Stoichiometry, base orientation, and nuclease accessibility of RecA.DNA complexes seen by polarized light in flow-oriented solution. Implications for the mechanism of genetic recombination

Modeling the Homologous Recombination Process: Methods, Successes and Challenges

Homologous recombination (HR) is a fundamental process common to all species. HR aims to faithfully repair DNA double strand breaks. HR involves the formation of nucleoprotein filaments on DNA single strands (ssDNA) resected from the break. The nucleoprotein filaments search for homologous regions in the genome and promote strand exchange with the ssDNA homologous region in an unbroken copy of the genome. HR has been the object of intensive studies for decades. Because multi-scale dynamics is a fundamental aspect of this process, studying HR is highly challenging, both experimentally and using computational approaches. Nevertheless, knowledge has built up over the years and has recently progressed at an accelerated pace, borne by increasingly focused investigations using new techniques such as single molecule approaches. Linking this knowledge to the atomic structure of the nucleoprotein filament systems and the succession of unstable, transient intermediate steps that takes place during the HR process remains a challenge; modeling retains a very strong role in bridging the gap between structures that are stable enough to be observed and in exploring transition paths between these structures. However, working on ever-changing long filament systems submitted to kinetic processes is full of pitfalls. This review presents the modeling tools that are used in such studies, their possibilities and limitations, and reviews the advances in the knowledge of the HR process that have been obtained through modeling. Notably, we will emphasize how cooperative behavior in the HR nucleoprotein filament enables modeling to produce reliable information.

Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson–Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.

Construction and evaluation of a kinetic scheme for RecA-mediated DNA strand exchange

The Escherichia coli RecA protein is the prototype of a class of proteins playing a central role in genomic repair and recombination in all organisms. The unresolved mechanistic strategy by which RecA aligns a single strand of DNA with a duplex DNA and mediates a DNA strand switch is central to understanding its recombinational activities. Toward a molecular-level understanding of RecA-mediated DNA strand exchange, we explored its mechanism using oligonucleotide substrates and the intrinsic fluorescence of 6-methylisoxanthopterin (6MI). Steady- and presteady-state spectrofluorometric data demonstrate that the reaction proceeds via a sequential four-step mechanism comprising a rapid, bimolecular association step followed by three slower unimolecular steps. Previous authors have proposed multistep mechanisms involving two or three steps. Careful analysis of the differences among the experimental systems revealed a previously undiscovered intermediate (N1) whose formation may be crucial in the kinetic discrimination of homologous and heterologous sequences. This observation has important implications for probing the fastest events in DNA strand exchange using 6MI to further elucidate the molecular mechanisms of recombination and recombinational repair.

Model of RecA-mediated homologous recognition

We consider theoretically the homology search between a long double-stranded DNA and a RecA-single-stranded DNA nucleofilament, emphasizing the polymeric nature of the search and the ability of double-stranded DNA to overcome the difference in pitch between itself and the nucleofilament by thermally activated stretching from the canonical B state to the metastable, stretched S state. Our analytical first-passage-time analysis agrees well with experimental data, predicts new dependencies on the intracellular fluid viscosity and ionic strength, and strongly suggests that initial homologous recognition involves a three base-pair seed.

Specific defects in double-stranded DNA unwinding and homologous pairing of a mutant RecA protein

The DNA molecules bound to RecA filaments are extended 1.5-fold relative to B-form DNA. This extended DNA structure may be important in the recognition of homology between single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). In this study, we show that the K286N mutation specifically impaired the dsDNA unwinding and homologous pairing activities of RecA, without an apparent effect on dsDNA binding itself. In contrast, the R243Q mutation caused defective dsDNA unwinding, due to the defective dsDNA binding of the C-terminal domain of RecA. These results provide new evidence that dsDNA unwinding is essential to homology recognition between ssDNA and dsDNA during homologous pairing.

Binding, annealing and strand exchange between oligonucleotides in different sites of the RecA protein filament

The efficiency of single-stranded (ss) oligonucleotides binding at the secondary site of the RecA protein filament is demonstrated to depend on the strandedness of DNA bound at the primary site. When the primary site is occupied by a ss-oligonucleotide, the binding of another ss-oligonucleotide at the secondary site is characterized by higher affinity and a lower rate of dissociation than is the case when the primary site is occupied by a double-stranded oligonucleotide. In contrast to a DNA strand exchange reaction suppressed by a heterologous oligonucleotide bound at the secondary site of the RecA filament, the occupation of the secondary site by a heterologous oligonucleotide does not prevent renaturation between the oligonucleotides bound at the primary site and complementary oligonucleotides from solution demonstrating that the binding of a DNA strand in the secondary site is not a necessary intermediate step in RecA-promoted DNA renaturation.

Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda

Although homologous recombination and DNA repair phenomena in bacteria were initially extensively studied without regard to any relationship between the two, it is now appreciated that DNA repair and homologous recombination are related through DNA replication. In Escherichia coli, two-strand DNA damage, generated mostly during replication on a template DNA containing one-strand damage, is repaired by recombination with a homologous intact duplex, usually the sister chromosome. The two major types of two-strand DNA lesions are channeled into two distinct pathways of recombinational repair: daughter-strand gaps are closed by the RecF pathway, while disintegrated replication forks are reestablished by the RecBCD pathway. The phage lambda recombination system is simpler in that its major reaction is to link two double-stranded DNA ends by using overlapping homologous sequences. The remarkable progress in understanding the mechanisms of recombinational repair in E. coli over the last decade is due to the in vitro characterization of the activities of individual recombination proteins. Putting our knowledge about recombinational repair in the broader context of DNA replication will guide future experimentation.

A molecular model for RecA-promoted strand exchange via parallel triple-stranded helices

A number of studies have concluded that strand exchange between a RecA-complexed DNA single strand and a homologous DNA duplex occurs via a single-strand invasion of the minor groove of the duplex. Using molecular modeling, we have previously demonstrated the possibility of forming a parallel triple helix in which the single strand interacts with the intact duplex in the minor groove, via novel base interactions (Bertucat et al., J. Biomol. Struct. Dynam. 16:535-546). This triplex is stabilized by the stretching and unwinding imposed by RecA. In the present study, we show that the bases within this triplex are appropriately placed to undergo strand exchange. Strand exchange is found to be exothermic and to result in a triple helix in which the new single strand occupies the major groove. This structure, which can be equated to so-called R-form DNA, can be further stabilized by compression and rewinding. We are consequently able to propose a detailed, atomic-scale model of RecA-promoted strand exchange. This model, which is supported by a variety of experimental data, suggests that the role of RecA is principally to prepare the single strand for its future interactions, to guide a minor groove attack on duplex DNA, and to stabilize the resulting, stretched triplex, which intrinsically favors strand exchange. We also discuss how this mechanism can incorporate homologous recognition.

The mutant RecA proteins, RecAR243Q and RecAK245N, exhibit defective DNA binding in homologous pairing

In homologous pairing, the RecA protein sequentially binds to single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), aligning the two DNA molecules within the helical nucleoprotein filament. To identify the DNA binding region, which stretches from the outside to the inside of the filament, we constructed two mutant RecA proteins, RecAR243Q and RecAK245N, with the amino acid substitutions of Arg243 to Gln and Lys245 to Asn, respectively. These amino acids are exposed to the solvent in the crystal structure of the RecA protein and are located in the central domain, which is believed to be the catalytic center of the homologous pairing activity. The mutations of Arg243 to Gln (RecAR243Q) and Lys245 to Asn (RecAK245N) impair the repair of UV-damaged DNA in vivo and cause defective homologous pairing of ssDNA and dsDNA in vitro. Although RecAR243Q is only slightly defective and RecAK245N is completely proficient in ssDNA binding to form the presynaptic filament, both mutant RecA proteins are defective in the formation of the three-component complex including ssDNA, dsDNA, and RecA protein. The ability to form dsDNA from complementary single strands is also defective in both RecAR243Q and RecAK245N. These results suggest that the region including Arg243 and Lys245 may be involved in the path of secondary DNA binding to the presynaptic filament.

