Calorimetric Analysis of Binding of two Consecutive DNA Strands to RecA Protein Illuminates Mechanism for Recognition Of Homology

Takahashi, Masayuki; Maraboeuf, Fabrice; Morimatsu, Katsumi; Selmane, Tassadite; Fleury, Fabrice; Nordén, Bengt

doi:10.1016/j.jmb.2006.10.042

Cited by 4 publications

(4 citation statements)

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“…Meanwhile, intercalators, being inserted into DNA duplexes, may significantly disturb and destabilize DNA structure in their neigborhood, thus facilitating PNA invasion. Most probably, the idea of duplex room-temperature metastability (in the form of length-dependent crossover between the first-and second-order phase transitions discussed above) can also be relevant to DNA strand-exchange reactions catalyzed by RecA/Rad51 type of enzymes (there is strong and specific protein-DNA coupling that significantly restructures one of the DNA strands, thus speeding up the search for the corresponding complementary strand to form the proper DNA duplex 57,58 ). Interestingly, this same concept ought to be crucial for understanding the modalities of self-assembly in DNA nanostructures addressable in terms of their DNA-base code (see, e.g., refs 59 and 60 and references therein) as well.…”

Section: Discussion: Thermodynamics Of Dna Hybridization From the Sta...mentioning

confidence: 99%

Physical Rationale Behind the Nonlinear Enthalpy−Entropy Compensation in DNA Duplex Stability

Starikov

Nordén

2009

J. Phys. Chem. B

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The physical-chemical sense of nonlinear entropy-enthalpy compensation based upon the standard thermodynamical parameters of high-temperature melting for doublet units in DNA duplexes has been considered. We are able to show that there are three, with no other constraints equally plausible, principal levels of DNA melting/hybridization description. First, DNA structure assembly/disassembly can be seen from the viewpoint of the conventional equilibrium thermodynamics without taking special care of the heat capacity DeltaC(p) value (by simply setting it equal to zero). Second, it is possible to assume that the DeltaC(p) is finite, but independent of temperature. At this approximation level the high-temperature DNA melting cannot be described, but only some special transition between metastable states of DNA duplexes in water solutions in the vicinity of ice melting point. Third, both the latter transition and the high-temperature DNA melting can be reproduced by one and the same approach, if the DeltaC(p) is assumed to be temperature dependent. These three approximation levels are equally justified from the nonlinear entropy-enthalpy compensation standpoint and by a generalized theory of temperature effects on themodynamical stability as is outlined here. Applicability of each of the approximation levels involved is discussed.

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Section: Discussion: Thermodynamics Of Dna Hybridization From the Sta...mentioning

confidence: 99%

Physical Rationale Behind the Nonlinear Enthalpy−Entropy Compensation in DNA Duplex Stability

Starikov

Nordén

2009

J. Phys. Chem. B

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“…Cite this article as Cold Spring Harb Perspect Biol 2015;7:a016444 the idea that the filament senses both WatsonCrick base pairing and DNA conformation in the recognition process, a mechanism referred to as "conformational proofreading" (Lee et al 2006;Takahashi et al 2007; see comments in Rambo et al 2010;Savir and Tlusty 2010;Ragunathan et al 2011). The atomic structure of the RecA-ssDNA filament, in its active, ATP-bound form, reveals that the ssDNA exists in a deformed conformation, with the sugar-phosphate backbone extended between trinucleotide units, which are held in a B-like conformation (Chen et al 2008; see comments by Kowalczykowski 2008).…”

Section: Dna Pairing and Annealingmentioning

confidence: 99%

DNA-Pairing and Annealing Processes in Homologous Recombination and Homology-Directed Repair

Morrical

2015

Cold Spring Harb Perspect Biol

113

127

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The formation of heteroduplex DNA is a central step in the exchange of DNA sequences via homologous recombination, and in the accurate repair of broken chromosomes via homology-directed repair pathways. In cells, heteroduplex DNA largely arises through the activities of recombination proteins that promote DNA-pairing and annealing reactions. Classes of proteins involved in pairing and annealing include RecA-family DNA-pairing proteins, single-stranded DNA (ssDNA)-binding proteins, recombination mediator proteins, annealing proteins, and nucleases. This review explores the properties of these pairing and annealing proteins, and highlights their roles in complex recombination processes including the double Holliday junction (DhJ) formation, synthesis-dependent strand annealing, and singlestrand annealing pathways-DNA transactions that are critical both for genome stability in individual organisms and for the evolution of species.

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“…Among various protein–DNA interactions, the interaction between DNA repair proteins such as RecA family proteins and single-stranded DNA (ssDNA) has received much attention in the biological and biomedical fields. The RecA family of proteins such as Rad51 and RecA catalyze a DNA strand exchange reaction between ssDNA and homologous double-stranded DNA (dsDNA), the so-called homologous recombination (HR). − The primary function of HR is to maintain genome stability during vegetative growth of prokaryotic cells or mitosis of eukaryotic cells. In this HR reaction, RecA protein (or Rad51) binds to ssDNA in an ATP-dependent manner and then forms a helical nucleofilament. − In this regard, the interaction between RecA protein and ssDNA/dsDNA has been extensively investigated in bulk phase ,, and at the single-molecule level. ,− …”

Section: Introductionmentioning

confidence: 99%

“…In this HR reaction, RecA protein (or Rad51) binds to ssDNA in an ATP-dependent manner and then forms a helical nucleofilament. 5−7 In this regard, the interaction between RecA protein and ssDNA/dsDNA has been extensively investigated in bulk phase 4,8,9 and at the single-molecule level. 3,10−13 However, most studies on RecA-DNA interaction have been performed on ssDNA, which can form a B-DNA duplex with Watson−Crick base pairing.…”

Section: Introductionmentioning

confidence: 99%

Interaction of G-Quadruplex with RecA Protein Studied in Bulk Phase and at the Single-Molecule Level

et al. 2013

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As in the human genome there are numerous repeat DNA sequences to adopt into non-B DNA structures such as hairpin, triplex, Z-DNA, G-quadruplex, and so on, an understanding of the interaction between DNA repair proteins and a non-B DNA forming sequence is very important. In this regard, the interaction between RecA protein and human telomeric 5'-TAGGG-(TTAGGG)3-TT-3' sequence and the G-quadruplex formed from this sequence has been investigated in bulk phase and at the single-molecule level. The RecA@ssDNA filament, which is formed by the interaction between RecA protein and a G-rich sequence, was dissociated by the addition of K(+) ions, and the dissociated G-rich sequence was quickly folded to a G-quadruplex structure, indicating that the G-quadruplex structure is more favorable than the RecA@ssDNA filament in the presence of K(+) ions. In addition, we demonstrate that the conformation of the G-quadruplex, which is heterogeneous in the absence of RecA, converged to the specific G-quadruplex with one double-chain-reversal loop upon association of RecA protein.

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Calorimetric Analysis of Binding of two Consecutive DNA Strands to RecA Protein Illuminates Mechanism for Recognition Of Homology

Cited by 4 publications

References 50 publications

Physical Rationale Behind the Nonlinear Enthalpy−Entropy Compensation in DNA Duplex Stability

Physical Rationale Behind the Nonlinear Enthalpy−Entropy Compensation in DNA Duplex Stability

DNA-Pairing and Annealing Processes in Homologous Recombination and Homology-Directed Repair

Interaction of G-Quadruplex with RecA Protein Studied in Bulk Phase and at the Single-Molecule Level

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