Extended Data Figure 1: Schematic of oligonucleotide probe design and synthesis.
From: Super-resolution imaging reveals distinct chromatin folding for different epigenetic states
A unique pair of index primers are used in a PCR reaction to selectively amplify the templates for the probe set of interest from a complex pool of custom, array-derived oligonucleotides. These templates are then amplified and converted to RNA in an in vitro transcription reaction. The RNA products are converted back to DNA in a reverse-transcription reaction using a primer labelled with an activator dye, Alexa-405, which incorporates the dye into the resulting single-stranded DNA probe. Finally, a 32-nucleotide oligonucleotide attached to Alexa-647 is hybridized to all of the probes. The photoswitchable dye, Alexa-647, is used for STORM imaging. The activator dye, Alexa-405, facilitates the 405-nm light induced reactivation of the Alexa-647 dye.
