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qSanger: Quantification of Genetic Variants in Bacterial Cultures by Sanger Sequencing

Prakash, Satya; Racovita, Adrian; Petrucci, Teresa; Galizi, Roberto; Jaramillo, Alfonso


Satya Prakash

Adrian Racovita

Teresa Petrucci

Alfonso Jaramillo


Genetic variations such as mutations and recombinations arise spontaneously in all cultured organisms. Although it is possible to identify nonneutral mutations by selection or counterselection, the identification of neutral mutations in a heterogeneous population usually requires expensive and time-consuming methods such as quantitative or droplet polymerase chain reaction and high-throughput sequencing. Neutral mutations could even become dominant under changing environmental conditions enforcing transitory selection or counterselection. We propose a novel method, which we called qSanger, to quantify DNA using amplitude ratios of aligned electropherogram peaks from mixed Sanger sequencing reads. Plasmids expressing enhanced green fluorescent protein and mCherry fluorescent markers were used to validate qSanger both in vitro and in cotransformed Escherichia coli via quantitative polymerase chain reaction and fluorescence quantifications. We show that qSanger allows the quantification of genetic variants, including single-base natural polymorphisms or de novo mutations, from mixed Sanger sequencing reads, with substantial reduction of labor and costs compared to canonical approaches.

Journal Article Type Article
Acceptance Date Dec 25, 2022
Online Publication Date Feb 7, 2023
Deposit Date Jun 7, 2023
Journal BioDesign Research
Print ISSN 2693-1257
Publisher American Association for the Advancement of Science
Peer Reviewed Peer Reviewed
Volume 5
Article Number 0007
Keywords Cell Biology, Agricultural and Biological Sciences (miscellaneous), Biochemistry, Genetics and Molecular Biology (miscellaneous), Biotechnology
Additional Information Received: 2022-08-25; Accepted: 2022-12-25; Published: 2023-02-07