To assess 5-HT axon terminal integrity after MDMA treatment, the density of 5-HT transporter (SERT) binding sites was measured by quantitative autoradiography using [125I]RTI-55 -2beta- 4-iodophenyl3 beta- 4-iodophenyl) tropane) (125I-RTI-55) as a ligand.
The highest enrichment levels of H3.3 around Pol II binding sites are measured exactly at the binding peak of RNA Pol II.
Atomic distances between corresponding binding residues within each binding site were measured in Deep View.
In these experiments, the effects of single base pair mutations of the a1- α2 consensus binding site were measured by assaying their ability to repress transcription of a heterologous promoter and by electrophoretic mobility shift DNA-binding assays (EMSA).
The immediate effect of the cyclopentyl group within the binding site is measured by the time series of the radius of gyration of the cyclopentyl group binding pocket composed by W1093.28, G902.61, and I3097.36 in Figure 6.
Amounts of [H]-E2 or [H]-T bound to binding sites were determined by measuring the radioactivity of 400 μL supernatant in 3 mL scintillation cocktail (Ultima Gold TM Packard BioScience, Groningen, the Netherlands), using a liquid scintillation counter (Tri Carb 1600; Canberra-Packard, Rodgau-Jugesheim, Germany).
Site-directed mutagenesis of the putative NF-κB binding sites were then generated, and the promoter activities of the corresponding constructs were measured.
Presence/absence, shape, signal intensity vs. background, diameter and DNA binding site capability were measured for each spot on the slide using files generated by Imagene software (BioDiscovery Inc., El Secundo, CA, USA).
Potential binding sites were elucidated by docking.
Ligand binding sites were predicted using 3DLigandSite.
