Sequence-specific DNA labelling for fluorescence microscopy

The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence -specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treat-ment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.

Automated summary

In this review, we summarize various sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatments and DNA denaturation. These methods include hairpin polyamides, triplex-forming oligonucleotides, dCas9 proteins, transcription activator-like effectors (TALEs), and DNA methyltransferases (MTases). The goal is to eventually replace the traditionally used fluorescence in situ hybridization (FISH) with less invasive and non-destructive methods that are compatible with live cell imaging, allowing for the examination of chromatin structure and dynamics in living cells, tissues, and organisms.