Non-B DNA has impacts on cell biology and genome fidelity. Yet it is important to test if non-B DNA is being formed in cells. G-quad structure being among the stable forms of non-B DNA what experiments are be used to test specific sequence regions for the formation of G-quad structure?
Dear John Tainer ,
you may be interested in this open access paper:
https://academic.oup.com/nar/article/47/8/3862/5403498?login=true
Whole-genome experimental maps of DNA G-quadruplexes in multiple species (2019)
This gives you a first insight into the G-quadruplex forming potential of given genomic loci of 12 model species. For in vivo validation, some luciferase assay would be necessary, please, see e.g.:
Article G-quadruplex formation in the Oct4 promoter positively regul...
Regarding G-quadruplex type (parallel, anti-parallel, hybrid), CD spectroscopy is routinely used:
https://onlinelibrary.wiley.com/doi/full/10.1002/ange.201709184?casa_token=H6rj7qKKNq8AAAAA%3ATzHAyxEFGUrabWZt05bGBdOOY46g14yzTBokhWyd-JOig7LC2ILuIT-WGFidtqn3WxroemZdmX23agA
Chapter CD Study of the G-Quadruplex Conformation
Unfortunately, revealing the 3D structure of a particular G-quadruplex in vivo is still impossible (as far as I know). Some methods for quantitative in vivo G4s imaging exist, e.g.
Quantitative Detection of G‐Quadruplex DNA in Live Cells Based on Photon Counts and Complex Structure Discrimination (https://onlinelibrary.wiley.com/doi/full/10.1002/anie.202002422?casa_token=uZPj-dmCAoUAAAAA%3A0bIY4hJ4QJKXgy6X0f30n0yj4iNGoxmix56W_3nZ2E-Ej2UYLcZfoUZkV2sZEfmsNm46NYfHgwJiUqI)
or antibody-based methods:
https://academic.oup.com/nar/article/42/2/860/1030319?login=true (1H6 antibody)
https://academic.oup.com/dnaresearch/article/27/5/dsaa024/5934508?login=true (BG4)
but they are non-specific to particular G4 (instead you see thousands of G4s in the whole genome/transcriptome of the cell)
Hope this help,
Martin
- Badges
- Science topic