DNA Renaturation at the Water-Phenol Interface

Details DNA Renaturation at the Water-Phenol Interface DNA Renaturation at the Water-Phenol Interface

2003-11-27

arxiv.org/abs/q-bio/0311038v1

Biology

Quantitative Biology

Biomolecules

Scientific paper

10.1140/epje/i2004-10011-7

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.

Affiliated with

Also associated with

No associations

Rating

DNA Renaturation at the Water-Phenol Interface does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with DNA Renaturation at the Water-Phenol Interface, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and DNA Renaturation at the Water-Phenol Interface will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-519410