In site-specific recombination reactions catalyzed by Tn3 resolvase, the right and left arms of the res site are always religated to the correct partner. This poses the problem of how resolvase aligns the two sites correctly for the cleavage/religation reaction. We show that the "accessory" binding subsites II and III of res are important for correct alignment of the adjoining crossover subsite (subsite I). Deletion of subsites II and III from one of the two res sites removes a barrier to recombination between incorrectly aligned crossover subsites. Correct alignment does not require any DNA sequence asymmetry in the crossover subsite, DNA supercoiling, or covalent linkage of the two res sites. Our results suggest that correct subsite I alignment is determined by local, resolvase-mediated interactions of subsites II and III of both partners, consistent with a current model of the synapse. Surprisingly, the topological selectivity for intramolecular resolution in a supercoiled substrate does not require subsites II and III in both recombination partners.

Transposons of the Tc1/mariner family have been used to integrate foreign DNA stably into the genome of a large variety of different cell types and organisms. Integration is at TA dinucleotides located essentially at random throughout the genome, potentially leading to insertional mutagenesis, inappropriate activation of nearby genes, or poor expression of the transgene. Here, we show that fusion of the zinc-finger DNA-binding domain of Zif268 to the C-terminus of ISY100 transposase leads to highly specific integration into TA dinucleotides positioned 6-17 bp to one side of a Zif268 binding site. We show that the specificity of targeting can be changed using Zif268 variants that bind to sequences from the HIV-1 promoter, and demonstrate a bacterial genetic screen that can be used to select for increased levels of targeted transposition. A TA dinucleotide flanked by two Zif268 binding sites was efficiently targeted by our transposase-Zif268 fusion, suggesting the possibility of designer ‘Z-transposases’ that could deliver transgenic cargoes to chosen genomic locations.

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The human nuclear gene (POLG) for the catalytic subunit of mitochondrial DNA polymerase (DNA polymerase γ) contains a trinucleotide CAG microsatellite repeat within the coding sequence. We have investigated the frequency of different repeat-length alleles in populations of diseased and healthy individuals. The predominant allele of 10 CAG repeats was found at a very similar frequency (approximately 88%) in both Finnish and ethnically mixed population samples, with homozygosity close to the equilibrium prediction. Other alleles of between 5 and 13 repeat units were detected, but no larger, expanded alleles were found. A series of 51 British myotonic dystrophy patients showed no significant variation from controls, indicating an absence of generalised CAG repeat instability. Patients with a variety of molecular lesions in mtDNA, including sporadic, clonal deletions, maternally inherited point mutations, autosomally transmitted mtDNA depletion and autosomal dominant multiple deletions showed no differences in POLG trinucleotide repeat-length distribution from controls. These findings rule out POLG repeat expansion as a common pathogenic mechanism in disorders characterised by mitochondrial genome instability.