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Review
. 2001 Jul 17;98(15):8425-32.
doi: 10.1073/pnas.111005198.

Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: a possible advantage of DNA over RNA as genomic material

T Shibata  1 , T Nishinaka, T Mikawa, H Aihara, H Kurumizaka, S Yokoyama, Y Ito
Affiliations
Review

Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: a possible advantage of DNA over RNA as genomic material

T Shibata et al. Proc Natl Acad Sci U S A. .

Abstract

Heteroduplex joints are general intermediates of homologous genetic recombination in DNA genomes. A heteroduplex joint is formed between a single-stranded region (or tail), derived from a cleaved parental double-stranded DNA, and homologous regions in another parental double-stranded DNA, in a reaction mediated by the RecA/Rad51-family of proteins. In this reaction, a RecA/Rad51-family protein first forms a filamentous complex with the single-stranded DNA, and then interacts with the double-stranded DNA in a search for homology. Studies of the three-dimensional structures of single-stranded DNA bound either to Escherichia coli RecA or Saccharomyces cerevisiae Rad51 have revealed a novel extended DNA structure. This structure contains a hydrophobic interaction between the 2' methylene moiety of each deoxyribose and the aromatic ring of the following base, which allows bases to rotate horizontally through the interconversion of sugar puckers. This base rotation explains the mechanism of the homology search and base-pair switch between double-stranded and single-stranded DNA during the formation of heteroduplex joints. The pivotal role of the 2' methylene-base interaction in the heteroduplex joint formation is supported by comparing the recombination of RNA genomes with that of DNA genomes. Some simple organisms with DNA genomes induce homologous recombination when they encounter conditions that are unfavorable for their survival. The extended DNA structure confers a dynamic property on the otherwise chemically and genetically stable double-stranded DNA, enabling gene segment rearrangements without disturbing the coding frame (i.e., protein-segment shuffling). These properties may give an extensive evolutionary advantage to DNA.

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Figures

Figure 1
Figure 1
A model for the extended single-stranded DNA structure induced by binding of RecA/Rad51. (A) The model structure and summary of NOE intensities. (B and C) Comparison of the model structure of the extended single-stranded DNA (B) with a part of B-form DNA (C). The extended single-stranded DNA structure, in which the distance between bases is ca. 5 Å, contains hydrophobic 2′ methylene-base interactions, instead of the base-base stacking found in B-form DNA (the distance between bases: 3.4 Å). [Reproduced with permission from ref. (Copyright 1997, National Academy of Sciences).]
Figure 2
Figure 2
Model of heteroduplex joint formation induced by the base rotation associated with sugar pucker interconversion. (Left) The side view. (Right) The bottom view. Single-stranded DNA approaches from the minor groove of the extended double-stranded DNA with the N-type (C3′ endo) sugar pucker (Lower Left) or from the major groove of the double-stranded DNA with the S-type (C2′ endo) sugar pucker (Upper Left). The interconversion of sugar puckers induces the horizontal rotation of bases, which tests whether a base in the single-stranded DNA is complementary to a base engaged in a base-pair interaction in the double-stranded DNA. Complementarity would result in a base-pair switch. Thermal molecular motions are predicted to be sufficient to induce the base rotation, because the kinetic barrier for the interconversion of sugar puckers and that for the disruption of each base pair are sufficiently low. [Reproduced with permission from ref. (Copyright 1998, National Academy of Sciences).]
Figure 3
Figure 3
Proposed ATP hydrolysis-independent and -dependent steps in heteroduplex joint formation and dissociation by RecA. Step 1: In the presence of ATP, RecA binds to single-stranded DNA (ssDNA) to form nucleoprotein filaments, resulting in the unfolding of secondary structures. Step 2: The nucleoprotein filament interacts with double-stranded DNA (dsDNA) without any need for sequence homology. These steps were well established by previous studies (see text). Step 3: A proposed ATP hydrolysis-independent reversible step. Repeated trials of base-pair switching induced by base rotation in the reaction lead to the formation of a core heteroduplex joint. The stability of the heteroduplex joint depends on the size of the base-paired region within the heteroduplex. Step 4: ATP hydrolysis-dependent unidirectional branch migration. Once a core heteroduplex is formed, the heteroduplex is extended in the 5′ to 3′ direction of parental single-stranded DNA (junction and direction are indicated by arrow i). When double-stranded DNA is under topological constraint (e.g., it is a closed circle or is anchored to the chromatin scaffold at points), the heteroduplex is extended until a supercoil is removed. Then, as the leading junction (indicated by arrow i) moves, the trailing junction (indicated by arrow ii) follows keeping the distance between the two junctions constant, and resulting in the migration of the heteroduplex. This step was characterized by various studies (see text). Step 4′: Proposed model of ATP hydrolysis-dependent dissociation at the end of the homologous sequence. If the heteroduplex joint is formed with a homologous sequence of a limited length, the heteroduplex joint is dissociated (41). This probably occurs by RecA-promoted migration of the trailing junction beyond the region of homology (41).
Figure 4
Figure 4
Possible stimulation of heteroduplex joint extension by continuous conversion of sugar puckers of the N type to the S type. Because the twist of extended double-stranded DNA is increased by sugar pucker interconversion from the N type to the S type, the sugar pucker type interconversion may create the rotational motion that stimulates branch migration. As extended double-stranded DNA with the N-type sugar puckers fits well with the active form (ATP form) of the RecA filament, and extended double-stranded DNA with S-type sugar puckers fits well with the inactive form (ADP form) of the RecA filament, ATP hydrolysis is predicted to stimulate rotation and, therefore, branch migration. It should be noted that this model is compatible with heteroduplex joint formation with single-stranded DNA approaching from the minor groove of double-stranded DNA with the N-type sugar pucker.
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