Atomistic Stability of Q-DNA: Molecular Dynamics Simulations and Structural Persistence Criteria
| dc.contributor.author | Barack Ndenga | |
| dc.date.accessioned | 2025-12-24T17:28:41Z | |
| dc.date.issued | 2025-12-24 | |
| dc.description | This work presents a systematic atomistic evaluation of candidate tetra-stranded genome architectures (Q-DNA) using explicit-solvent molecular dynamics simulations. A reproducible simulation protocol is defined and applied to representative Q-DNA architectures spanning parallel, paired-duplex, and interwoven braid topologies, with canonical B-DNA and G-quadruplex motifs used as stability benchmarks. Structural persistence is quantified using standard MD observables, including root-mean-square deviation (RMSD), hydrogen-bond occupancy, generalized helical twist, and local breathing modes. Based on these metrics, the study identifies a top three set of Q-DNA architectures that remain coherent under thermal fluctuations at atomic resolution and derives sequence-level design recommendations that favor stability and robustness. By bridging abstract theoretical models with atomistic simulations, this contribution establishes physical plausibility criteria for tetra-stranded hereditary polymers and provides a computational foundation for future experimental exploration, synthetic genetics, and alternative genome architectures relevant to origins-of-life and astrobiology research. Resource type: computational/theoretical manuscript Intended audience: molecular biophysics, computational biology, synthetic genetics, and theoretical genome architecture communities | |
| dc.description.abstract | Theoretical plausibility of a canonical tetra-stranded genome must ultimately be confronted with atomistic stability. Even if topological, thermodynamic, and electrostatic conditions are satisfied in principle, a viable Q-DNA architecture must persist under thermal fluctuations at atomic resolution. In this work, I define a reproducible molecular dynamics (MD) protocol to evaluate candidate tetra-stranded Q-DNA architectures and establish quantitative criteria for structural persistence. I apply this framework to three representative Q-DNA architectures and compare their behavior to canonical B-DNA and well-characterized G-quadruplex motifs. Using standard MD observables—RMSD, hydrogen-bond occupancy, helical twist, and breathing modes—I identify a top three set of Q-DNA architectures that remain structurally coherent over simulation timescales and derive sequence-level design recommendations for future experimental and computational studies. Keywords: Q-DNA, molecular dynamics, tetra-stranded DNA, atomistic stability, structural persistence, G-quadruplex comparison | |
| dc.description.provenance | Submitted by Barack Ndenga (ndengabarack@gmail.com) on 2025-12-24T17:28:41Z No. of bitstreams: 2 94th .pdf: 297105 bytes, checksum: 5e78b4ba6469f9d254ab90c82519309f (MD5) license_rdf: 1166 bytes, checksum: d700fae5b268849d8bbda3dffdc09cde (MD5) | en |
| dc.description.provenance | Made available in DSpace on 2025-12-24T17:28:41Z (GMT). No. of bitstreams: 2 94th .pdf: 297105 bytes, checksum: 5e78b4ba6469f9d254ab90c82519309f (MD5) license_rdf: 1166 bytes, checksum: d700fae5b268849d8bbda3dffdc09cde (MD5) Previous issue date: 2025-12-24 | en |
| dc.description.sponsorship | None | |
| dc.identifier.uri | https://africarxiv.ubuntunet.net/handle/1/10666 | |
| 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 | Atomistic Stability of Q-DNA: Molecular Dynamics Simulations and Structural Persistence Criteria | |
| dc.type | Article |