dorsal/arxiv
View SchemaDNA Renaturation at the Water-Phenol Interface
| Authors | Arach Goldar, Jean-Louis Sikorav |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0311038 |
| URL | https://arxiv.org/abs/q-bio/0311038 |
| DOI | 10.1140/epje/i2004-10011-7 |
Abstract
We study DNA adsorption and renaturation in a water-phenol two-phase system, with or without shaking. In very dilute solutions, single-stranded DNA is adsorbed at the interface in a salt-dependent manner. At high salt concentrations the adsorption is irreversible. The adsorption of the single-stranded DNA is specific to phenol and relies on stacking and hydrogen bonding. We establish the interfacial nature of a DNA renaturation at a high salt concentration. In the absence of shaking, this reaction involves an efficient surface diffusion of the single-stranded DNA chains. In the presence of a vigorous shaking, the bimolecular rate of the reaction exceeds the Smoluchowski limit for a three-dimensional diffusion-controlled reaction. DNA renaturation in these conditions is known as the Phenol Emulsion Reassociation Technique or PERT. Our results establish the interfacial nature of PERT. A comparison of this interfacial reaction with other approaches shows that PERT is the most efficient technique and reveals similarities between PERT and the renaturation performed by single-stranded nucleic acid binding proteins. Our results lead to a better understanding of the partitioning of nucleic acids in two-phase systems, and should help design improved extraction procedures for damaged nucleic acids. We present arguments in favor of a role of phenol and water-phenol interface in prebiotic chemistry. The most efficient renaturation reactions (in the presence of condensing agents or with PERT) occur in heterogeneous systems. This reveals the limitations of homogeneous approaches to the biochemistry of nucleic acids. We propose a heterogeneous approach to overcome the limitations of the homogeneous viewpoint.
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"abstract": "We study DNA adsorption and renaturation in a water-phenol two-phase system,\nwith or without shaking. In very dilute solutions, single-stranded DNA is\nadsorbed at the interface in a salt-dependent manner. At high salt\nconcentrations the adsorption is irreversible. The adsorption of the\nsingle-stranded DNA is specific to phenol and relies on stacking and hydrogen\nbonding. We establish the interfacial nature of a DNA renaturation at a high\nsalt concentration. In the absence of shaking, this reaction involves an\nefficient surface diffusion of the single-stranded DNA chains. In the presence\nof a vigorous shaking, the bimolecular rate of the reaction exceeds the\nSmoluchowski limit for a three-dimensional diffusion-controlled reaction. DNA\nrenaturation in these conditions is known as the Phenol Emulsion Reassociation\nTechnique or PERT. Our results establish the interfacial nature of PERT. A\ncomparison of this interfacial reaction with other approaches shows that PERT\nis the most efficient technique and reveals similarities between PERT and the\nrenaturation performed by single-stranded nucleic acid binding proteins. Our\nresults lead to a better understanding of the partitioning of nucleic acids in\ntwo-phase systems, and should help design improved extraction procedures for\ndamaged nucleic acids. We present arguments in favor of a role of phenol and\nwater-phenol interface in prebiotic chemistry. The most efficient renaturation\nreactions (in the presence of condensing agents or with PERT) occur in\nheterogeneous systems. This reveals the limitations of homogeneous approaches\nto the biochemistry of nucleic acids. We propose a heterogeneous approach to\novercome the limitations of the homogeneous viewpoint.",
"arxiv_id": "q-bio/0311038",
"authors": [
"Arach Goldar",
"Jean-Louis Sikorav"
],
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],
"doi": "10.1140/epje/i2004-10011-7",
"title": "DNA Renaturation at the Water-Phenol Interface",
"url": "https://arxiv.org/abs/q-bio/0311038"
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