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Structural maintenance of chromosome (SMC) protein complexes, such as condensin, cohesin, and SMC5/6, are vital in many genetic processes, including mitotic chromosome organization and segregation, regulation of sister chromatid pairing, DNA damage repair and replication, and regulation of gene expression ( 1–6). We discuss our findings in terms of a scrunching model where a stepwise DNA loop extrusion is generated by an ATP-binding-induced engagement of the hinge and the globular domain of the SMC complex. Using ATP-binding-impaired and ATP-hydrolysis-deficient mutants, we find that ATP binding is the primary step-generating stage underlying DNA loop extrusion. Using Molecular Dynamics simulations, we demonstrate that this is due to the structural flexibility of the DNA polymer at these low forces. These large steps show that, strikingly, condensin typically reels in DNA in very sizeable amounts with ∼200 bp on average per single extrusion step at low force, and occasionally even much larger, exceeding 500 bp per step.
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The measured median step sizes range between 20–40 nm at forces of 1.0–0.2 pN, respectively, comparable with the holocomplex size. Here, using high-resolution magnetic tweezers, we resolve single steps in the loop extrusion process by individual yeast condensins. Its ATP-dependent motor mechanism remains unclear but likely involves steps associated with large conformational changes within the ∼50 nm protein complex. The condensin SMC protein complex organizes chromosomal structure by extruding loops of DNA.