Complementary recognition in condensed DNA: Accelerated DNA renaturation

Sikorav, Jean‐Louis; Church, George M.

doi:10.1016/0022-2836(91)90595-w

Cited by 104 publications

(87 citation statements)

References 61 publications

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“…Presumably, such coaggregates, held together by transient protein-protein, protein-DNA, and DNA-DNA interactions, act to reduce the sampling volume. An increase in the effective DNA concentration has indeed been shown to accelerate DNA catenation (28) and renaturation processes (29).…”

Section: Discussionmentioning

confidence: 99%

Ordered intracellular RecA–DNA assemblies: A potential site of in vivo RecA-mediated activities

Levin-Zaidman

Frenkiel-Krispin

Shimoni

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

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The inducible SOS response increases the ability of bacteria to cope with DNA damage through various DNA repair processes in which the RecA protein plays a central role. Here we present the first study of the morphological aspects that accompany the SOS response in Escherichia coli. We find that induction of the SOS system in wild-type bacteria results in a fast and massive intracellular coaggregation of RecA and DNA into a lateral macroscopic assembly. The coaggregates comprise substantial portions of both the cellular RecA and the DNA complement. The structural features of the coaggregates and their relation to in vitro RecA-DNA networks, as well as morphological studies of strains carrying RecA mutants, are all consistent with the possibility that the intracellular assemblies represent a functional entity in which RecA-mediated DNA repair and protection activities occur.biocrystallization ͉ DNA repair ͉ homology search ͉ stress response R ecA-mediated DNA recombination and repair processes proceed through several sequential phases (1-3). A presynaptic filament in which RecA molecules coat a single-stranded DNA substrate is initially formed. The filament acts then as a sequence-specific DNA-binding entity, capable of searching and binding dsDNA sites that are homologous to the RecA-coated segment. Within the resulting joint species, DNA strand exchange and heteroduplex extension processes are promoted. The mechanism that enables a rapid search for DNA homology in vivo, within a highly crowded and complex genome, remains enigmatic.To reach its target, any sequence-specific DNA-binding protein must overcome two general obstacles: a minute cellular concentration of the target, and a vast excess of nontarget, yet still competitive, DNA sites. The search for a homologous DNA site conducted by the RecA-DNA presynaptic filament shares these hurdles, but is further encumbered by the uniquely adverse diffusion characteristics of its components. A DNA target corresponds to a segment that is part of, and embedded within, the chromosome. This, and the large structural asymmetry of DNA, conspire to minimize the diffusion constant of DNA sites (4, 5). In a homology search executed by the RecA-DNA filament, both the searching and the target entities are chromosomal DNA sites whose small diffusion constants drastically attenuate their encounter rate. How then does a RecA-mediated intracellular search evade the kinetic impediments that are intrinsic to the nature of its components?Here we show that damages inflicted on bacterial DNA lead to a rapid formation of an ordered intracellular assembly that accommodates both RecA and DNA. We suggest that the striated morphology of this RecA-DNA assembly is capable of promoting an in vivo homology search by attenuating both the sampling volume and the dimensionality of the process. Moreover, RecA was shown to protect chromosomal DNA from degradation (6) through unknown mechanisms. The tight crystalline packaging that is progressively assumed by the intracellular RecA-DNA assemblies as ...

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Section: Discussionmentioning

confidence: 99%

Ordered intracellular RecA–DNA assemblies: A potential site of in vivo RecA-mediated activities

Levin-Zaidman

Frenkiel-Krispin

Shimoni

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

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“…Krasnow and Cozzarelli [17] found virtually an absolute dependence of the rates of enzymatic DNA catenation on polyamine-induced DNA aggregation. In a comprehensive experimental and theoretical study of DNA condensation, Sikorav and Church [41] demonstrated 10-100-fold increases in reaction rates in DNA renaturation reactions under several condensing conditions, including condensation by crowding. Similarly large increases in cohesion rates between sticky-ended DNA fragments occur under condensing conditions [3].…”

