Process for the scaleable purification of plasmid DNA

Abstract

The present invention relates to a nonchromatographic-based process for the isolation of clinical grade plasmid DNA from bacterial cells. The exemplified methods described herein outline a scaleable, economically favorable protocol for the purification of clinical grade plasmid DNA from E. coli which includes CTAB-based precipitation of DNA in combination with adsorption of impurities to calcium silicate.

What is claimed is:  
     
         1 . A method of purifying supercoiled plasmid DNA from a cell lysate of a large scale microbial fermentation which comprises: 
 (a) precipitating supercoiled plasmid DNA by a detergent-induced precipitation; and,    (b) redissolving the precipitate in a salt solution.    
     
     
         2 . A method of  claim 1  wherein the detergent of step (a) is hexadecyltrimethylammonium bromide (CTAB).  
     
     
         3 . A method of  claim 2  wherein hexadecyltrimethylammonium bromide is added in a two step process, wherein a first hexadecyltrimethylammonium-induced precipitation occurs to precipitate out debris and non-supercoiled plasmid DNA and a second hexadecyltrimethylammonium bromide-induced precipitation occurs to precipitate the supercoiled plasmid DNA.  
     
     
         4 . A method of  claim 3  wherein the first and the second hexadecyltrimethylammonium bromide-induced precipitation steps occur in a standard STET buffer.  
     
     
         5 . A method of  claim 4  wherein the precipitated, supercoiled DNA is resuspended in a buffer solution and further concentrated by a process selected from the group consisting of alcohol precipitation and ultrafiltration.  
     
     
         6 . A method of  claim 5  wherein the supercoiled DNA is concentrated by ethanol precipitation.  
     
     
         7 . A method of  claim 3  wherein the precipitated, supercoiled DNA is resuspended in a buffer and further concentrated by a process selected from the group consisting of alcohol precipitation and ultrafiltration.  
     
     
         8 . A method of  claim 7  wherein the supercoiled DNA is concentrated by ethanol precipitation.  
     
     
         9 . A method of  claim 2  wherein the first and the second hexadecyltrimethylammonium bromide-induced precipitation steps occur in a standard STET buffer.  
     
     
         10 . A method of  claim 2  wherein the cell lysate is clarified prior to addition of the hexadecyltrimethylammonium bromide (CTAB).  
     
     
         11 . A method of  claim 10  wherein the cell lysate is clarified by addition of diatomaceous earth.  
     
     
         12 . A method of  claim 11  wherein the supercoiled DNA is further concentrated by a process selected from the group consisting of alcohol precipitation and ultrafiltration.  
     
     
         13 . A method of  claim 12  wherein the supercoiled DNA is concentrated by ethanol precipitation.  
     
     
         14 . A method of purifying supercoiled plasmid DNA from a cell lysate of a microbial fermentation which comprises adding hydrated, crystallized calcium silicate to the cell lysate to adsorb residual impurities away from the supercoiled plasmid DNA.  
     
     
         15 . A method of  claim 14  wherein the cell lysate is clarified prior to addition of the hydrated, crystallized calcium silicate.  
     
     
         16 . A method of  claim 15  wherein the cell lysate is clarified by addition of diatomaceous earth.  
     
     
         17 . A method of  claim 16  wherein the supercoiled DNA is further concentrated by a process selected from the group consisting of alcohol precipitation and ultrafiltration.  
     
     
         18 . A method of  claim 17  wherein the supercoiled DNA is concentrated by ethanol precipitation.  
     
     
         19 . A method of  claim 14  wherein the supercoiled DNA is further concentrated by a process selected from the group consisting of alcohol precipitation and ultrafiltration.  
     
     
         20 . A method of  claim 19  wherein the supercoiled DNA is concentrated by ethanol precipitation.  
     
     
         21 . A method of  claim 14  wherein the hydrated, crystallized calcium silicate is added in a stepwise manner.  
     
     
         22 . A method of  claim 21  wherein the cell lysate is clarified prior to addition of the hydrated, crystallized calcium silicate.  
     
