ArticleFrontiers in genetics2022
An Integrated Algorithm for Designing Oligodeoxynucleotides for Gene Synthesis.
Article in Frontiers in genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- A Physics-Inspired Approach to Improve Oligonucleotide Design and Gene Synthesis.Computational and structural biotechnology journal · 2026Article
- CertPrime: a new oligonucleotide design tool for gene synthesis.Computational and structural biotechnology journal · 2025Article
- A depth-first search algorithm for oligonucleotide design in gene assembly.Frontiers in genetics · 2022Article
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2 authors.
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Abstract
The design and construction of large synthetic genes can be a slow, difficult, and confusing process, especially in the key step of oligodeoxynucleotide design. Herein we present an integrated algorithm to design oligonucleotide sets for gene synthesis by both ligase chain reaction and polymerase chain reaction. It offers much flexibility with no constraints on the gene to be synthesized. Firstly, it divides the long-input DNA sequence by a greedy algorithm based on the length of the oligodeoxynucleotide overlap region. Secondly, it tunes the length of the overlap region iteratively in an attempt to minimize the melting temperature variance of overlap. Thirdly, dynamic programming algorithm is used to achieve the uniform melting temperature of the oligodeoxynucleotide overlaps. Finally, the oligodeoxynucleotides with homologous melting temperature necessary for ligase chain reaction-based or two-step assembly PCR-based synthesis of the desired gene are outputted.
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