No sliding during homology search by RecA protein

The RecA protein of Escherichia coli is a prototype of the RecA/Rad51 family of proteins that exist in virtually all the organisms. In a process called DNA synapsis, RecA first polymerizes onto a single-stranded DNA (ssDNA) molecule; the resulting RecA-ssDNA complex then searches for and binds to a double-stranded DNA (dsDNA) molecule containing the almost identical, or "homologous, " sequence. The RecA-ssDNA complex thus can be envisioned as a sequence-specific binding entity. How does the complex search for its target buried within nonspecific sequences? One possible mechanism is the sliding mechanism, in which the complex first binds to a dsDNA molecule nonspecifically and then linearly diffuses, or slides, along the dsDNA. To understand the mechanism of homology search by RecA, this sliding model was tested. A plasmid containing four homologous targets in tandem was constructed and used as the dsDNA substrate in the synapsis reaction. If the sliding is the predominant search mode, the two outermost targets should act as more efficient targets than the inner targets. No such positional preference was observed, indicating that a long range sliding of the RecA-ssDNA complex does not occur. These and other available data can be adequately explained by a simple three-dimensional random collision mechanism.

DNA strand exchange mediated by the Escherichia coli RecA protein initiates in the minor groove of double-stranded DNA

The Escherichia coli RecA protein can recognize sequence homology between a single-stranded DNA (ssDNA) and homologous double-stranded DNA (dsDNA). One model for the homology recognition invokes a DNA triplex intermediate in which specific hydrogen bonds connect the ssDNA with groups in the major groove of dsDNA. Using photo-cross-linking methods, we have analyzed the arrangement of DNA strands after the local strand exchange. The results showed that the displaced strand sits in the major groove of the hybrid duplex product. This arrangement indicates that the ssDNA invades the minor groove of dsDNA and hence argues against the involvement of triplex intermediates. The results support an alternative model for the homology recognition that invokes melting of the dsDNA and annealing of the one strand to the invading ssDNA.

Effects of minor and major groove-binding drugs and intercalators on the DNA association of minor groove-binding proteins RecA and deoxyribonuclease I detected by flow linear dichroism

Linear and circular dichroic spectroscopies have been employed to investigate the effects of small DNA ligands on the interactions of two proteins which bind to the minor groove of DNA, viz. RecA protein from Escherichia coli and deoxyribonuclease I (bovine pancreas). Ligands representing three specific non-covalent binding modes were investigated: 4',6-diamidino-2-phenylindole and distamycin A (minor groove binders), methyl green (major groove binder), and methylene blue, ethidium bromide and ethidium dimer (intercalators). Linear dichroism was demonstrated to be an excellent detector, in real time, of DNA double-strand cleavage by deoxyribonuclease I. Ligands bound in all three modes interfered with the deoxyribonuclease I digestion of dsDNA, although the level of interference varied in a manner which could be related to the ligand binding site, the ligand charge appearing to be less important. In particular, the retardation of deoxyribonuclease I cleavage by the major groove binder methyl green demonstrates that accessibility to the minor groove can be affected by occupancy of the opposite groove. Binding of all three types of ligand also had marked effects on the interaction of RecA with dsDNA in the presence of non-hydrolyzable cofactor adenosine 5'-O-3-thiotriphosphate, decreasing the association rate to varying extents but with the strongest effects from ligands having some minor groove occupancy. Finally, each ligand was displaced from its DNA binding site upon completion of RecA association, again demonstrating that modification of either groove can affect the properties and behaviour of the other. The conclusions are discussed against the background of previous work on the use of small DNA ligands to probe DNA-protein interactions.

Second-site RecA-DNA interactions: lack of identical recognition

The RecA protein plays crucial roles in recombination and repair. In vitro, it polymerizes on single-stranded DNA and promotes homologous recognition of duplex DNA and subsequent strand exchange. How the RecA filament recognizes homologous duplex DNA is not yet clear. Recent research has indicated the possibility of recognition between identical DNA strands in the RecA filament which may be involved in a triple-stranded structure prior to strand exchange. Here we address this type of recognition by the RecA filament with a variety of physical techniques. By a gel retardation assay, we find interaction of identical DNAs in RecA filaments to be strongly dependent on the DNA length. Fluorescence measurements (emission quenching and resonance energy transfer) show that two identical DNA strands do not make tight contacts in the RecA complex and are similar in magnitude to heterologous interactions. This conclusion is supported by caloriometric measurements, which show a large exothermic enthalpy change upon the recognition of complementary strands by the RecA filament, but not for binding of identical strands. Spectroscopic techniques, linear and circular dichroism, indicate that the complexes between RecA and pairs of either identical or complementary DNA strands still have rather similar overall structures. The present study thus reveals no significant interactions between identical single strands of DNA in the RecA filament in vitro.