     
         23 . A method of  claim 22  wherein the cell lysate is clarified by addition of diatomaceous earth.  
     
     
         24 . A method of  claim 23  wherein the supercoiled DNA is further concentrated by a process selected from the group consisting of alcohol precipitation and ultrafiltration.  
     
     
         25 . A method of  claim 24  wherein the supercoiled DNA is concentrated by ethanol precipitation.  
     
     
         26 . A method of purifying supercoiled plasmid DNA from a cell lysate of a microbial fermentation, which comprises: 
 (a) precipitating the supercoiled plasmid DNA by a detergent-induced precipitation;    (b) redissolving the precipitate in a salt solution;    (c) adding hydrated, crystallized calcium silicate to the resuspended supercoiled plasmid to adsorb residual impurities away from the supercoiled plasmid DNA, resulting in a solution containing the supercoiled plasmid DNA; and,    (d) concentrating the supercoiled plasmid DNA.    
     
     
         27 . A method of  claim 26  wherein the detergent of step (a) is hexadecyltrimethylammonium bromide.  
     
     
         28 . A method of  claim 27  wherein hexadecyltrimethylammonium bromide is added in a two step process, wherein a first hexadecyltrimethylammonium-induced precipitation occurs to precipitate out debris and non-supercoiled plasmid DNA and a second hexadecyltrimethylammonium bromide-induced precipitation occurs to precipitate the supercoiled plasmid DNA.  
     
     
         29 . A method of  claim 28  wherein the first and the second hexadecyltrimethylammonium bromide-induced precipitation steps occur in a standard STET buffer.  
     
     
         30 . A method of  claim 29  wherein the supercoiled DNA is concentrated in step (d) by a process selected from the group consisting of alcohol precipitation and ultrafiltration.  
     
     
         31 . A method of  claim 30  wherein the supercoiled DNA is concentrated by ethanol precipitation.  
     
     
         32 . A method of  claim 28  wherein the cell lysate is clarified prior to addition of the hydrated, crystallized calcium silicate.  
     
     
         33 . A method of  claim 32  wherein the cell lysate is clarified by addition of diatomaceous earth.  
     
     
         34 . A method of  claim 33  wherein the supercoiled DNA is further concentrated by a process selected from the group consisting of alcohol precipitation and ultrafiltration.  
     
     
         35 . A method of  claim 34  wherein the supercoiled DNA is concentrated by ethanol precipitation.  
     
     
         36 . A method of  claim 26  wherein the cell lysate is clarified prior to addition of the hydrated, crystallized calcium silicate.  
     
     
         37 . A method of  claim 36  wherein the cell lysate is clarified by addition of diatomaceous earth.  
     
     
         38 . A method of  claim 37  wherein the supercoiled DNA is further concentrated by a process selected from the group consisting of alcohol precipitation and ultrafiltration.  
     
     
         39 . A method of  claim 38  wherein the supercoiled DNA is concentrated by ethanol precipitation.  
     
     
         40 . A method for the purification of supercoiled plasmid DNA from a microbial fermentation, which comprises: 
 (a) harvesting microbial cells from a fermentation broth;    (b) adding to the harvested microbial cells a sufficient amount of a lysis solution;    (c) heating the microbial cells of step b) to a temperature between 70° C. and 100° C. in a flow-through heat exchanger to form a cell lysate;    (d) cooling the cell lysate;    (e) clarifying the cell lysate using filtration with diatomaceous earth;    (f) precipitating residual cell debris and impurities with a first hexadecyltrimethylammonium-induced precipitation;    (g) selectively precipitating supercoiled plasmid DNA with a second hexadecyltrimethylammonium-induced precipitation;    (h) redissolving the supercoiled plasmid DNA in a well defined buffer of optimized ionic strength and salt composition;    (i) adsorbing residual impurities onto calcium silicate within the buffer of step (h);    (j) precipitating supercoiled plasmid DNA with ethanol;    (k) filtering to collect and wash the precipitate;    (l) drying to remove ethanol;    (m) redissolving purified supercoiled plasmid DNA in a physiologically acceptable formulation buffer; and,    (n) sterilizing by filtration through a 0.22 μm filter.    
     
