Concentration of mammalian genomic DNA using two-phase aqueous micellar systems

• Published in: Biotechnology and bioengineering Vol. 102; no. 6; pp. 1613 - 1623
• Main Authors: Mashayekhi, Foad, Meyer, Aaron S., Shiigi, Stacey A., Nguyen, Vu, Kamei, Daniel T.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 15.04.2009; Wiley; Wiley Subscription Services, Inc
• Subjects: Algorithms; Biological and medical sciences; Biomarkers, Tumor - isolation & purification; Biotechnology; cancer biomarkers; Cells; Chemical Fractionation - methods; Deoxyribonucleic acid; diagnostics; DNA; DNA - isolation & purification; Fundamental and applied biological sciences. Psychology; Genetic markers; genomic DNA; Genomics; HeLa Cells; Humans; liquid-liquid extraction; Mammals; Micelles; Models, Chemical; Neoplasms - diagnosis; Polyethylene Glycols - chemistry; Salts - chemistry; Studies; Temperature; Time Factors; Triton X-114; two-phase aqueous micellar systems; genomic DNA; two-phase aqueous micellar systems; Genomics; liquid-liquid extraction; Biological marker; Concentration; Malignant tumor; cancer biomarkers; Vertebrata; diagnostics; Mammalia; DNA; Extraction; Diagnosis; Genome; Triton X-114; Cancer
• ISSN: 0006-3592; 1097-0290
• DOI: 10.1002/bit.22188

The concentration of biomarkers, such as DNA, prior to a subsequent detection step may facilitate the early detection of cancer, which could significantly increase chances for survival. In this study, the partitioning behavior of mammalian genomic DNA fragments in a two‐phase aqueous micellar system was investigated using both experiment and theory. The micellar system was generated using the nonionic surfactant Triton X‐114 and phosphate‐buffered saline (PBS). Partition coefficients were measured under a variety of conditions and compared with our theoretical predictions. With this comparison, we demonstrated that the partitioning behavior of DNA fragments in this system is primarily driven by repulsive, steric, excluded‐volume interactions that operate between the micelles and the DNA fragments, but is limited by the entrainment of micelle‐poor, DNA‐rich domains in the macroscopic micelle‐rich phase. Furthermore, the volume ratio, that is, the volume of the top, micelle‐poor phase divided by that of the bottom, micelle‐rich phase, was manipulated to concentrate DNA fragments in the top phase. Specifically, by decreasing the volume ratio from 1 to 1/10, we demonstrated proof‐of‐principle that the concentration of DNA fragments in the top phase could be increased two‐ to nine‐fold in a predictive manner. Biotechnol. Bioeng. 2009;102: 1613–1623. © 2008 Wiley Periodicals, Inc.