A path for coevolution of recombinational DNA repair, transposition, and the common nucleotides

The development of isoguanosine: from discovery, synthesis, and modification to supramolecular structures and potential applications

First systematical review of isoguanosine, an unnatural base, as an isomer of guanosine shows significant differences in diverse properties.

Direct evaluation of a kinetic model for RecA-mediated DNA-strand exchange: the importance of nucleic acid dynamics and entropy during homologous genetic recombination

The Escherichia coli RecA protein is the prototype of a class of proteins that play central roles in genomic repair and recombination in all organisms. The unresolved mechanistic strategy by which RecA aligns a single strand of DNA with a duplex DNA and mediates a DNA strand switch is central to understanding homologous recombination. We explored the mechanism of RecA-mediated DNA-strand exchange using oligonucleotide substrates with the intrinsic fluorophore 6-methylisoxanthopterin. Pre-steady-state spectrofluorometric analysis elucidated the earliest transient intermediates formed during recombination and delineated the mechanistic strategy by which RecA facilitates this process. The structural features of the first detectable intermediate and the energetic characteristics of its formation were consistent with interactions between a few bases of the single-stranded DNA and the minor groove of a locally melted or stretched duplex DNA. Further analysis revealed RecA to be an unusual enzyme in that entropic rather than enthalpic contributions dominate its catalytic function, and no unambiguously active role for the protein was detected in the earliest molecular events of recombination. The data best support the conclusion that the mechanistic strategy of RecA likely relies on intrinsic DNA dynamics.

A selfish origin for recombination

Recent findings of molecular biology show that recombination is initiated by interactions between homologous chromosomes and that an allele can induce the initiation of recombination on the homolog. Since gene conversion at the site of initiation is strong enough to promote the transmission of that allele, recombination may be a way for a self-promoting element to spread, even if it gives no advantage to the individual or to the population. I develop a simple model and discuss available molecular evidence in support of this hypothesis. A consequent argument is that with asexual reproduction the evolution of recombination leads to an intragenomic conflict, and a possible outcome of this conflict may be the origin of sexual reproduction.