Locations of functional domains in the RecA protein. Overlap of domains and regulation of activities

We review the locations of various functional domains of the RecA protein of Escherichia coli, including how they have been assigned, and discuss the potential regulatory roles of spatial overlap between different domains. RecA is a multifunctional and ubiquitous protein involved both in general genetic recombination and in DNA repair: it regulates the synthesis and activity of DNA repair enzymes (SOS induction) and catalyses homologous recombination and mutagenesis. For these activities RecA interacts with a nucleotide cofactor, single-stranded and double-stranded DNAs, the LexA repressor, UmuD protein, the UmuD'2C complex as well as with RecA itself in forming the catalytically active nucleofilament. Attempts to locate the respective interaction sites have been advanced in order to understand the various functions of RecA. An intriguing question is how these numerous functional sites are contained within this rather small protein (38 kDa). To assess more clearly the roles of the respective sites and to what extent the sites may be interacting with each other, we review and compare the results obtained from various biological, biochemical and physico-chemical approaches. From a three-dimensional model it is concluded that all sites are concentrated to one part of the protein. As a consequence there are significant overlaps between the sites and it is speculated that corresponding interactions may play important roles in regulating RecA activities.

Differential proximity probing of two DNA binding sites in the Escherichia coli recA protein using photo-cross-linking methods

The DNA strand-exchange reaction catalyzed by the Escherichia coli RecA protein occurs between the two DNA binding sites that are functionally distinct. Site I is the site to which a DNA molecule (normally single-stranded DNA) binds first; this first binding makes site II available for additional DNA-binding (normally double- stranded DNA). Photo-cross linking was employed to identify the amino acid residues located close to the bound DNA molecule(s). A ssDNA oligo containing multiple 5-iodouracil residues (IdU) was cross-linked to RecA by irradiation with a XeC1 pulse laser (308 nm), and the cross-linked peptides were purified and sequenced. To differentiate the two DNA binding sites, we used two protocols for making RecA-ssDNA complexes: (1) IdU-containing oligo was mixed with a stoichiometric excess of RecA, a condition which favors the binding of the oligo to site I, and (2) RecA was first allowed to bind to a nonphotoreactive oligo and then chased with the IdU-containing oligo, a condition which favors the binding of the IdU-oligo to site II. We observed that when RecA was in excess (site I probing), cross-linking occurred to Met-164 which is located in the disordered loop 1 of the RecA crystal structure [Story, R.M., Weber, I.T., & Steitz, T.A. (1992) Nature 355, 318-325]. When site II was probed, the majority of cross-linking occurred to Met-202 or Phe-203, located in loop 2. These results support the idea that, as predicted by Story and co-workers (1992), the disordered loops are involved in DNA binding. The results also suggest that the two sites are not only functionally but also physically distinct.

The central aromatic residue in loop L2 of RecA interacts with DNA. Quenching of the fluorescence of a tryptophan reporter inserted in L2 upon binding to DNA

To determine the role of the central aromatic residue in one of the DNA binding domains in Escherichia coli RecA protein, we have constructed a protein in which a tryptophan fluorescence reporter is inserted in the place of phenylalanine residue 203 in loop L2, a putative DNA binding site, and measured its fluorescence. The modified protein is active both in vivo and in vitro. The binding of nucleotide cofactor (ATP or its analog adenosine 5'-O-3-thiotriphosphate) does not modify the fluorescence. By contrast, the binding of DNA, both in the absence and presence of cofactor, strongly decreases the fluorescence in intensity (40-65%) and shifts the emission peak from 344 to 337 nm. The change occurs both with single- and double-stranded DNA and also upon the binding of a second single-stranded DNA. The results indicate that the residue 203 is in fact close to the first and second DNA binding sites. However, the quenching is not total and depends only slightly on the nature of DNA bases, thus suggesting an indirect interaction with DNA bases.

