot rely exclusively on pairwise interactions without collapsing into a duplex-dominant description. In this work, I introduce a multi-body pairing framework for four-stranded genomes, formalized using interaction hypergraphs rather than simple base-pair graphs. I define classes of four-strand hydrogen-bonding units, analyze their energetic and informational degeneracy, and derive sequence–structure compatibility rules required for genome-scale coherence. The result is a dictionary of Q-recognition units and a set of design constraints that make tetra-stranded encoding possible, distinct, and testable. Keywords: Q-DNA, hydrogen bonding, non-Watson–Crick pairing, hypergraphs, multi-body interactions, sequence constraints | |
| dc.description.provenance | Submitted by Barack Ndenga (ndengabarack@gmail.com) on 2025-12-23T22:25:29Z No. of bitstreams: 2 92nd .pdf: 285196 bytes, checksum: 58424428249f852a23b87aee68d3d548 (MD5) license_rdf: 1166 bytes, checksum: d700fae5b268849d8bbda3dffdc09cde (MD5) | en |
| dc.description.provenance | Made available in DSpace on 2025-12-23T22:25:29Z (GMT). No. of bitstreams: 2 92nd .pdf: 285196 bytes, checksum: 58424428249f852a23b87aee68d3d548 (MD5) license_rdf: 1166 bytes, checksum: d700fae5b268849d8bbda3dffdc09cde (MD5) Previous issue date: 2025-12-23 | en |
| dc.description.sponsorship | None | |
| dc.identifier.uri | https://africarxiv.ubuntunet.net/handle/1/10664 | |
| dc.language.iso | en | |
| dc.publisher | Publisher | |
| dc.rights | Attribution-NonCommercial-ShareAlike 3.0 United States | en |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc-sa/3.0/us/ | |
| dc.title | Four-Strand Pairing Beyond Watson–Crick: Interaction Hypergraphs, Controlled Degeneracy, and Sequence Constraints | |
| dc.type | Article |