Mismatch detection in homologous strand exchange amplified by hydrophobic effects
Journal article, 2021

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.

hydrophobic catalysis

mismatch detection

DNA strand exchange

PEG

Author

Bengt Nordén

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

T. Brown

University of Oxford

Bobo Feng

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

Biopolymers

0006-3525 (ISSN) 1097-0282 (eISSN)

Vol. 112 4 e23426

Subject Categories

Biochemistry and Molecular Biology

Microbiology

Other Industrial Biotechnology

DOI

10.1002/bip.23426

PubMed

33780001

More information

Latest update

5/12/2021