Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2000-07-03
2003-09-09
Fredman, Jeffrey (Department: 1637)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091200, C536S023100, C536S024500, C536S024300
Reexamination Certificate
active
06617108
ABSTRACT:
BACKGROUND OF THE INVENTION
I. Field of the Invention
The present invention relates to the general field of biochemical assays and separations, generally classified in U.S. Patent Class 435.
II. Description of the Prior Art
Interest in nucleic acid purification has increased with human trials of plasmid-based vaccines (e.g., for influenza, HIV, and malaria) and therapeutics (e.g., insulin and vascularization promoters) as well as the steady expansion of DNA sequencing activities. (references 1 and 2) This invention embodies a rapid, scaleable, nuclease-free (preferably RNAse free), cost effective method of nucleic acid purification using selective precipitation by compaction agents.
Prior Art will include the following:
1. Parasrampuria, D. and Hunt, A., (1998), Therapeutic issues in gene therapy; part 1: vectors. Biopharm. 11:38-45.
2. Anderson, F., (1998), Human Gene Therapy. Nature. 392: 25-30.
3. Horn, N. A., Meek, J. A., Budahazi, G., and Marquet M. 1995. Cancer gene therapy using plasmid DNA: purification of DNA for human clinical trials. Human Gene Therapy. 6:565-573.
4. Gosule, L. C. and Schellman, J. A., (1976), Compact form of DNA induced by spermidine. Nature. 259:333-335.
5. Arscott, P. G., Li, A. Z., and Bloomfield, V. A., (1990), Condensation of DNA by trivalent cations. 1. Effects of DNA length and topology on the size and shape of condensed particles. Biopolymers. 30:619-630.
6. Wilson, R. W. and Bloomfield, V. A., (1979), Counter-ion induced condensation of deoxyribonucleic acid. A light scattering study. Biochemistry. 18:2192-2196.
7. Bednar, J., Furrer, P., Stasiak, A., Dubochet, J., Egelman, E. H., and Bates, A. D., (1994), The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix: possible implications for DNA structure in vivo. Journal of Molecular Biology. 235:825-847.
8. Rolland, A., (1998), From genes to gene medicines: recent advances in nonviral gene delivery. Critical Review of Therapeutic Drug Carrier Systems. 15:143-198.
9. Hoopes, B. C. and McClure, W. R., (1981), Studies on the selectivity of DNA precipitation by spermine. Nucleic Acids Research. 9:5493-5504.
10. Sambrook, J., Fritsch, E. F., and Maniatis, T., (1989), Molecular cloning, a laboratory manual. Second edition, Cold Spring Harbor Laboratory Press.
11. Horn, N., Marquet, M., Meek, J., and Budahazi, G., (1996), Process for reducing RNA concentration in a mixture of biological material using diatomaceous earth. U.S. Pat. No. 5,576,196.
12. Lev, Z., (1987), A procedure for large-scale isolation of RNA-free plasmid and phage DNA without the use of RNAse. Analytical Biochemistry. 160:332-336.
13. Drevin, I., Larsson, L., and Johansson, B. L., (1989), Column performance of Q-Sepharose HP in analytical- and preparative-scale chromatography. Journal of Chromatography. 477:337-344.
14. Horn et al; U.S. Pat. No. 5,707,812, Purification of Plasmid DNA During Column Chromatography, which is understood to teach addition of short chain polymeric alcohol to promote isolation of plasmid DNA.
15. Hubert, P., and Dellacherie, E., (1980), Use of water-soluble biospecific polymers for the purification of proteins, Journal of Chromatography, 184, 325-333.
16. Irwin, J. A., and Tipton, K. F., (1995), Affinity precipitation: a novel approach to protein purification, Essays in Biochemistry, 29, 137-156.
17. Widom, J., and Baldwin, R. L., (1983), Monomolecular condensation of &lgr;-DNA induced by Cobalt Hexammine, Biopolymers, 22, 1595-1620.
18. Nunn, C. S., and Neidle, S. 1996. The high resolution crystal structure of the DNA decamer d(AGGCATGCCT). J. Mol. Biol. 256:340-351.
19. Kieft, J. S. and Tinoco, I. 1997. Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine.
Structure.
5(5):713-721.
20. Pitulle, C., Hedenstierna, K. O., and Fox, G. E. 1995. A novel approach for monitoring genetically engineered microorganisms by using artificial, stable RNAs. Applied Environmental Microbiology. 61(10): 3661-3666.
