Bear with me on this please!
I have made some plasmid enhancer deletions and have found a difference between 93bp of an enhancer and 70bp of an enhancer on luciferase expression in vivo.
I'm trying to determine what this difference is due to- whether it's due to the spacing issue or due to a transcription factor binding site.
I am about to add on 23bp of a scrambled sequence on the end of my 70bp enhancer but my supervisor has alerted me to the fact that there are 10.4-12 nucleotides per turn (depending on the form on the DNA) and so adding on 23bp might just be enough to get through 2 complete turns of the helix and thus, my spacing issue question may not be answered appropriately. This is easy to get over- change the amount of nt at the end of my 70bp sequence.
However, he also mentioned that there is an in vitro assay for looking at DNA helix conformations and the turns etc- can anyone tell me what to look for? It's definitey not ChIP... I've tried googling a variety of search terms but couldn't come up with anything that looked appropriate.