DNA supercoil introduced to directly visualize individual plectonemes along supercoiled DNA which would further allow to study the interactions of DNA processing proteins with supercoiled DNA. In that study, Sytox Orange (an intercalating dye), has been used to induce supercoiling on surface tethered DNA molecules. DNA supercoiling is important for DNA packaging within all cells. Because the length of DNA can be thousands of times that of a cell, packaging this genetic material into the cell or nucleus (in eukaryotes) is a difficult feat. Supercoiling of DNA reduces the space and allows for DNA to be packaged. In prokaryotes, plectonemic supercoils are
Single-cell DNA template strand sequencing Library construction proceeds as normal for Illumina paired-end sequencing. Multiplexing PCR primers are then ligated to the PCR amplicons with hexamer barcodes identifying which cell each fragment they are derived from. Unlike single cell sequencing protocols, Strand-seq does not utilize multiple displacement amplification or MALBAC for DNA amplification. Rather, it is solely dependent on PCR. The majority of current applications for Strand-seq start by aligning sequenced reads to a reference genome. Alignment can be performed using a variety of short-read aligners such as BWA and Bowtie. By aligning Strand-seq reads from a single cell to the reference genome, the inherited