21. Setterquist, R. A, Smith, G. K., Oakley, T. H., Lee, Y. H., and Fox, G. E. 1996. Sequence, overproduction and purification of Vibrio proteolyticus ribosomal protein L18 for in vitro and in vivo studies. Gene. 183(1-2):237-242.
22. Yang, Y. and Fox, G. E. 1996. An Archaea 5S rRNA analog is stablely expressed in
Escherichia coli
. Gene. 168: 81-85.
23. Sioud, M. and Drlica, K. 1991. Prevention of human immunodeficiency virus type 1 integrase expression in
Escherichia coli
by a ribozyme. Proc. Natl. Acad. Sci. USA 88:7303-7307.
24. Couture, L. A. and Stinchcomb, D. T. 1996. Anti-gene therapy: the use of ribozymes to inhibit gene function. TIG. 12(12):510-514.
25. Christoffersen, R. E., and Marr J. J., (1995), Ribozymes as human therapeutic agents, Journal of Medicinal Chemistry, 38(12), 2023-2037.
26. Weiss, B., Davidkova, G. and Zhou L. W., (1999), Antisense RNA gene therapy for studying and modulating biological processes, Cell. Mol. Life Sci., 55, 334-358.
27. Kumar, M. and Carmichael, G. G., (1998), Antisense RNA: function and fate of duplex RNA in cells of higher eukaryotes, Microbiology and Molecular Biology Reviews, 62(4), 1415-1434.
28. Matthews, H. R., (1993), Polyamines, chromatin structure and transcription, BioEssays, 15(8), 561-566.
29. Hedemstierna, K. O. F., Lee, H. Y., Yang, Y., and Fox, G. E, (1993), A prototype stable RNA identification cassette for monitoring plasmids of genetically engineered microorganisms. System. Appl. Microbiol. 16, 280-286.
30. Pitulle, C., Dsouza, L., and Fox, G. E. 1997. A low molecular weight artificial RNA of unique size with multiple probe target regions. System. Appl. Microbiol. 20:133-136.
31. Uchiyama, S., Imamura, T., Nagai, S., and Konishi, K. 1981. Separation of low molecular weight RNA species by high-speed gel filtration. J. Biochem. 90:643-648.
32. Lee, K. M. and Marshall, A. G. 1986. High-speed preparative-scale separation and purification of ribosomal 5S and 5.8S RNA's via Sephacryl S-300 gel filtration chromatography. Preparative Biochemistry 16(3):247-258.
33. Hori, S. and Ohtani, S. 1990. Separation of high-molecular mass RNAs by high-performance liquid chromatography on hydroxyapatite. Journal of Chromatography. 515:611-619.
34. Fair, W. R., and Wehner, N., (1971) Antibacterial action of spermine: effect on urinary tract pathogens, Applied Environmental Microbiology, 21(1), 6-8
35. Scopes, R. K., (1993) Protein purification: principles and practice, Springer-Verlag, 379 pages.
36. Blackburn, G. M., and Gait, M. J., (1996),
Nucleic Acids in Chemistry and Biology
, Oxford University Press, pages 337-346.
37. Saenger, W., (1988),
Principles of Nucleic Acid Structure
, Springer-Verlag, pages 432-434.
38. Ma, C., Sun, L., and Bloomfield, V. A., (1995), “Condensation of Plasmids Enhanced by Z-DNA Conformation of d(CG)
n
Inserts”, Biochemistry, vol. 34(11), 3521-3528.
39 U.S. Pat. No. 5,622,822, to Tobias et al, Issued Apr. 22, 1997, (Assigned Johnson & Johnson), Methods for capture and selective release of nucleic acids using polyethyleneimine and an anionic phosphate ester surfactant and amplification of same teaches that nucleic acids can be made available for amplification or other treatment after lysis by contacting the lysate with polyethyleneimine to form a precipitate with the nucleic acids. The nucleic acids are then released from the precipitate by contact with a strong base, and the released nucleic acids are kept in solution with an anionic phosphate ester surfactant.
II. Problems Presented by Prior Art
Most current methods of plasmid separation are relatively time-consuming and require the use of adsorbents, toxic substances, nucleases, and/or filtration media to separate plasmid from protein, genomic DNA, endotoxins and especially the abundant RNA present in cell lysates.
This technique offers several important improvements over current methods: no RNAse and/or other enzymes are used, the technique requires no chromatographic medium, and the technique is directly scaleable if larger
Murphy Jason
Willson, III Richard C.
Fredman Jeffrey
Technology Licensing Co. LLC
Willson, Jr. Richard Coale
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