Four-Strand Pairing Beyond Watson–Crick: Interaction Hypergraphs, Controlled Degeneracy, and Sequence Constraints
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Barack Ndenga
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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
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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
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