Abstract:
The present invention relates to a method for isolating nucleic acid from a sample. Known methods for the isolation of nucleic acid from these materials may comprise the use of a chaotropic substance, for example to lyse cells present in the starting material, and free the nucleic acid therefrom. When a nucleic acid containing material is treated with a chaotrope and contacted with a nucleic acid binding solid phase, the nucleic acid will bind to the solid phase in the presence of the chaotrope and the solid phase with the nucleic acid bound thereto can thus be separated from the remainder of the sample. The method of the present invention for the isolation of nucleic acid from nucleic acid containing starting material is a method wherein the starting material is contacted with a chaotropic substance and, either simultaneously or subsequently, with a nucleic acid binding solid phase, where after the nucleic acid binding solid phase is subjected to a washing procedure and, optionally, the nucleic acid is eluted from the nucleic acid binding solid phase, characterized in that the washing procedure comprises the steps of washing the solid phase with subsequently ode ore more high salt buffer solution(s), optionally an alcoholic solution and a low salt buffer solution.

Description:
This is the national phase application of PCT/E99/00482, filed Jan. 26, 1999. 
    
    
     FIELD OF THE INVENTION 
     The present invention relates to a method for isolating nucleic acid from a sample. 
     BACKGROUND OF THE INVENTION 
     Recent developments in molecular biology such as, nucleic acid amplification methods, recombinant DNA techniques and sequencing methods rely on isolated nucleic acids as input material. Thus there is an ongoing need to improve the methods presently used for the purification of nucleic acid from complex samples. Of course these methods should be as simple and fast as possible and should result in a high recovery of the nucleic acid from the starting material. Furthermore it would be desirable to have methods that can be readily automated. Starting materials from which DNA is to be isolated are usually complex biological materials in which the nucleic acid is present surrounded by cellular material such as proteins or lipids. Such materials may be, for example, whole blood, blood serum, buffy coat, urine, faeces, liquor cerebrospinalis, sperm, saliva, cell cultures etc. 
     Known methods for the isolation of nucleic acid from these materials may comprise the use of a chaotropic substance, for example to lyse cells present in the starting material, and free the nucleic acid therefrom. By chaotropic substance is meant any substance capable of altering the secondary, tertiary and/or quatemary structure of proteins and nucleic acids, but leaving at least the primary structure intact. Examples of chaotropic substances are guanidinium (iso) thiocyanate and guanidine hydrochloride. Also sodium iodine, potassium iodine, sodium (iso)thiocyanate, urea or mutual combinations therewith are suitable. 
     When a nucleic acid containing material is treated with a chaotrope and contacted with a nucleic acid binding solid phase, the nucleic acid will bind to the solid phase in the presence of the chaotrope and the solid phase with the nucleic acid bound thereto can thus be separated from the remainder of the sample. Solid phases used in these processes usually comprise siliceous material such as glass particles, either porous or non-porous, silica gel, glass fiber, filters made of siliceous material, diatomeceous earth, etc. Such a method, based on the use of a chaotropic substance and a nucleic acid binding solid phase is described in EP389063, the contents of which are herewith incorporated by reference. In this patent a method for the isolation of nucleic acid is described based on the use of a chaotropic substance and silica or a derivative thereof. The method can be used for the isolation of nucleic acid from complex biological starting material. With the method as described in EP 389063 nucleic acid is bound to silica in the presence of a chaotrope. Thereafter the solid phase with the nucleic acid bound thereto is separated from the liquid and washed. 
     In practice, washing is usually performed in a sequence of washing steps, The solid phase is usually washed with a high salt buffer, that resembles the binding buffer in its constitution. One or more wash step with a lower alkyl alcohol, such as ethanol 70% are part of the washing procedure, to remove proteins, lipids and the like that may also have been bound to the silica. The washing procedure may also involve an additional wash step with acetone to remove any remaining impurities from the silica. The volatile acetone is removed again by drying the solid phase prior to the elution of the nucleic acid therefrom with a low salt buffer. 
     Prior art procedures have the disadvantage that they are still rather time consuming due to these complicated washing procedures involved. Especially the use of organic solvents like acetone also makes it more difficult to automate the process. The volatile nature of the solvents used puts severe constraints on a possible apparatus to be designed for performing these methods in an automated manner. 
