In the present invention, viruses, plasmids or both are constructed which contain viral DNA, either at least one head-to-head ITR junction, recombinase recognition sites positioned such that site-specific recombination between recombinase recognition sites in separate plasmids results in generation of infectious viral DNA at high-efficiency in cotransfected host cells that have been engineered to express a site-specific recombinase, or both. Because of the high-efficiency and specificity of the Cre enzyme, the FLP enzyme, or both, suitably engineered plasmids can be readily recombined to produce infectious virus at high-efficiency in cotransfected 293 cells, without, at the same time, producing wild-type adenovirus, with the attendant problems for removal thereof. Use of recombinases besides Cre or FLP, and recombinase recognition sites besides lox or frt sites, and use of cells other than 293 cells are also disclosed and enabled, as are kits incorporating the site-specific vector system, as well as compositions and methods for using such compositions as vaccines or in gene therapeutic applications. Enhancements in the efficiency of both site-specific and homologous recombination are provided by inclusion of at least one head-to-head ITR junction.Selon cette invention, on construit des virus et/ou des plasmides qui contiennent un ADN viral et dans lesquels il existe soit au moins une jonction ITR tête-à-tête ou des sites de reconnaissance de recombinases, disposés de manière à ce que la recombinaison spécifique aux sites entre les sites de reconnaissance de recombinases dans les plasmides séparés mène à la génération hautement efficace dun ADN viral infectieux dans les cellules hôtes cotransférées manipulées pour exprimer une recombinase spécifique au site, soit les deux. Grâce à lefficacité et à la spécificité élevées de lenzyme Cre, de lenzyme FLP ou des deux, on peut aisément recombiner les plasmides manipulés en conséquence pour produire très efficacement un vir