     
         41 . A method of  claim 40  wherein steps (j)-(n) are omitted and the buffer of step (i) is washed, sterilized and the DNA is concentrated by ethanol precipitation, resulting in a powder precipitate containing the supercoiled plasmid DNA.  
     
     
         42 . The method of  claim 40  wherein the microbial cells of step (b) are heated in step (c) to a temperature from about 70° C. to about 80° C.  
     
     
         43 . A method of  claim 42  wherein hexadecyltrimethylammonium bromide is added in a two step process, wherein a first hexadecyltrimethylammonium-induced precipitation occurs to precipitate out debris and non-supercoiled plasmid DNA and a second hexadecyltrimethylammonium bromide-induced precipitation occurs to precipitate the supercoiled plasmid DNA.  
     
     
         44 . A method of  claim 43  wherein the first and the second hexadecyltrimethylammonium bromide-induced precipitation steps occur in a standard STET buffer.  
     
     
         45 . The method of  claim 41  wherein the microbial cells of step (b) are heated in step (c) to a temperature from about 70° C. to about 80° C.  
     
     
         46 . A method of  claim 45  wherein hexadecyltrimethylammonium bromide is added in a two step process, wherein a first hexadecyltrimethylammonium-induced precipitation occurs to precipitate out debris and non-supercoiled plasmid DNA and a second hexadecyltrimethylammonium bromide-induced precipitation occurs to precipitate the supercoiled plasmid DNA.  
     
     
         47 . A method of  claim 46  wherein the first and the second hexadecyltrimethylammonium bromide-induced precipitation steps occur in a standard STET buffer.  
     
     
         48 . A method for the purification of supercoiled plasmid DNA from a cell lysate of a large scale microbial fermentation, which comprises: 
 (a) harvesting microbial cells from a fermentation broth;    (b) adding to the harvested microbial cells a sufficient amount of a lysis solution;    (c) heating the microbial cells of step b) to a temperature between 70° C. and 100° C. in a flow-through heat exchanger to form a cell lysate;    (d) cooling the cell lysate;    (e) clarifying the cell lysate using filtration with diatomaceous earth;    (f) precipitating supercoiled plasmid DNA with hexadecyltrimethylammonium;    (g) redissolving the supercoiled plasmid DNA in a well defined buffer of optimized ionic strength and salt composition;    (h) adsorbing residual impurities onto calcium silicate within the buffer of step (g);    (i) precipitating supercoiled plasmid DNA with ethanol;    (j) filtering to collect and wash the precipitate;    (k) drying to remove ethanol;    (l) redissolving purified supercoiled plasmid DNA in a physiologically acceptable formulation buffer; and,    (m) sterilizing by filtration through a 0.22 μm filter.    
     
     
         49 . A method of  claim 48  wherein steps (j)-(n) are omitted and the buffer of step (i) is washed, sterilized and the DNA is concentrated by ethanol precipitation, resulting in a powder precipitate containing the supercoiled plasmid DNA.  
     
     
         50 . The method of  claim 48  wherein the microbial cells of step (b) are heated in step (c) to a temperature from about 70° C. to about 80° C.  
     
     
         51 . A method of  claim 50  wherein the first and the second hexadecyltrimethylammonium bromide-induced precipitation steps occur in a standard STET buffer.  
     
     
         52 . The method of  claim 49  wherein the microbial cells of step (b) are heated in step (c) to a temperature from about 70° C. to about 80° C.  
     
     
         53 . A method of  claim 52  wherein the first and the second hexadecyltrimethylammonium bromide-induced precipitation steps occur in a standard STET buffer.  
     
