Size-dependent isolation of DNA fragments from sheared genomic DNA via dSPRI.

AMPure XP SPRI beads bind DNA fragments in a size dependent manner according to the concentration of salts and polyethylene glycol (PEG) in the reaction [4]–[7], which can easily be changed by using different volume ratios of DNA to SPRI bead solutions. A two-step procedure is employed to isolate targeted DNA size fractions. Panels A to H present Bioanalyzer DNA-1000 assays showing the sheared genomic DNA used as starting material (black), the larger size DNA fragments discarded in separation 1 (red), and the size fraction purified and recovered after separation 2 (blue). Panel I is a table summarizing the conditions and results displayed in panels A to H. All Bioanalyzer DNA-1000 traces after separation 1 (panel J), and after separation 2 (panel K), are respectively displayed on a graph for the conditions presented in panels A to H. The conditions displayed in panel H were used to obtaine the Illumina composite reads discussed in the text. The wider DNA fragment size distribution from panel H allowed to better analyze the effects of shorter versus longer overlapping regions on consensus reads.