Figure 5
The Role of TFAM-induced bubbles on DNA compaction and transcription initiation.
(a) Effect of large hinge formation (star) due to TFAM oligomerization on DNA compaction. Large oligomers bend DNA more effectively. Note that small hinges (crosses) develop only when the oligomers diffuse extremely slowly. For monomers, small hinges are evident only upon specific binding (see below). (b) Persistent length of the DNA as a function of TFAM concentration, calculated using equation (5), in comparison with experimental results of Ref. 17. (c) Schematic illustration of LSP activation by TFAM. TFAM first assists TFBM2 and mitoRNAP to excite the transcription bubble and then a nucleation of the bubble induced by Box A and the transcription bubble stabilizes the transcription machinery. The small bubble at the end of Box B and the large bubble at the end of Box A act as flexible hinges allowing the DNA to rotate. The interaction between the tail and TFB2M can stabilize a U-turn in agreement with the experimental works of Ref. 18. (d) Same as in c but for the HSP activation. Note that in this case the interaction of the tail with TFB2M prevents rotation around the large flexible hinge and thus a U-turn is not possible, as also observed in Ref. 18.
