期刊
BIOPOLYMERS
卷 112, 期 4, 页码 -出版社
WILEY
DOI: 10.1002/bip.23426
关键词
DNA strand exchange; mismatch detection; PEG; hydrophobic catalysis
资金
- Biotechnology and Biological Sciences Research Council
- European Research Council
- Swedish Research Council
- Ruth and Nils-Erik Stenback Foundation
This study investigates the effect of a semi-hydrophobic environment represented by poly(ethylene glycol) on the strand exchange process of DNA, specifically focusing on the role of the concentration of the co-solute in accelerating the exchange from mismatched to matched strands. The results suggest that the semi-hydrophobic environment affects the process through various mechanisms, including weakening base stacking, strengthening base-pair hydrogen bonds, and stabilizing unstacked mismatched bases with intercalated hydrophobic co-solvent molecules.
In contrast to DNA replication and transcription where nucleotides are added and matched one by one, homologous recombination by DNA strand exchange tests whole sequences for complementarity, which requires elimination of mismatched yet thermodynamically stable intermediates. To understand the remarkable sequence specificity of homologous recombination, we have studied strand exchange between a 20-mer duplex containing one single mismatch (placed at varied positions) with the matching single strand in presence of poly(ethylene glycol) representing a semi-hydrophobic environment. A FRET-based assay shows that rates and yields of strand exchange from mismatched to matched strands rapidly increase with semi-hydrophobic co-solute concentration, contrasting previously observed general strand exchange accelerating effect of ethyl glycol ethers. We argue that this effect is not caused simply by DNA melting or solvent-induced changes of DNA conformation but is more complex involving several mechanisms. The catalytic effects, we propose, involve strand invasion facilitated by reduced duplex stability due to weakened base stacking (longitudinal breathing). Secondly, decreased water activity makes base-pair hydrogen bonds stronger, increasing the relative energy penalty per mismatch. Finally, unstacked mismatched bases (gaps) are stabilized through partly intercalated hydrophobic co-solvent molecules, assisting nucleation of strand invasion at the point of mismatch. We speculate that nature long ago discovered, and now exploits in various enzymes, that sequence recognition power of nucleic acids may be modulated in a hydrophobic environment.
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