Computer-Aided Planning for the Verification of Large Batches of DNA Constructs.
Computer-aided manufacturing
DNA assembly
DNA verification
Restriction digest analysis
Sanger sequencing
Synthetic Biology
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2021
2021
Historique:
entrez:
6
1
2021
pubmed:
7
1
2021
medline:
30
3
2021
Statut:
ppublish
Résumé
Restriction digest analysis and Sanger sequencing are among the most commonly used techniques to check the sequence of synthetic DNA constructs. However, both require careful preparation to select restriction enzymes or DNA primers adapted to the expected constructs sequences. In projects involving manufacturing of large batches of synthetic constructs, the task can be tedious and error-prone. This chapter demonstrates the use of two free and open-source web applications providing fast and automated selection of enzymes and sequencing primers for DNA construct verification.
Identifiants
pubmed: 33405221
doi: 10.1007/978-1-0716-1032-9_7
doi:
Substances chimiques
DNA
9007-49-2
DNA Restriction Enzymes
EC 3.1.21.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
167-174Références
Casini A, Storch M, Baldwin GS, Ellis T (2015) Bricks and blueprints: methods and standards for DNA assembly. Nat Rev Mol Cell Biol 16(9):568–576. https://doi.org/10.1038/nrm4014
doi: 10.1038/nrm4014
pubmed: 26081612
Potapov V, Ong JL, Kucera RB, Langhorst BW, Bilotti K, Pryor JM et al (2018) Comprehensive profiling of four base overhang ligation fidelity by T4 DNA ligase and application to DNA assembly. ACS Synth Biol 7(11):2665–2674. https://doi.org/10.1021/acssynbio.8b00333
doi: 10.1021/acssynbio.8b00333
pubmed: 30335370
Shapland EB, Holmes V, Reeves CD, Sorokin E, Durot M, Platt D et al (2015) Low-cost, high-throughput sequencing of DNA assemblies using a highly multiplexed Nextera process. ACS Synth Biol 4(7):860–866. https://doi.org/10.1021/sb500362n
doi: 10.1021/sb500362n
pubmed: 25913499
Sanger F, Coulson AR (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94(3):441–448. https://doi.org/10.1016/0022-2836(75)90213-2
doi: 10.1016/0022-2836(75)90213-2
pubmed: 1100841
Dharmadi Y, Patel K, Shapland E, Hollis D, Slaby T, Klinkner N et al (2014) High-throughput, cost-effective verification of structural DNA assembly. Nucleic Acids Res 42(4):e22. https://doi.org/10.1093/nar/gkt1088
doi: 10.1093/nar/gkt1088
pubmed: 24203706
Hancock JM, Zvelebil MJ, Hancock JM (2004). PRIMER3. In: Dictionary of bioinformatics and computational biology. https://doi.org/10.1002/9780471650126.dob0560.pub2