Section: Reaction Rates Involving Dnamentioning

confidence: 99%

Macromolecular crowding and the mandatory condensation of DNA in bacteria

1996

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Cellular DNA in bacteria is localized into nucleoids enclosed by cytoplasm. The forces which cause condensation of the DNA into nucleoids are poorly understood. We suggest that direct and indirect macromolecular crowding forces from the surrounding cytoplasm are critical factors for nucleoid condensation, and that within a bacterial cell these crowding forces are always present at such high levels that the DNA is maintained in a condensed state. The DNA affected includes not only the preexisting genomic DNA but also DNA that is newly introduced by viral infection, replication or other means.Key words: Cytoplasmic macromolecule; DNA condensation; Escherichia coli; Macromolecular crowding; Mandatory condensation; Nucleoid DNA condensation in bacteria: general considerationsThe genomic DNA of bacteria is condensed into one or a few nucleoids per cell [1] that are in direct contact with a surrounding cytoplasm containing very high concentrations of macromolecules (e.g. ,~ 340 mg/ml of total RNA and protein [2]). The term 'condensation' is used to indicate adoption of a relatively concentrated, compact state occupying a fraction of the volume available. The DNA of the bacterial nucleoid is estimated to have a local concentration of ,'-50-100 mg DNA/ml (see footnote 6 of [3]) and to occupy 1/8 to 1/5 of the volume within the cell envelope [1].Condensation of DNA within bacterial ceils has been observed by light microscopy of both living and fixed cells, as well as by electron microscopy [4][5][6][7][8] (reviewed in [9,10]). Condensation of DNA in isolated nucleoids is indicated by microscopy as well as by hydrodynamic properties [11][12][13]. Condensation of DNA in model in vitro systems has been assayed by aggregation, as described below. Condensing forcesThe origins and magnitudes of the forces which cause DNA condensation are poorly understood. Supercoiling, macromolecular crowding and the binding of histone-like proteins and of polyamines have all been suggested to contribute to DNA condensation. It is unclear how important each of these fac-*Corresponding author: Fax: (1) (301) 496-0201.0014-5793196/$12.00 © 1996 Federation of European Biochemical Societies. PH SO0 1 4-5793(96)00725-9 tors is in causing DNA condensation in vivo. Model studies of the binding of histone-like proteins under dilute solution conditions indicate that the cellular amounts of DNA-binding proteins in bacteria are 5-10-fold lower than those required for condensation (see [14] for references and discussion). The polyamines putrescine and spermidine can occur in large amounts in E. coli [15]. Spermidine but not putrescine can condense DNA from aqueous solution [16], although the binding reaction is relatively salt-sensitive [17,18] and so may make a restricted contribution over much of the range of intracellular salt concentrations observed in growing cells [19,20]. Enzymatic supercoiling directly yields more compact forms [21].Macromolecular crowding ('crowding', reviewed in [22,23]) can cause DNA condensation by two distinctly dif...

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“…[31][32][33][34][35][36] DNA is also soluble in the presence of molecular solvents such as ethanol, dimethyl sulfoxide (DMSO), dimethylformamide (DMF) and acetonitrile (ACN), which can significantly accelerate DNA hybridization. [37][38][39][40] At the same time, these molecular solvents contain hydrophobic groups that can solvate the DNA bases and reduce DNA duplex stability. As a solvent, ILs are unique in many aspects.…”

Section: Introductionmentioning

confidence: 99%

Exploring the thermal stability of DNA-linked gold nanoparticles in ionic liquids and molecular solvents

2012

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While water is the most commonly used solvent for DNA, many co-solvents have been added for various applications. Ionic liquids (ILs) are molten salts at around room temperature. ILs have been tested as a green solvent for many reactions and many biopolymers can also be dissolved in ILs. In this work, we study DNAlinked gold nanoparticles (AuNPs) in seven types of ILs. DNA-functionalized AuNPs possess 10 a high density of negative charges and thus may generate new physical properties in ILs. We have identified the role of ILs to transit from salts to increase DNA duplex stability to solvents to decrease DNA melting temperature. The onset of this transition depends on the structure of ILs, where more hydrophobic cations destabilize DNA at lower IL concentrations. This trend is opposite to molecular solvents (e.g. ethanol, DMSO, ACN and DMF) that destabilize DNA at low solvent concentration. 15 Specific DNA base pairing is disrupted at high DMSO concentrations, and AuNPs are held together by non-specific interactions. The other tested molecular solvents are able to maintain DNA base pairs, although strong non-specific interactions are also present. Several ILs can release proton and thus drastically change pH, which also changes the melting temperature of DNA. This study also reveals the feasibility of using ILs as solvents for DNA-functionalized nanomaterials.

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Complementary recognition in condensed DNA: Accelerated DNA renaturation

Cited by 104 publications

References 61 publications

Ordered intracellular RecA–DNA assemblies: A potential site of in vivo RecA-mediated activities

Ordered intracellular RecA–DNA assemblies: A potential site of in vivo RecA-mediated activities

Macromolecular crowding and the mandatory condensation of DNA in bacteria

Exploring the thermal stability of DNA-linked gold nanoparticles in ionic liquids and molecular solvents

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