     
         54 . A method for the purification of supercoiled plasmid DNA from a cell lysate of a large scale microbial fermentation, which comprises: 
 (a) harvesting microbial cells from a fermentation broth;    (b) adding to the harvested microbial cells a sufficient amount of lysozyme/alkaline/KOAc to promote cell lysis, forming a cell lysate;    (c) clarifying the cell lysate using filtration with diatomaceous earth;    (d) precipitating residual cell debris and impurities with a first hexadecyltrimethylammonium-induced precipitation;    (e) selectively precipitating supercoiled plasmid DNA with a second hexadecyltrimethylammonium-induced precipitation;    (f) redissolving the supercoiled plasmid DNA in a well defined buffer of optimized ionic strength and salt composition;    (g) adsorbing residual impurities onto calcium silicate with the buffer of step (f);    (h) precipitating supercoiled plasmid DNA with ethanol;    (i) filtering to collect and wash the precipitate;    (j) drying to remove ethanol;    (k) redissolving purified supercoiled plasmid DNA in a physiologically acceptable formulation buffer; and,    (l) sterilizing by filtration through a 0.22 μm filter.    
     
     
         55 . A method of  claim 54  wherein steps (h)-(l) are omitted and the remaining buffer of step (i) is washed, sterilized and the supercoiled plasmid DNA is concentrated by ethanol precipitation, resulting in a powder precipitate containing the supercoiled plasmid DNA.  
     
     
         56 . A method of  claim 53  wherein hexadecyltrimethylammonium bromide is added in a two step process, wherein a first hexadecyltrimethylammonium-induced precipitation occurs to precipitate out debris and non-supercoiled plasmid DNA and a second hexadecyltrimethylammonium bromide-induced precipitation occurs to precipitate the supercoiled plasmid DNA.  
     
     
         57 . A method of  claim 56  wherein the first and the second hexadecyltrimethylammonium bromide-induced precipitation steps occur in a standard STET buffer.  
     
     
         58 . A method of  claim 55  wherein hexadecyltrimethylammonium bromide is added in a two step process, wherein a first hexadecyltrimethylammonium-induced precipitation occurs to precipitate out debris and non-supercoiled plasmid DNA and a second hexadecyltrimethylammonium bromide-induced precipitation occurs to precipitate the supercoiled plasmid DNA.  
     
     
         59 . A method of  claim 58  wherein the first and the second hexadecyltrimethylammonium bromide-induced precipitation steps occur in a standard STET buffer.  
     
     
         60 . A method for the purification of supercoiled plasmid DNA from a cell lysate of a large scale microbial fermentation, which comprises: 
 (a) harvesting microbial cells from a large scale fermentation;    (b) adding to the harvested microbial cells a sufficient amount of lysozyme/alkaline/KOAc to promote cell lysis, forming a cell lysate;    (c) clarifying the cell lysate using filtration with diatomaceous earth;    (d) precipitating supercoiled plasmid DNA with hexadecyltrimethylammonium;    (e) redissolving the supercoiled plasmid DNA in a well defined buffer of optimized ionic strength and salt composition;    (f) adsorbing residual impurities onto hydrated, crystallized calcium silicate;    (h) precipitating supercoiled plasmid DNA with ethanol;    (i) filtering to collect and wash the precipitate;    (j) drying to remove ethanol;    (k) redissolving purified supercoiled plasmid DNA in a physiologically acceptable formulation buffer; and,    (l) sterilizing by filtration through a 0.22 μm filter.    
     
     
         61 . A method of  claim 60  wherein steps (j)-(n) are omitted and the buffer of step (i) is washed, sterilized and the DNA is concentrated by ethanol precipitation, resulting in a powder precipitate containing the supercoiled plasmid DNA.  
     
     
         62 . A method of  claim 60  wherein the first and the second hexadecyltrimethylammonium bromide-induced precipitation steps occur in a standard STET buffer.  
     
     
         63 . A method of  claim 61  wherein the first and the second hexadecyltrimethylammonium bromide-induced precipitation steps occur in a standard STET buffer.