Real-Time Detection of Single-Molecule DNA Compaction by Condensin I

Abstract

Background: Condensin is thought to contribute to large-scale DNA compaction during mitotic chromosome assembly. It remains unknown, however, how the complex reconfigures DNA structure at a mechanistic level.Results: We have performed single-molecule DNA nanomanipulation experiments to directly measure in real-time DNA compaction by the Xenopus laevis condensin I complex. Condensin can bind to the nanomanipulated DNA in the absence of ATP, but it compacts the DNA only in the presence of hydrolyzable ATP. Linear compaction is evidenced by a reduction in the end-to-end extension of nanomanipulated DNA. The reaction results in total compaction of the DNA (i.e., zero end-to-end extension). Discrete and reversible DNA compaction events are observed in the presence of competitor DNA when the DNA is subjected to weak stretching forces (F = 0.4 picoNewton [pN]). The distribution of step sizes is broad and displays a peak at ∼60 nm (∼180 bp) as well as a long tail. This distribution is essentially unaffected by the topological state of the DNA substrate. Increasing the force to F = 10 pN drives the system toward step-wise reversal of compaction. The distribution of step sizes observed upon disruption of condensin-DNA interactions displays a sharp peak at ∼30 nm (∼90 bp) as well as a long tail stretching out to hundreds of nanometers.Conclusions: The DNA nanomanipulation assay allows us to demonstrate for the first time that condensin physically compacts DNA in an ATP-hydrolysis-dependent manner. Our results suggest that the condensin complex may induce DNA compaction by dynamically and reversibly introducing loops along the DNA.