000163860 001__ 163860 000163860 005__ 20251107115329.0 000163860 0247_ $$2doi$$a10.1016/j.csbj.2025.10.004 000163860 0248_ $$2sideral$$a146006 000163860 037__ $$aART-2025-146006 000163860 041__ $$aeng 000163860 100__ $$aLuna-Cerralbo, David 000163860 245__ $$aCertPrime: a new oligonucleotide design tool for gene synthesis 000163860 260__ $$c2025 000163860 5060_ $$aAccess copy available to the general public$$fUnrestricted 000163860 5203_ $$aThe 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. 000163860 536__ $$9info:eu-repo/grantAgreement/ES/DGA/E30-20R$$9info:eu-repo/grantAgreement/ES/DGA/IDMF 2021-0009$$9info:eu-repo/grantAgreement/ES/MICINN/PID2020-113582GB-I00$$9info:eu-repo/grantAgreement/ES/MICINN/PID2023-147734NB-I00 000163860 540__ $$9info:eu-repo/semantics/openAccess$$aby-nc-nd$$uhttps://creativecommons.org/licenses/by-nc-nd/4.0/deed.es 000163860 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/publishedVersion 000163860 700__ $$aSerrano, Ana 000163860 700__ $$aBlasco-Machín, Irene 000163860 700__ $$aHamdan, Fadi 000163860 700__ $$aMartínez-Oliván, Juan 000163860 700__ $$aBroset, Esther 000163860 700__ $$0(orcid)0000-0002-5833-8798$$aBruscolini, Pierpaolo$$uUniversidad de Zaragoza 000163860 7102_ $$12004$$2405$$aUniversidad de Zaragoza$$bDpto. Física Teórica$$cÁrea Física Teórica 000163860 773__ $$g29 (2025), 286-295$$pComput. struct. biotechnol. j.$$tComputational and Structural Biotechnology Journal$$x2001-0370 000163860 8564_ $$s3123020$$uhttps://zaguan.unizar.es/record/163860/files/texto_completo.pdf$$yVersión publicada 000163860 8564_ $$s2377430$$uhttps://zaguan.unizar.es/record/163860/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada 000163860 909CO $$ooai:zaguan.unizar.es:163860$$particulos$$pdriver 000163860 951__ $$a2025-11-07-10:26:09 000163860 980__ $$aARTICLE