A method for preparing a minicircle nucleic acid vector composition substantially free of contaminating nucleic acids, the method comprising: transfecting a genetically modified bacterial cell lacking functional endonuclease I and comprising a coding sequence for araE under control of a constitutive promoter, a genomically integrated coding sequence for a unidirectional site-specific recombinase under the control of an inducible promoter and optionally comprising a genomically integrated coding sequence for a restriction endonuclease not endogenous to the bacterial cell under the control of an inducible promoter, with a circular parental plasmid comprising: (i) a polynucleotide of interest flanked by att B and att P recombination sites recognized by a unidirectional site-specific recombinase; (ii) at least one restriction endonuclease site recognized by a restriction endonuclease not endogenous to the bacterial cell; wherein present in said bacterial cell are sequences encoding the unidirectional site-specific recombinase and the restriction endonuclease not endogenous to the bacterial cell; incubating the bacterial cells under conditions and for a period of time sufficient to express the unidirectional site-specific recombinase and allow the unidirectional site-specific recombinase to recombine the att B and att P recombination sites; and to express the restriction endonuclease and allow the restriction endonuclease to digest the restriction endonuclease site, wherein the incubating provides a minicircle nucleic acid vector comprising the polynucleotide of interest and a product hybrid sequence of the unidirectional site-specific recombinase; purifying the minicircle nucleic acid vector to provide a minicircle nucleic acid vector composition substantially free of contaminating nucleic acids and devoid of plasmid backbone sequences. transfecting a genetically modified bacterial cell lacking functional endonuclease I and comprising a coding sequence for araE under control of a constitutive promoter, a genomically integrated coding sequence for a unidirectional site-specific recombinase under the control of an inducible promoter and optionally comprising a genomically integrated coding sequence for a restriction endonuclease not endogenous to the bacterial cell under the control of an inducible promoter, with a circular parental plasmid comprising: (i) a polynucleotide of interest flanked by att B and att P recombination sites recognized by a unidirectional site-specific recombinase; (ii) at least one restriction endonuclease site recognized by a restriction endonuclease not endogenous to the bacterial cell; (i) a polynucleotide of interest flanked by att B and att P recombination sites recognized by a unidirectional site-specific recombinase; (ii) at least one restriction endonuclease site recognized by a restriction endonuclease not endogenous to the bacterial cell; wherein present in said bacterial cell are sequences encoding the unidirectional site-specific recombinase and the restriction endonuclease not endogenous to the bacterial cell; incubating the bacterial cells under conditions and for a period of time sufficient to express the unidirectional site-specific recombinase and allow the unidirectional site-specific recombinase to recombine the att B and att P recombination sites; and to express the restriction endonuclease and allow the restriction endonuclease to digest the restriction endonuclease site, wherein the incubating provides a minicircle nucleic acid vector comprising the polynucleotide of interest and a product hybrid sequence of the unidirectional site-specific recombinase; purifying the minicircle nucleic acid vector to provide a minicircle nucleic acid vector composition substantially free of contaminating nucleic acids and devoid of plasmid backbone sequences.