Partitioning behavior of short DNA fragments in polymer/salt aqueous two‐phase systems

The development of liquid biopsy as a minimally invasive technique for tumor profiling has created a need for efficient biomarker extraction systems from body fluids. The analysis of circulating cell‐free DNA (cfDNA) is especially promising, but the low amounts and high fragmentation of cfDNA found in plasma pose challenges to its isolation. While the potential of aqueous two‐phase systems (ATPS) for the extraction and purification of various biomolecules has already been successfully established, there is limited literature on the applicability of these findings to short cfDNA‐like fragments. This study presents the partitioning behavior of a 160 bp DNA fragment in polyethylene glycol (PEG)/salt ATPS at pH 7.4. The effect of PEG molecular weight, tie‐line length, neutral salt additives, and phase volume ratio is evaluated to maximize DNA recovery. Selected ATPS containing a synthetic plasma solution spiked with human serum albumin and immunoglobulin G are tested to determine the separation of DNA fragments from the main plasma protein fraction. By adding 1.5% (w/w) NaCl to a 17.7% (w/w) PEG 400/17.3% (w/w) phosphate ATPS, 88% DNA recovery was achieved in the salt‐rich bottom phase while over 99% of the protein was removed. Graphical and Lay Summary The extraction of DNA fragments from blood samples is crucial for cancer management as it eliminates the need for invasive surgeries to obtain tumor information. This study investigates using aqueous two‐phase systems (ATPS) to separate short DNA fragments from plasma proteins by examining factors such as polymer type and salt concentration that influence DNA distribution behavior. The findings provide a foundation for developing an ATPS‐based DNA extraction method from plasma.