Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA molecules

Abstract

Rad51 protein (Rad51) is central to recombinational repair of double-strand DNA breaks. It polymerizes onto DNA and promotes strand exchange between homologous chromosomes. We visualized the real-time assembly and disassembly of human Rad51 nucleoprotein filaments on double-stranded DNA by single-molecule fluorescence microscopy. Rad51 assembly extends the DNA by Ϸ65%. Nucleoprotein filament formation occurs via rapid nucleation followed by growth from these nuclei. Growth does not continue indefinitely, however, and nucleoprotein filaments terminate when Ϸ2 m in length. The dependence of nascent filament formation on Rad51 concentration suggests that 2-3 Rad51 monomers are involved in nucleation. Rad51 nucleoprotein filaments are stable and remain extended when ATP hydrolysis is prevented; however, when permitted, filaments decrease in length as a result of conversion to ADP-bound nucleoprotein complexes and partial protein dissociation. Dissociation of Rad51 from dsDNA is slow and incomplete, thereby rationalizing the need for other proteins that facilitate disassembly.nucleation ͉ RecA protein ͉ recombination ͉ self-assembly ͉ single-molecule G enomes are continually attacked by both endogenous and exogenous agents that damage DNA. DNA damage in the form of DNA breaks can lead to chromosome translocations, cell cycle arrest, and apoptosis. Homologous recombination is an essential biological process that ensures the accurate repair of DNA breaks and thereby contributes to genomic integrity. The recombinational repair of DNA with a break occurs by a multistep process (1-3). The first step requires resection of the broken duplex DNA by a helicase and/or nuclease to produce a region of 3Ј-terminated single-strand DNA (ssDNA) at the ends of the break (1, 4). These ssDNA tails serve as substrates for the assembly of a DNA strand exchange protein, such as RecA in bacteria or Rad51 in eukaryotes (2,3,5). This nucleoprotein filament finds homology in an intact DNA molecule and promotes DNA strand invasion to form an intermediate, termed a joint molecule. Pairing by both processed ends of the broken DNA, and their subsequent replication, results in formation of Holliday junctions. These Holliday junctions undergo branch migration and are resolved enzymatically to produce the repaired DNA.Rad51 protein (Rad51) assembles on either single-or doublestranded DNA (dsDNA) to produce a nucleoprotein filament that, at saturation, comprises 1 Rad51 monomer for every 3 nucleotides or base-pairs of DNA. Electron microscopy and X-ray crystallography show the Rad51 nucleoprotein filament to be a right-handed helical structure in which the DNA is stretched by Ϸ50% over its normal B-form length (6, 7). This filament displays ATP hydrolysis activity when assembled on either ssDNA or dsDNA. Rad51 promotes the homologous pairing of ssDNA with dsDNA; however, migration of the nascent DNA heteroduplex is relatively slow. This DNA strand exchange activity is substantially enhanced by RPA, and is regulated by several mediator proteins (Brca2...

Direct observation of twisting steps during Rad51 polymerization on DNA

“…We observed that the polymerization of hRad51 on dsDNA requires a minimal concentration of approximately 100 nM to initiate. This is consistent with previous results independently obtained both with conventional MT (20) and in single-molecule videomicroscopy (21) confirming the existence of a threshold concentration for hRad51 polymerization initiation. The threshold in ref.…”

“…In additions, the flow used in ref. 21 to keep molecules extended involves a stretching, which is nonuniform but can be high enough, especially at some places, to significantly increase hRad51 binding rate. Besides this minor discrepancy, data in refs.…”

“…Reported values range from 3 to 7 bp per protein for RecA (5,(7)(8)(9)) and 2 to 3 and 4 to 5 bp per protein for Rad51 (4,(10)(11)(12). The kinetics of RecA and Rad51 polymerization were recently the subject of several singlemolecule studies (13)(14)(15)(16)(17)(18)(19)(20)(21). There is consensus about a nucleation and growth mechanism for both RecA (14)(15)(16)22) and Rad51 (19)(20)(21), and about a highly cooperative nucleation step requiring the simultaneous binding of several proteins.…”

“…The kinetics of RecA and Rad51 polymerization were recently the subject of several singlemolecule studies (13)(14)(15)(16)(17)(18)(19)(20)(21). There is consensus about a nucleation and growth mechanism for both RecA (14)(15)(16)22) and Rad51 (19)(20)(21), and about a highly cooperative nucleation step requiring the simultaneous binding of several proteins. The stoichiometry of this nucleus, however, is not well established for Rad51, and values ranging from 2-3 (21) to 4-6 (19, 20) protein monomers were proposed.…”

Two distinct conformational states define the interaction of human RAD 51‐ ATP with single‐stranded DNA

“…This process is highly dependent on the tension in the dsDNA template: disassembly stalls completely at forces above 50 pN. In addition, although the NPF can readily form in the presence of both ATP (van Mameren et al , 2009b) and ADP (Hilario et al , 2009), hRAD51 disassembly from dsDNA is critically dependent on ATP hydrolysis (van Mameren et al , 2009b). X‐ray crystallography has identified the location of the ATP‐binding pocket between adjacent monomers in the NPF (Conway et al , 2004).…”