DNA-binding surface of RecA protein photochemical cross-linking of the first DNA binding site on RecA filament

The first DNA-binding site (site I) of RecA protein on the filament has been mapped. RecA protein was covalently cross-linked with a 55-base synthetic single-stranded DNA which was a good substrate for the RecA-mediated strand exchange reaction. The cross-linking sites of protein were determined in the regions spanning RecA residues 64-68, 89-106, 178-183, 199-216 and 257-280. The cross-linking in the residues 64-68, 89-106, 199-216 and 257-280 would be due to the cross-linking of Tyr65, Tyr103, disordered loop 2, and Tyr264, respectively. These regions form a DNA-binding surface centered around the beta-sheet spanning residues 243-257. In the P6(1) crystal filament, the DNA-binding surface is near the RecA-RecA interface but are not in the filament axis. The data implicate a mechanism whereby the DNA binding surface would be led into the filament axis by a conformational change from inactive filament as the P6(1) structure to active filament as the RecA-DNA-ATP complex.

Binding of RecA to anti-parallel poly(dA).2poly(dT) triple helix DNA

Binding of RecA protein to conventional anti-parallel poly(dA).2poly(dT) triplex DNA has been studied using flow linear dichroism spectroscopy. The association requires the presence of cofactor analog adenosine 5'-O-3-thiotriphosphate (ATP gamma S) and occurs with a rate similar to that for the association of RecA to double-stranded poly(dA).poly(dT) DNA. The binding of RecA to DNA stiffens the nucleotide chain, as evidenced from high orientation already at low shear rates, and the complex with triplex DNA appears to be at least as stiff as that with the duplex DNA. Therefore, the observation of a lower magnitude of the LD spectrum at 260 nm, in the triplex-RecA compared to the duplex-RecA complex, but retained magnitude of protein LD at 280 nm, indicates a markedly impaired orientation of nucleo-bases, possibly reflecting a perturbation by RecA on the third strand making its bases deviate strongly from perpendicularity. The circular dichroism spectrum, appearing immediately after dissociation of RecA by SDS, suggests an intact triplex structure, meaning that complexation with RecA has not dissociated the third strand. In conclusion, binding of RecA to triplex DNA does not modify the main organisation of the strands, but could affect the base-base interactions between them. Tilted bases could reflect a conformational change that RecA imposes also on the biological intermediate triplex structure to relax the base-base hydrogen bonding between the DNA strands.

Fluorescence-detected interactions of oligonucleotides in RecA complexes

A technique has been developed to probe directly RecA-DNA interactions by the use of the fluorescent chromophore, (+)anti-benzo(a)pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), covalently attached to DNA. The 24-mer oligonucleotide 5'-d(CTACTAAACATGTACAAATCATCC) was specifically modified on the exocyclic nitrogen of the central guanine, to yield a trans-adduct. Upon interaction of the modified oligonucleotide with RecA we find an increase in BPDE fluorescence and a rather high fluorescence anisotropy, suggesting a restricted motion of the BPDE-oligonucleotide in the protein filament. In the presence of the cofactor ATP gamma S, binding of two oligonucleotides, identical or complementary in sequence, in the RecA filament is possible. The RecA-DNA complex is, however, more stable when the sequences are complementary; in addition, a shift in the BPDE emission peaks is observed. In the presence of ATP (and an ATP regeneration system), the RecA-DNA interaction between two complementary oligonucleotides is changes, and we now find protein-mediated renaturation to occur.

Occurrence of three-stranded DNA within a RecA protein filament

A RecA protein-generated triple-stranded DNA species can be observed by electron microscopy, within narrowly defined conditions. Three-stranded DNA is detected only when initiation of normal DNA strand exchange is precluded by heterologous sequences within the duplex DNA substrate, when ATP is hydrolyzed, and when the DNA is cross-linked with a psoralen derivative prior to removal of RecA filaments. When adenosine 5'-O-(thiotriphosphate) is used, only the product hybrid duplex DNA can be cross-linked within the RecA filament. The third strand is either displaced or interwound in a conformation that does not permit cross-linking. When ATP is hydrolyzed by RecA, all three strands are cross-linked within the filament in a complex pattern that suggests a dynamic structure. This structure is altered when RecA protein is removed before cross-linking. Hsieh et al. (1990) and Rao et al. (1991, 1993) have proposed, on the basis of nuclease protection and chemical modification studies, that a stable triple-stranded DNA species can persist after removal of RecA protein. We have been unable to visualize these triple-stranded structures by the methods used in the present investigation. When RecA removal was followed immediately by interstrand cross-linking, only the two strands of the hybrid duplex DNA were cross-linked.

