I am attempting to analyze nuclear DNA damage induced by an ectopically-expressed endonuclease. This nuclease recognizes an eight-base sequence, and forms a double-stranded break with a two-base overhang on each strand (see attached image). Histone 2AX phosphorylation is a commonly used marker for double-stranded breaks. Can H2AX be used to visualize DSBs with this topology, or is H2AX only phosphorylated in response to blunt strand breaks without overhangs?
No matter whether you have an overhang, histones adjacent to a DSB will be phosphorylated. BTW, a "clean" double strand break does not refer to a DSB without overhangs. An endonuclease like yours will produce a "clean" DSB, unlike what would be produced by ionizing radiation. The latter leads to ends that have to be heavily processed due to chemical modification of the DNA and proteins crosslinked to the DNA by the radical chemistry.
@Armin
You are quite right, I have amended the title of the question for clarity.
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