Major scaffold protein involved in loop formation is:
Chromosome condensation during prophase requires scaffold proteins shaping 30 nanometer fiber loops into cylindrical chromatids 700 nanometers wide. Topoisomerase II alpha, type II enzyme cleaving both DNA strands, passing duplex through break and resealing, resolves sister chromatid catenations, adjusts supercoiling and forms axial scaffold along chromatid center overlapping condensin complex. Immunofluorescence shows topoisomerase II colocalizes with condensin along axis. DNA polymerase synthesizes DNA, RNA polymerase transcribes, ligase joins Okazaki fragments, but scaffold architecture and loop compaction depend critically on topoisomerase II plus condensin activity during mitotic entry.
Ref: Earnshaw and Laemmli 1983 Scaffold; Alberts et al., Molecular Biology of the Cell, Chapter 19: Scaffold Protein Topoisomerase II