Extended Data Fig. 7: Spo11 sets up a topological trap for DNA crossings.
From: Spo11 generates gaps through concerted cuts at sites of topological stress
As mounting evidence stresses similarities between the Spo11 complex and type IIB topoisomerases1,33,41 our ‘topological trap’ model strives to explain how Spo11 induces (d)DSBs at DNA crossings. To explain the encounter between the complex and a DNA crossing, we suggest that Spo11 traps a second strand in the tip of bent DNA, a principle that if corroborated, could explain how type II topoisomerases arrive at crossings in general. a, When axis-anchored64 Spo11 encounters a DNA strand (G-segment, grey), the tethering of the G-strand to the presumed Mer2, Mei4, Rec114 dependent condensate65 forms a physical barrier, which can capture an additional strand. Spo11 bends the DNA at the binding site, but does not cleave the DNA. This will draw a second strand (T-segment, brown) into the tip of the bend, and provoke the formation of a DNA crossing. After the arrival of the second strand (T-segment), Spo11 undergoes a conformational change, and entraps both strands. This movement accompanies the cleavage reaction as for topoisomerase VI41, which results in the breakage of both single strands of the G-segment, setting the T-segment free. b, If the G-segment interacts with two or more Spo11 complexes before it encounters a T-strand, the formation of a gap and the corresponding release of a dDSB fragment can occur. Spo11 prefers motifs that mediate DNA bending in defined angles35. Two such bending angles will add up to form a flat U-shape (second panel from top), only if these bending motifs are in phase, resulting in cleavage products of periodic length. DNA between the two tethering Spo11 complexes is in close proximity to the condensate—an additional constraint that may cause the observed GC preference in short fragments. The ensuing steps are completely analogous to single DSB formation in a, with one additional requirement. A dDSB will only occur when a T-strand crosses both G-strand tethers. As shown in the second and third panel, it is important that the T-strand enters below both G-strand arms, which triggers the conformational change of the Spo11 complexes to clamp down the crossings and cleave the G-segment in a concerted fashion. If the T-segment crosses below one, but above the other, grey arm, only a single crossing is trapped and the structure resolves with a single DSB. The two DNA crossings between the G- and T-strands generate the dDSB irrespective of how many Spo11 complexes tether the G segment. Because of the torsional stiffness of DNA at that scale, measured by the twist persistence length, phosphodiester bonds are presented at the same angle to Spo11 at periodic distances (top panel in b). The twist persistence length for dsDNA ranges from 120 to 300 bp, increasing with the stress acting on DNA66,67. These numbers are in good agreement with the maximal range (around 335 bp) over which we could detect periodicity (Extended Data Fig. 3d).
