biostudies-literatureGenna VEuropean Molecular Biology OrganizationJuan De La Cierva FellowshipEuropean Research CouncilH2020 BioExcel Center of ExcellenceMINECO Severo Ochoa Award of ExcellenceBiomolecular and Bioinformatics Resources PlatformSpanish Ministry of Sciencegkaf170https://www.ebi.ac.uk/biostudies/studies/S-EPMC11897885biostudies-literatureUnknown53(5)By combining in silico, biophysical, and in vitro experiments, we decipher the topology, physical, and potential biological properties of hybrid-parallel nucleic acids triplexes, an elusive structure at the basis of life. We found that hybrid triplex topology follows a stability order: r(Py)-d(Pu)·r(Py) > r(Py)-d(Pu)·d(Py) > d(Py)-d(Pu)·d(Py) > d(Py)-d(Pu)·r(Py). The r(Py)-d(Pu)·d(Py) triplex is expected to be preferred in the cell as it avoids the need to open the duplex reducing the torsional stress required for triplex formation in the r(Py)-d(Pu)·r(Py) topology. Upon a massive collection of melting data, we have created the first predictor for hybrid triplex stability. Leveraging this predictor, we conducted a comprehensive scan to assess the likelihood of the human genome and transcriNucleic acids researchSystematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism.PMC11897885ALTF 103-2018RTI2018-096704-B-100IJC2019-040468-I/25A04100Castellazzi CVillegas NBrun-Heath ILabrador MGandioso AHospital AGenna VMateo LSala APortella GAloy POrozco MGonzalez JTerrazas MEritja RAvino ASerrano-Chacon IGonzalez CfalseSystematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism.By combining in silico, biophysical, and in vitro experiments, we decipher the topology, physical, and potential biological properties of hybrid-parallel nucleic acids triplexes, an elusive structure at the basis of life. We found that hybrid triplex topology follows a stability order: r(Py)-d(Pu)·r(Py) > r(Py)-d(Pu)·d(Py) > d(Py)-d(Pu)·d(Py) > d(Py)-d(Pu)·r(Py). The r(Py)-d(Pu)·d(Py) triplex is expected to be preferred in the cell as it avoids the need to open the duplex reducing the torsional stress required for triplex formation in the r(Py)-d(Pu)·r(Py) topology. Upon a massive collection of melting data, we have created the first predictor for hybrid triplex stability. Leveraging this predictor, we conducted a comprehensive scan to assess the likelihood of the human genome and transcri2025-01-01T00:00:00Z2025 Feb2026-04-18T03:20:02.157Z2025-04-04T01:29:16.694ZS-EPMC118978854007193610.1093/nar/gkaf170