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. 2025 Jan 23;26(1):27.
doi: 10.1186/s12859-025-06049-9.

BAC-browser: the tool for synthetic biology

Tatiana A Semashko  1   2 , Gleb Y Fisunov  3   4 , Georgiy Y Shevelev  5 , Vadim M Govorun  3
Affiliations

BAC-browser: the tool for synthetic biology

Tatiana A Semashko et al. BMC Bioinformatics. .

Abstract

Background: Currently, synthetic genomics is a rapidly developing field. Its main tasks, such as the design of synthetic sequences and the assembly of DNA sequences from synthetic oligonucleotides, require specialized software. In this article, we present a program with a graphical interface that allows non-bioinformatics to perform the tasks needed in synthetic genomics.

Results: We developed BAC-browser v.2.1. It helps to design nucleotide sequences and features the following tools: generate nucleotide sequence from amino acid sequences using a codon frequency table for a specific organism, as well as visualization of restriction sites, GC composition, GC skew and secondary structure. To assemble DNA sequences, a fragmentation tool was created: regular breakdown into oligonucleotides of a certain length and breakdown into oligonucleotides with thermodynamic alignment. We demonstrate the possibility of DNA fragments assemblies designed in different modes of BAC-browser.

Conclusions: The BAC-browser has a large number of tools for working in the field of systemic genomics and is freely available at the link with a direct link https://sysbiomed.ru/upload/BAC-browser-2.1.zip .

Keywords: Genome browser; LCR assembly; PCR assembly; Sequence editor; Synthetic biology; Synthetic genomics.

PubMed Disclaimer

Conflict of interest statement

Declarations. Ethical approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Splitting the nucleotide sequence into oligonucleotides without gaps in the BAC-browser. A The window of the browser with splitting into oligonucleotides. Oligonucleotides are shown in pink, and sticky ends optimized for the thermodynamics of duplex formation are highlighted in gray. B The Assembly design window with available parameters on the left side and thermodynamic parameters for splitting on the right side
Fig. 2
Fig. 2
Splitting the nucleotide sequence into oligonucleotides with gaps in the BAC-browser. Also, this sequence was previously split on three overlapping fragments, each of which will be assembled from oligonucleotides separately. A The window of the browser with splitting into oligonucleotides. Oligonucleotides are shown in pink, and sticky ends optimized for the thermodynamics of duplex formation are highlighted in gray. Three fragments F1-F3 are shown in grey. B The Assembly design window with available parameters on the left side and thermodynamic parameters for splitting on the right side
Fig. 3
Fig. 3
Genes assemblies using oligonucleotides generated with different algorithms by BAC-browser. The figure shows the varying annealing temperature at the first stage of assembly, L1 is a DNA ladder. The bottom panel under each EF gel shows the amount of DNA in the sample. A LCR assembly of gp49 with regular split and camR with thermodynamic ungapped split under different conditions; B PCR assembly of gp49 with regular split, camR with thermodynamic ungapped split and fragment of bseRI gene with thermodynamic gapped split under different conditions
Fig. 4
Fig. 4
Specificity of genes assemblies by PCR methods under different conditions. The figure shows the varying annealing temperature at the first stage of assembly, L1 and L2 are DNA ladders. Oligos for three genes were mixed together in first round of assembly, and the gene of interest was amplified using flanking primers in second round
Fig. 5
Fig. 5
BseRI full-gene assembly, L2 is a DNA ladder. A PCR assembly of bseRI first gene fragment with thermodynamic gapped split under different conditions; B PCR assembly of bseRI second gene fragment with thermodynamic gapped split under different conditions; C PCR assembly of bseRI first gene fragment with thermodynamic gapped split under different conditions; D PCR assembly of bseRI full gene from three gene fragments assembled under different conditions
See this image and copyright information in PMC

References

    1. Deaner M, Alper HS. Promoter and terminator discovery and engineering. Adv Biochem Eng Biotechnol. 2016;162:21–44. 10.1007/10_2016_8. - PubMed
    1. Bohrer CH, Fursova NA, Larson DR. Enhancers: a focus on synthetic biology and correlated gene expression. ACS Synth Biol. 2024;13(10):3093–108. 10.1021/ACSSYNBIO.4C00244. - PubMed
    1. Pfleger BF, Pitera DJ, Smolke CD, Keasling JD. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol. 2006;24(8):1027–32. 10.1038/NBT1226. - PubMed
    1. Wang HH, et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature. 2009;460(7257):894. 10.1038/NATURE08187. - PMC - PubMed
    1. Zhang W, Mitchell LA, Bader JS, Boeke JD. Synthetic genomes. Annu Rev Biochem. 2020;89:77–101. 10.1146/ANNUREV-BIOCHEM-013118-110704. - PubMed

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