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