Size-selective DNA separation: Recovery spectra help determine the sodium chloride (NaCl) and polyethylene glycol (PEG) concentrations required

• Published in: Biotechnology journal Vol. 9; no. 10; pp. 1241 - 1249
• Main Authors: He, Zhangyong, Xu, Hong, Xiong, Min, Gu, Hongchen
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY-VCH Verlag 01-10-2014; WILEY‐VCH Verlag
• Subjects: Desired DNA interval; DNA - chemistry; DNA - isolation & purification; Molecular Weight; Paramagnetic particles; Particle Size; Polyethylene glycol; Polyethylene Glycols - chemistry; Recovery spectra; Sodium Chloride - chemistry; Spectrophotometry - methods; Desired DNA interval; Recovery spectra; Polyethylene glycol; Paramagnetic particles
• ISSN: 1860-6768; 1860-7314
• DOI: 10.1002/biot.201400234

In the presence of sodium chloride (NaCl), DNA fragments can be size‐selectively separated by varying the final concentration of polyethylene glycol (PEG). This separation strategy in combination with the use of paramagnetic particles provides a valuable platform for achieving the desired DNA size interval, which is important in automated library preparation for high‐throughput DNA sequencing. Here, we report the establishment of recovery spectra of DNA fragments that enable the determination of suitable NaCl and PEG concentrations for size‐selective separation. Firstly, at a given NaCl concentration, the recovery equation was obtained by fitting the DNA recovery ratios versus the PEG concentrations using the logistic function to determine the required parameters. Secondly, the slope function of the recovery equation was achieved by deducing its first derivative. Therefore, the recovery spectrum can be generated using the slope function based on those parameters. According to the recovery spectra of different length DNA fragments, suitable NaCl and PEG concentrations can be determined, respectively, by calculating their resolution values and recovery ratios. The strategy was effectively applied to the size‐selective separation of 532‐, 400‐, and 307‐bp fragments at the selected reagent concentrations with recoveries of 96.9, 64.7, and 85.9%, respectively. Our method enables good predictions of NaCl and PEG concentrations for size‐selective DNA separation.
DNA fragments can be size‐selectively separated using carboxyl‐coated paramagnetic particles by varying the final concentrations of polyethylene glycol (PEG) and sodium chloride (NaCl). In this work, the authors report a recovery spectrum approach that can help determine the NaCl and PEG concentrations required for size‐selective separation of DNA fragments. The study demonstrates good predictions of NaCl and PEG concentrations for size‐selective DNA separation.