163860 20251107115329.0 doi 10.1016/j.csbj.2025.10.004 sideral 146006 ART-2025-146006 eng Luna-Cerralbo, David CertPrime: a new oligonucleotide design tool for gene synthesis 2025 The design of oligonucleotides with uniform hybridisation temperatures is essential for successful gene synthesis. However, current computational tools for oligonucleotide design face significant limitations, including difficulties in processing long DNA sequences, poor adaptability to specific experimental conditions, limited control over oligonucleotide length, and challenges in minimising spurious dimer formation. To address these issues, we developed CertPrime (https://oligodesign.bifi.es), an innovative tool designed for scalable and efficient handling of long DNA sequences. CertPrime enables precise customisation of experimental parameters, provides flexibility to limit the maximum oligonucleotide length, and generates designs with reduced deviations in melting temperatures across overlapping regions compared to existing tools. We experimentally compared CertPrime designs with benchmark design methods for a complex DNA sequence and found that CertPrime designs led to more efficient gene assembly, significantly reducing the occurrence of non-specific bands. These results make CertPrime a powerful and versatile tool for oligonucleotide design in gene synthesis applications. Access copy available to the general public Unrestricted info:eu-repo/grantAgreement/ES/DGA/E30-20R info:eu-repo/grantAgreement/ES/DGA/IDMF 2021-0009 info:eu-repo/grantAgreement/ES/MICINN/PID2020-113582GB-I00 info:eu-repo/grantAgreement/ES/MICINN/PID2023-147734NB-I00 info:eu-repo/semantics/openAccess by-nc-nd https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Serrano, Ana Blasco-Machín, Irene Hamdan, Fadi Martínez-Oliván, Juan Broset, Esther Bruscolini, Pierpaolo Universidad de Zaragoza (orcid)0000-0002-5833-8798 2004 405 Universidad de Zaragoza Dpto. Física Teórica Área Física Teórica 29 (2025), 286-295 Comput. struct. biotechnol. j. Computational and Structural Biotechnology Journal 2001-0370 3123020 http://zaguan.unizar.es/record/163860/files/texto_completo.pdf Versión publicada 2377430 http://zaguan.unizar.es/record/163860/files/texto_completo.jpg?subformat=icon icon Versión publicada oai:zaguan.unizar.es:163860 articulos driver 2025-11-07-10:26:09 ARTICLE