Interactions between DNA molecules bound to RecA filament. Effects of base complementarity.

Wittung, Pernilla; Nordén, Bengt; Kim, S. K.; Takahashi, Masayuki

doi:10.1016/s0021-9258(17)37532-4

Cited by 25 publications

(2 citation statements)

References 29 publications

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“…Interactions within the RecA Filament Studied by Fluorescence Spectroscopy. Fluorescence spectroscopy has been found useful for studying interactions between DNA strands in RecA filaments in situ, this is to say, without the need for deproteinization or electrophoretic separation (Wittung et al, 1994(Wittung et al, , 1995. The spectroscopic properties of a fluorescent probe attached to DNA report on the immediate environment of the probe and can thus provide information about interactions occurring in the RecA filament in real time.…”

Section: Resultsmentioning

confidence: 99%

Second-Site RecA−DNA Interactions: Lack of Identical Recognition

et al. 1996

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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.

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Section: Resultsmentioning

confidence: 99%

Second-Site RecA−DNA Interactions: Lack of Identical Recognition

et al. 1996

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“…Within this filament, ssDNA occupies the primary binding site of the recombinase. A secondary binding site accommodates double-stranded DNA (dsDNA) in such a way that its sequence can be rapidly scanned for homology by the resident single strand (3)(4)(5)(6)(7)(8). The recombinase energetically activates the dsDNA by extending its backbone 1.5-fold relative to B-form DNA (4,(9)(10)(11).…”

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confidence: 99%

The Synaptic Complex of RecA Protein Participates in Hybridization and Inverse Strand Exchange Reactions

Gamper

Nulf

Corey³

et al. 2003

Biochemistry

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RecA protein catalyzes strand exchange between homologous single-stranded and double-stranded DNAs. In the presence of ATPgammaS, the post-strand exchange synaptic complex is a stable end product that can be studied. Here we ask whether such complexes can hybridize to or exchange with DNA, 2'-OMe RNA, PNA, or LNA oligonucleotides. Using a gel mobility shift assay, we show that the displaced strand of a 45 bp synaptic complex can hybridize to complementary oligonucleotides with different backbones to form a four-stranded (double D-loop) joint that survives removal of the RecA protein. This hybridization reaction, which confirms the single-stranded character of the displaced strand in a synaptic complex, might initiate recombination-dependent DNA replication if it occurs in vivo. We also show that either strand of the heteroduplex in a 30 bp synaptic complex can be replaced with a homologous DNA oligonucleotide in a strand exchange reaction that is mediated by the RecA filament. Consistent with the important role that deoxyribose plays in strand exchange, oligonucleotides with non-DNA backbones did not participate in this reaction. The hybridization and strand exchange reactions reported here demonstrate that short synaptic complexes are dynamic structures even in the presence of ATPgammaS.

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Analysing DNA complexes by circular and linear dichroism

Nordén¹,

Kurucsev²

1994

J of Molecular Recognition

213

167

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The application of linear and circular dichroism (LD and CD) in nucleic acid research is illustrated by recent results aimed at answering specific structural problems in the interaction of DNA with molecules of biological importance. We first consider the circumstances under which ligands, such as DAPI (4',6-diamidino-2-phenylindole), change their preferred binding mode in the minor groove to major groove binding or intercalation. As an extension of this problem we refer to the switch between groove binding and intercalation of structurally similar ligands such as ellipticines and trigonal ruthenium complexes. We also explore the use of LD and CD in the determination of the structure of the complex formed between the polynucleotide poly(dA) and the novel 'peptide nucleic acid', consisting of nucleic acid bases joined by a polyamide homomorphous with the deoxyribose-phosphate backbone of DNA. Finally, the structure and interaction of the recombination enzyme RecA with DNA is discussed, in particular the influence of the presence of intercalators, groove binders or covalent DNA adducts.

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Interactions between DNA molecules bound to RecA filament. Effects of base complementarity.

Cited by 25 publications

References 29 publications

Second-Site RecA−DNA Interactions: Lack of Identical Recognition

Second-Site RecA−DNA Interactions: Lack of Identical Recognition

The Synaptic Complex of RecA Protein Participates in Hybridization and Inverse Strand Exchange Reactions

Analysing DNA complexes by circular and linear dichroism

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