Analysis of the DNA binding site of Escherichia coli RecA protein

To investigate the DNA binding site of RecA protein, we constructed 15 recA mutants having alterations in the regions homologous to the other ssDNA binding proteins. The in vivo analyses showed that the mutational change at Arg243, Lys248, Tyr264, or simultaneously at Lys6 and Lys19, or Lys6 and Lys23 caused severe defects in the recA functions, while other mutational changes did not. Purified RecA-K6A-K23A (Lys6 and Lys23 changed to Ala and Ala, respectively) protein was indistinguishable from the wild-type RecA protein in its binding to DNA. However, the RecA-R243A (Arg243 changed to Ala) and RecA-Y264A (Tyr264 changed to Ala) proteins were defective in binding to both ss- and ds-DNA. In self-oligomerization property, RecA-R243A was proficient but RecA-Y264A was deficient, suggesting that the RecA-R243A protein had a defect in DNA binding site and the RecA-Y264A protein was defective in its interaction with the adjacent RecA molecule. The region of residues 243-257 including the Arg243 is highly homologous to the DNA binding motif in the ssDNA binding proteins, while the eukaryotic RecA homologues have a similar structure at the amino-terminal side proximal to the nucleotide binding core. The region of residues 243-257 would be a part of the DNA binding site. The other parts of this site would be the Tyr103 and the region of residues 178-183, which were cross-linked to ssDNA. These three regions lie in a line in the crystal structure.

Properties of RecA-oligonucleotide complexes

The interaction of RecA protein with short single-stranded oligonucleotides is characterised by flow linear dichroism (LD), isoelectric focusing (IEF) and electron microscopy (EM). From LD and EM it is evident that RecA forms long filaments with at least some 50 oligonucleotides in a 'train formation'. The tendency to form trains is substantially lower when an amino group is attached to the 5' end of the oligonucleotide, suggesting that the modification impairs protein-protein interactions at the interface between two oligomers. From LD it is also evident that no bridging occurs between RecA-oligonucleotide complexes containing more than one oligomer strand per RecA filament. This property make them manageable in polyacrylamide gels, hence allowing characterisation by IEF. RecA was found acidic with a pI of 5.0. The pI was not dependent on the presence of bound cofactor (ATP gamma S) and oligonucleotides suggesting that protonation of the protein readily occurs to compensate for the negative charges provided by bound cofactor and DNA.

Spectroscopic observation of renaturation between polynucleotides with RecA in the presence of ATP hydrolysis

To obtain mechanistic insights about RecA-promoted base pairing between complementary polynucleotides, the complex formation of RecA with poly(dA) and poly(dT) in the presence of ATP (and ATP-regenerating system) has been studied. The reaction was followed using a fluorescent probe, benzopyrenediolepoxide (BPDE), covalently attached to less than 1% of the adenine bases of poly(dA). BPDE is sensitive to its environment and has been found useful for detection of interactions between DNA strands, in the three binding positions of the RecA filament, in the presence of adenosine 5'-O-3-thiotriphosphate (ATP[S]) [Wittung, P., Nordén, B. & Takahashi, M. (1994) J. Biol. Chem. 269, 5799-5803]. The emission spectrum of RecA:BPDE-poly(dA) formed in the presence of ATP is similar to that observed with ATP[S] supporting similar structures of the complexes. However, the fluorescence anisotropy is considerably reduced, suggesting a higher degree of freedom of DNA in the presence of ATP hydrolysis. Upon addition of a complementary strand, poly(dT), to a preformed filament of RecA:BPDE-poly(dA) in the presence of ATP, the fluorescence intensity slowly decreases and a change of emission profile consistent with Watson-Crick base pairing is observed. This contrasts with the case of ATP[S] in which normal base pairing is never observed. Hence, ATP hydrolysis appears necessary for the RecA filament to be able to promote true renaturation. The renaturation reaction is found more effective when one of the complementary DNA strands is bound in the primary RecA DNA-binding position and the other is added as the third strand, but the reaction can also occur between DNA strands in any combination of binding positions in the RecA filament. This observation suggests the importance of the third DNA-binding position of the RecA filament. Renaturation between DNA strands in the other two combinations of binding positions is speculated to have a role in aborting the strand-exchange reaction when the strands are insufficiently complementary.

