Mechanism of DNA strand exchange at liposome surfaces investigated using mismatched DNA

Mismatch detection in homologous strand exchange amplified by hydrophobic effects

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.

Cholesterol-induced physicochemical changes in dodecylamine-based metallosomes: drug entrapping ability and interactions with biological molecules

Multivesicular metallosomes have been synthesized from metal functionalized amphiphiles. They have been thoroughly characterized and explored for their entrapment efficiency towards drug and other biomolecules.

Wavelength-selective light-triggered strand exchange reaction

We prepared an oligodeoxynucleotide (ODN) bearing two 4-hydroxy-2-mercaptobenzimidazole nucleobase analogues (SB(NV) and SB(NB)) modified with different photolabile groups. This ODN enabled a light-triggered strand exchange reaction in a wavelength-selective manner.

Glyco Star Polymers as Helical Multivalent Host and Biofunctional Nano-Platform

A series of amylose-based star polymers (1, 2, 4, and 8 arms) as a new glyco biomaterial was synthesized by a click reaction and enzymatic polymerization of specific primers with phosphorylase. The molecular weights were controlled by the enzymatic reaction. Further polymerization resulted in a viscous solution and, especially, for the 8-arm primer, a hydrogel was obtained due to effective cross-linking between the multiarmed structures. The star polymers with a degree of polymerization of about 60 per arm acted as an allosteric multivalent host for hydrophobic molecules by helical formation. A cationic 8-arm star polymer catalyzed DNA strand exchange as a nucleic acid chaperone. Amylose-based star polymers are promising building blocks for producing advanced hybrid glyco biomaterials.

Evidence for hydrophobic catalysis of DNA strand exchange

DNA strand exchange is catalysed by a hydrophobic environment which destabilises base stacking and promotes DNA breathing.

DNA strand exchange reaction activated by cationic comb-type copolymers having ureido groups

Ureido modification of cationic graft copolymers accelerated DNA strand exchange reaction relative to unmodified copolymers.

Linker histone H1 stimulates DNA strand exchange between short oligonucleotides retaining high sensitivity to heterology

The interaction of human linker histone H1(0) with short oligonucleotides was characterized. The capability of the histone to promote DNA strand exchange in this system has been demonstrated. The reaction is reversible at saturating amounts of H1 corresponding to complete binding of the oligonucleotide substrates with the histone. In our conditions the complete saturation of DNA with the histone occurs at a ratio of one protein molecule per about 60 nucleotides irrespectively of DNA strandedness. In contrast to the DNA strand exchange promoted by RecA-like enzymes of homologous recombination the H1 promoted reaction exhibits low tolerance to interruptions of homology between oligonucleotide substrates comparable to those for the case of spontaneous strand exchange between free DNA molecules at elevated temperatures and the exchange promoted by some synthetic polycations.