DNA renaturation at the water-phenol interface.

ABSTRACT

We study the renaturation of complementary single-stranded DNAs in a water-phenol two-phase system, with or without shaking. In very dilute solutions, each single-stranded DNA is strongly adsorbed at the interface at high salt concentrations. The adsorption of the single-stranded DNA is specific to phenol and relies on stacking and hydrogen bonding. We establish the interfacial nature of DNA renaturation at high salt, either with vigorous shaking (in which case the reaction is known as the Phenol Emulsion Reassociation Technique or PERT) or without. In the absence of shaking, the renaturation involves a surface diffusion of the single-stranded DNA chains. A comparison of PERT with other known renaturation reactions shows that PERT is the most efficient one and reveals similarities between PERT and the renaturation performed by single-stranded nucleic acid binding proteins. The most efficient renaturation reactions (either with PERT or in the presence of condensing agents) occur in heterogeneous systems, in contrast with standard thermal renaturation, which takes place in the bulk of a homogeneous phase. This work highlights the importance of aromaticity in molecular biology. Our results lead to a better understanding of the partitioning of nucleic acids, and should help to design improved extraction procedures for damaged nucleic acids. We present arguments in favor of interfacial scenarios involving phenol in prebiotic chemistry.