Linear-dichroism spectroscopy for the study of structural properties of proteins

This review gives an experiment directed survey of the application of linear-dichroism (LD) spectroscopy to the study of proteins. LD spectroscopy is a relatively simple technique that provides information on the orientation of chromophores in molecules, on molecular characteristics such as shape, size and electronic properties, and on binding parameters in molecular complexes. Since LD is only observed when the molecules are non-randomly oriented in the sample, particular attention is paid to various orientation techniques, viz. in electric and flow fields, in polymer films and gels, and by light induction (photoselection). Examples are given on bacteriorhodopsin and retinals, chlorosomes, lens crystallins, aspartate aminotransferase, and the interaction of gene32- and recA-protein with DNA.

Structure of UvrABC excinuclease-UV-damaged DNA complexes studied by flow linear dichroism. DNA curved by UvrB and UvrC

The interaction between UvrABC excinuclease from Escherichia coli and ultraviolet light-(UV) damaged DNA was studied by flow linear dichroism. The dichroism signal from DNA was drastically decreased in intensity upon incubation with UvrA and UvrB or whole enzyme in the presence of effector ATP. The change was specific for UV-damaged DNA, and a concluded suppressed DNA orientation suggests the wrapping of DNA around the protein. The incubation with the UvrC subunit alone also somewhat reduces the signal, however, in this case the change was smaller and not specific for UV-damaged DNA. The structural modification of DNA, promoted by the (UvrA2-UvrB) complex, probably facilitates or stabilizes the interaction of the UvrC subunit with DNA for the excision.

Coordination and internal exchange of two DNA molecules in a RecA filament in the presence of hydrolysing ATP. Information on ATP-RecA-DNA structure from linear dichroism spectroscopy

Solution structure of complexes between DNA and recombinase RecA from Escherchia coli, in the presence of the physiological cofactor ATP, is probed by flow linear dichroism (LD) spectroscopy. A problem of ADP accumulation which promotes dissociation of DNA-RecA is circumvented by using an ATP-regenerating system. The LD features indicate that the local structure of the complex is very similar to that found in the presence of the non-hydrolysable analog of ATP, adenosine-5'-O-[gamma-thio]triphosphate (ATP[gamma S]); the DNA bases are oriented with their planes preferentially perpendicular to the long axis of the filament, while the indole chromophores of the two tryptophan residues of RecA are rather parallel to this reference direction. A much smaller overall amplitude of the LD spectrum, compared to ATP[gamma S], is interpreted as a result of fast dissociation of RecA due to hydrolysis of ATP, producing transiently naked DNA regions which act like flexible joints, diminishing the macroscopic orientation of the RecA filaments. However, the ATP hydrolysis is not found to prevent simultaneous accommodation of two non-complementary DNA molecules in the RecA complex, as judged from the LD behaviour upon successive addition of two different polynucleotides or modified DNA strands. A notable difference from corresponding complexes formed with ATP[gamma S] is that, in the presence of ATP hydrolysis, the order in which the two DNA molecules have been added is insignificant as judged from virtually identical resulting structures; this observation indicates that exchange of DNA occurs between the two DNA accommodation sites within the RecA filament.

Stable synapsis of homologous DNA molecules mediated by the Escherichia coli RecA protein involves local exchange of DNA strands

Escherichia coli RecA protein promotes stable synapsis between a single-stranded DNA and a homologous duplex DNA, resulting in the formation of a complex of RecA with three DNA strands. To gain insight into the molecular interactions responsible for DNA synapsis, the base-pairing status within the synaptic complex was analyzed by using dimethylsulfate and potassium permanganate as probes. The results indicate that the original base pairs in the parental duplex are disrupted; one strand is displaced and the other strand appears to be involved in Watson-Crick base-pairing with the incoming single-stranded DNA. The state of base-pairing thus resembles that of the end products of strand exchange and not a canonical DNA triple helix involving non-Watson-Crick base-pairing. The results also indicate that this local strand exchange can occur without homology at the ends of the DNA substrates (i.e., when axial rotation of the product heteroduplex with respect to the axis of the parental duplex is obstructed). Taken together, these results suggest that exchange of DNA strands mediated by RecA occur at or before the stage of stable DNA synapsis by a process that does not require DNA rotation.

