Generation of minicircle DNA with physiological supercoiling

1. A method for producing supercoiled DNA minicircles, comprising:

a) engineering a plasmid DNA molecule comprising site-specific recombination sites;

b) transforming the plasmid into a cell suitable for site-specific recombination to occur, under conditions such that topoisomerase IV decatenation activity is inhibited, thereby producing a plurality of catenated DNA circles, wherein at least one of the circles in each catenane is a supercoiled DNA minicircle of less than about 1 kb in size;

c) decatenating the catenated site-specific recombination products, thereby releasing the supercoiled DNA minicircles from the catenanes; and

d) isolating the supercoiled DNA minicircles.

2. The method of claim 1 , wherein the catenated site-specific recombination products are decatenated by a site-specific endonuclease that does not cleave the supercoiled DNA minicircles.

3. The method of claim 1 , wherein nicked minicircles are also produced, and wherein the supercoiled DNA minicircles are separated from the nicked DNA minicircles.

4. The method of claim 1 , wherein the site-specific recombination sites are selected from the group consisting of: attB, attP, loxP sites, γδ res sites, FRT sites, hixL, hixR, TN3 res sites, Tn21 res sites, psi sites and cer sites.

5. The method of claim 1 , wherein the site-specific recombination utilizes an enzyme selected from the group consisting of: γδ resolvase, Hin recombinase, P1 Cre, yeast 2 micron Flp, Tn3 resolvase, Tn21 resolvase, λ integrase and XerCD.

6. The method of claim 1 , wherein the minicircles comprise one or more putative binding sites for one or more proteins of interest.

7. The method of claim 6 , wherein the one or more proteins of interest are selected from the group consisting of: topoisomerases, site-specific recombinases, restriction endonucleases, transcription factors, remodeling factors, DNA bending proteins, helicases, polymerases and DNA repair proteins.

8. The method of claim 1 , wherein the supercoiled DNA minicircle is attached to a solid support matrix.

9. The method of claim 1 , wherein topoisomers of the supercoiled minicircles are separated from each other, thereby producing substantially purified DNA minicircles, wherein the DNA minicircles have the same linking number.

10. The method of claim 9 , wherein the DNA minicircles have a ΔLk of between about +6 to about −6.

11. The method of claim 10 , wherein the DNA minicircles have a ΔLk of between about −1 to about −6.

12. The method of claim 1 , wherein the site-specific recombination sites are separated by about 100 base pairs to about 1000 base pairs.

13. The method of claim 12 , wherein the site-specific recombination sites are separated by about 342 base pairs.

14. A method for producing a population of supercoiled DNA minicircles

a) engineering a plasmid DNA molecule comprising site-specific recombination sites;

b) transforming the plasmid into a cell suitable for site-specific recombination to occur, under conditions such that topoisomerase IV decatenation activity is inhibited, thereby producing a plurality of catenated DNA circles, wherein at least one of the circles in each catenane is a supercoiled DNA minicircle of less than about 1 kb in size;

c) recovering the supercoiled DNA minicircles from the cell;

d) treating the supercoiled DNA minicircles with an enzyme that introduces nicks into the DNA minicircle; and

e) ligating the nicked minicircle in the presence of a DNA intercalator that introduces supercoils,

thereby producing a population of supercoiled DNA minicircles.

15. The method of claim 14 , wherein the enzyme that introduces nicks into the DNA minicircle is a nicking endonuclease.

16. The method of claim 14 , wherein the DNA intercalator is ethidium bromide.