Claims for Patent: 7,910,337

Summary for Patent: 7,910,337

Title:	Method for identifying drug-sensitizing antisense DNA fragments and use thereof
Abstract:	The invention provides a method for generating and selecting drug-sensitizing antisense DNA fragments. In one embodiment, the method includes identifying a gene of interest using knowledge of bacterial physiology, biochemistry, genetics, genomics, and other means. The method includes PCR amplification of a gene of interest using genomic DNA as a template; fragmentation of the DNA by sonication or other means; selecting DNA fragments no longer than 400 base pairs; ligating the DNA fragments into a suitable expression plasmid with a selectable marker; transforming the plasmids containing the DNA fragments into the organism from which the gene of interest originated; and selecting clones from transformed cells that show a phenotypic difference of the clone grown in the presence of the inducer relative to the phenotype in the absence of inducer.
Inventor(s):	Haselbeck; Robert (San Diego, CA), Hilgers; Mark (San Diego, CA), Shaw; Karen (Poway, CA), Brown-Driver; Vickie (Solana Beach, CA), Gc; Kedar (San Diego, CA), Finn; John M. (Encinitas, CA), Stidham; Mark (San Diego, CA)
Assignee:	Trius Therapeutics, Inc. (San Diego, CA)
Application Number:	11/636,394
Patent Claims:	1. A method for generating and selecting drug-sensitizing antisense DNA fragments comprising: selecting a gene of interest using means other than genomic surveys of antisense-defined proliferation genes, amplification of the gene of interest using genomic DNA as a template, fragmentation of the DNA by sonication or other means; selecting DNA fragments no longer than 400 base pairs; ligating the DNA fragments into a suitable expression plasmid with a selectable marker; transforming the plasmids containing the DNA fragments into the organism from which the gene of interest originated; and selecting clones from transformed cells that show a discernible phenotypic difference of the clone grown in the presence of the inducer relative to the phenotype in the absence of inducer. 2. The method of claim 1, wherein the discernible phenotype is relative sensitivity to a growth inhibiting compound. 3. The method of claim 1, wherein the discernible phenotype is requirement of a nutrient to the growth medium. 4. The method of claim 1, wherein the discernible phenotype is visible morphology such as shape. 5. The method of claim 1, wherein the discernible phenotype is relative sensitivity to osmotic stress. 6. The method of claim 1 wherein the discernible phenotype is colony size. 7. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of DNA biosynthesis. 8. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of RNA biosynthesis. 9. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of protein biosynthesis. 10. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of fatty acid biosynthesis. 11. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of cell wall biosynthesis. 12. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of amino acid biosynthesis. 13. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of nucleotide biosynthesis. 14. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of vitamin biosynthesis. 15. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of isoprenoid biosynthesis. 16. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of co-factor biosynthesis. 17. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of MurB. 18. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of UppS. 19. The method of claim 1, wherein the drug is an antibiotic acting through inhibition of DHFR. 20. The method of claim 1, wherein the drug is a beta-lactam antibiotic. 21. The method of claim 1, wherein the drug is a diaminopyrimidine antibiotic. 22. The method of claim 1, wherein the drug is macrolide antibiotic. 23. The method of claim 1, wherein the drug is daptomycin. 24. The method of claim 1, wherein the drug is a fluoroquinolone antibiotic including ciprofloxacin. 25. The method of claim 1, wherein the drug is a tetracycline. 26. The method of claim 1, wherein the drug is an oxazolidinone. 27. The method of claim 1, wherein the drug is fosfomycin. 28. The method of claim 1, wherein the drug is fosmidomycin. 29. The method of claim 1, wherein the drug is mupirocin. 30. The method of claim 1, wherein the drug is a lipopeptide. 31. The method of claim 1, wherein the drug is a glycopeptide. 32. The method of claim 1, wherein the drug is vancomycin. 33. The method of claim 1, wherein the drug is trimethoprim. 34. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene murB-2 and is comprised of the sequence specified for SEQ ID:1 Ba-murB2-C1. 35. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene murB-2 and is comprised of the sequence specified for SEQ ID:2 Ba-murB2-H1. 36. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene murB-2 and is comprised of the sequence specified for SEQ ID:3 Ba-murB2-D1. 37. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene murB-2 and is comprised of the sequence specified for SEQ ID:4 Ba-murB2-D2. 38. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene metS and is comprised of the sequence specified for SEQ ID:5 Ba-metRS1-H1. 39. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene metS and is comprised of the sequence specified for SEQ ID:6 Ba-metRS1-H2. 40. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene metS and is comprised of the sequence specified for SEQ ID:7 Ba-metRS1-H6. 41. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene metS and is comprised of the sequence specified for SEQ ID:8 Ba-metRS1-E4. 42. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene uppS and is comprised of the sequence specified for SEQ ID:9 Ba-uppS-UG9. 43. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene uppS and is comprised of the sequence specified for SEQ ID:10 Ba-uppS-UA3. 44. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene dfrA and is comprised of the sequence specified for SEQ ID:11 Ba-dfrA-2G1. 45. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Bacillus anthracis gene dfrA and is comprised of the sequence specified for SEQ ID:12 Ba-dfrA-2G6. 46. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Staphylococcus aureus gene murB and is comprised of the sequence specified for SEQ ID:13 Sa-murB-E9. 47. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Staphylococcus aureus gene murB and is comprised of the sequence specified for SEQ ID:14 Sa-murB-F7. 48. The method of claim 1, wherein said antisense-oriented fragment is a fragment of the Staphylococcus aureus gene murB and is comprised of the sequence specified for SEQ ID:15 Sa-murB-B9.

Details for Patent 7,910,337

Applicant	Tradename	Biologic Ingredient	Dosage Form	BLA	Approval Date	Patent No.	Expiredate
Emergent Biodefense Operations Lansing Llc	BIOTHRAX	anthrax vaccine adsorbed	Injection	103821	11/12/1998		2026-03-15