Structure of RecA-DNA complexes studied by combination of linear dichroism and small-angle neutron scattering measurements on flow-oriented samples

By combining anisotropy of small-angle neutron scattering (SANS) and optical anisotropy (linear dichroism, l.d.) on flow-oriented RecA-DNA complexes, the average DNA-base orientation has been determined in RecA complexes with double-stranded (ds) as well as single-stranded (ss) DNA. From the anisotropy of the two-dimensional SANS intensity representation, the second moment orientation function S is obtained. Knowledge of S is crucial for the interpretation of l.d. spectra in terms of orientation of the DNA bases and the aromatic amino acid residues. The DNA-base planes are essentially perpendicular to the fibre axis of the complex between RecA and dsDNA in the presence of cofactor ATP gamma S. A somewhat tilted base geometry is found for the RecA-ATP gamma S complexes with single-stranded poly(dT) and poly(d epsilon A). This behaviour contrasts the RecA-ssDNA complex formed without cofactor which displays a poor orientation of the bases. Well-ordered bases in the ssDNA-RecA complex is possibly reflecting the role of RecA in preparing a nucleotide strand for base-pairing in the search-for-homology process. While the central SANS intensity is essentially independent of the pitch of the helical complex, a secondary intensity maximum, which becomes focused upon flow orientation, is found to be a sensitive measure of the pitch. The pitch values for the complexes compare well with cryo-electron microscopy results but are slightly larger than those seen for uranyl-stained samples.

Linear dichroism spectroscopy of nucleic acids

This review will consider solution studies of structure and interactions of DNA and DNA complexes using linear dichroism spectroscopy, with emphasis on the technique of orientation by flow. The theoretical and experimental background to be given may serve, in addition, as a general introduction into the state of the art of linear dichroism spectroscopy, particularly as it is applied to biophysical problems.

Properties of RecA441 protein reveal a possible role for RecF and SSB proteins in Escherichia coli

We examined the possibility that the recA441 mutation, which partially suppresses the UV sensitivity of uvr recF mutant bacteria, exerts its effect by coding for an altered RecA protein that competes more efficiently than the RecA+ protein with SSB for ssDNA in vivo. Using an assay measuring recombination between UV-damaged lambda DNA and intact homologous DNA, we found that the introduction of the recA441 mutation partially suppressed the defects in recombination in bacteria lacking RecF activity but not in bacteria with excess SSB, although recombination was affected more in recF mutants than in bacteria overproducing SSB. These results therefore do not support the hypothesis that RecA441 protein, or RecA protein with the help of RecF protein, is required during recombination of UV-damaged DNA to compete with SSB for ssDNA.

Co-ordination of multiple DNA molecules in RecA fiber evidenced by linear dichroism spectroscopy

Polarized light spectroscopy has been used to study the interaction of RecA protein with DNA. Several different DNA complexes have been identified and characterized with respect to stoichiometries, base orientation and nuclease accessibility. By using spectroscopically distinguishable DNAs, we determined the number of DNA molecules co-ordinated by the RecA fiber in each of these complexes, and established their base pairing abilities. Based on these observations, we discuss the molecular mechanism of the RecA-mediated strand exchange reaction.

Head to head dimer model; an alternative model for the strand exchange reaction by RecA protein of Escherichia coli

The RecA protein of E coli promotes a strand exchange reaction in vitro which appears to be similar to homologous genetic recombination in vivo. A model for the mechanism of strand transfer reaction by RecA protein has been proposed by Howard-Flanders et al based on the assumption that the RecA monomer has two distinctive DNA binding sites both of which can bind to ssDNA as well as dsDNA. Here, I propose an alternative model based on the assumption that RecA monomer has a single domain for binding to a polynucleotide chain with a unique polarity. In addition, the model is based on a few mechanical assumptions that, in the presence of ATP, two RecA molecules form a head to head dimer as the basic binding unit to DNA, and that the binding of RecA protein to a polynucleotide chain induces a structural change of RecA protein that causes a higher state of affinity for another RecA molecule that is expressed as cooperativy. The model explains many of the biochemical capabilities of RecA protein including the polar polymerization of RecA protein on single stranded DNA and polar strand transfer of DNA by the protein as well as the formation of a joint DNA molecule in a paranemic configuration. The model also presents the energetics in the strand transfer reaction.