Journal
ACS SYNTHETIC BIOLOGY
Volume 3, Issue 8, Pages 525-528Publisher
AMER CHEMICAL SOC
DOI: 10.1021/sb4001323
Keywords
software; synthetic biology; biologically neutral sequences; linkers
Categories
Funding
- EPSRC [EP/G036004/1, EP/H019154/1]
- EU Framework Program 7 [ST-FLOW] [KBBE.2011.5-289326]
- BBSRC [BB/L027852/1, BB/J020036/1, BB/M00550X/1] Funding Source: UKRI
- EPSRC [EP/H019154/1, EP/J02175X/1, EP/K034359/1, EP/L011573/1, EP/G036004/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/J020036/1, BB/M00550X/1, BB/L027852/1] Funding Source: researchfish
- Engineering and Physical Sciences Research Council [EP/J02175X/1, EP/H019154/1, EP/G036004/1, EP/L011573/1, EP/K034359/1] Funding Source: researchfish
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R2oDNA Designer is a web application that stochastically generates orthogonal sets of synthetic DNA sequences designed to be biologically neutral. Biologically neutral sequences may be used for directing efficient DNA assembly by overlap-directed methods, as a negative control for functional DNA, as barcodes, or potentially as spacer regions to insulate biological parts from local context. The software creates optimized sequences using a Monte Carlo simulated annealing approach followed by the elimination of sequences homologous to host genomes and commonly used biological parts. An orthogonal set is finally determined by using a network elimination algorithm. Design constraints can be defined using either a web-based graphical user interface (GUI) or uploading a file containing a set of text commands.
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