Hi all,
Hope someone can help me with some issue the bothers me.
I was told that sonication usually does not shear DNA that is strongly bound by some protein due to previous cross-linking.
Considering chromatin structure, this means that the shearing should occur at the linker DNA and not at the DNA which surrounds nucleosomes.
So, why does the product of cross-linking followed by sonication does not show a similar pattern as MNase digestion when it is run on gel ? (MNase shows bands of mono-poly nucleosomes, and the second shows smear)
The way I see it , if 'nucleosome-linkerDNA-nucleosome' follow the structure of '150bp-40bp-150bp' (more or less) then I should see a gap in the gel for fragment which are less than 150bp and for fragments that are in the range of 230-340bp.
To clarify, I "can get" fragments of 150bp up to 230bp considering linker DNA is found at both the enter and exit of the DNA at the nucleosomes (40 + 150 + 40). But how, for example can be in the gel a fragment of 300bp ?
If anyone has an explanation or can point me to a publication that deals with it, I would be so grateful.
Hope someone can help me with some issue the bothers me.
I was told that sonication usually does not shear DNA that is strongly bound by some protein due to previous cross-linking.
Considering chromatin structure, this means that the shearing should occur at the linker DNA and not at the DNA which surrounds nucleosomes.
So, why does the product of cross-linking followed by sonication does not show a similar pattern as MNase digestion when it is run on gel ? (MNase shows bands of mono-poly nucleosomes, and the second shows smear)
The way I see it , if 'nucleosome-linkerDNA-nucleosome' follow the structure of '150bp-40bp-150bp' (more or less) then I should see a gap in the gel for fragment which are less than 150bp and for fragments that are in the range of 230-340bp.
To clarify, I "can get" fragments of 150bp up to 230bp considering linker DNA is found at both the enter and exit of the DNA at the nucleosomes (40 + 150 + 40). But how, for example can be in the gel a fragment of 300bp ?
If anyone has an explanation or can point me to a publication that deals with it, I would be so grateful.