     Thus a need exists for methods that are less complicated as far as the washing procedure is concerned and thus easier to perform in an automated manner. The present invention provides such a method. The present invention resembles prior art methods in that it is based on the binding of nucleic acid to a solid phase in the presence of a chaotropic substance. However, with the method of the present invention the washing procedure has been simplified and the need for washing with acetone or drying the solid phase prior to elution is eliminated. 
     SUMMARY OF THE INVENTION 
     The method of the present invention for the isolation of nucleic acid from nucleic acid containing starting material is a method wherein the starting material is contacted with a chaotropic substance and, either simultaneously or subsequently, with a nucleic acid binding solid phase, where after the nucleic acid binding solid phase is subjected to a washing procedure and, optionally, the nucleic acid is eluted from the nucleic acid binding solid phase, characterized in that the washing procedure comprises the steps of washing the solid phase with subsequently 
     one or more high salt buffer solution(s) 
     optionally an alcoholic solution 
     a low salt buffer solution. 
     DETAILED DESCRIPTION OF THE INVENTION 
     In nucleic acid isolation methods guanidine(iso)thiocyanate is often used in lysis buffers. 
     However, in cases where the nucleic acid to be isolated is intended to be used as input material for amplification reactions the guanidine ions may disturb the amplification reaction if they are not washed away properly. The high salt buffer used in the washing procedure of the method of the present invention preferably is NaSCN. By washing with NaSCN the guanidine ions that were present in the lysis buffer are replaced by natrium (sodium) ions of the high salt wash buffer. 
     With the method of the invention(one on the high salt buffer(s) used may comprise 1-10 M NaSCN/10 mM tris. The pH of such buffers may vary from 6 to 8 with an optimum around 6.5. Good results were obtained with a buffer having a NaSCN concentration of 10 2-5M/10 mM tris and a pH of 6.5. 
     Another high salt buffer that may be used in the washing procedure that is part of the method of the present invention may comprise NaCl preferably in a concentration between 1-10M. A preferred NaCl buffer comprises 2-5M NaCl/10 mM tris and has a pH of about 6.5. 
     To facilitate the transfer from chaotropic high salt buffer to the low salt buffer used in the washing procedure, it is advantageous to wash the solid phase with the nucleic acid bound thereto first with a NaSCN containing buffer (which will result in the replacement of guanidine ions by natrium ions) and subsequently with a NaCl buffer (resulting in the replacement of thiocyanate with chloride ions). 
     Thus the washing procedure may comprise the subsequent steps of, 
     washing with a first high salt buffer comprising 1-10M NaSCN/10 mM tris, with a pH approximately between 6 and 8 and 
     washing with a second high salt buffer comprising 1-10M NaCl/10 mM tris, with a pH approximately between 6 and 8, with a preference for a concentration of 2-5M of NaSCN and NaCl respectively and a pH of 6.5 for both buffers. 
     The wash steps with the high salt buffers may be followed by washing with a lower alkyl alcohol, for example, ethanol or isopropanol, to decrease the concentration of the salts (i.e. NaSCN and NaCl) from the solid phase in the sample. Furthermore, the alcohol wash steps decrease the concentration of lipids in the sample. In the case ethanol is used the preferred concentration range is about 60-70% ethanol. A most preferred concentration of ethanol is 63%. In the case of isopropanol an concentration of about 50% is preferred. The method may comprise more than one wash step with the alcoholic solution. Good results were obtained with a method comprising two subsequent washes with 70% ethanol. 
     The washing procedure of the method according to the present invention involves washing with a low salt buffer solution after washing with (one or more) high salt buffer(s) and optionally with a lower alkyl alcohol. With the use of the low salt buffer ethanol is removed from the solid phase. The use of the low salt buffer eliminates the need for an acetone wash and subsequent drying prior to elution of the nucleic acid from the solid phase. Elution normally is carried out with a low salt buffer or water. It is therefore surprising that the washing of the solid phase with a low salt buffer solution as performed with the method according to the invention, does not result in elution of a substantial part of the nucleic acid from the solid phase. 
     A preferred low salt buffer used with the method of the invention comprises 2-30 mM NaCl/10 mM tris. Good results were obtained with a low salt buffer comprising 15 mM NaCl/10 mM tris and having a pH of 6-8. 
     After washing with the low salt buffer, the nucleic acid may directly be eluted from the solid phase. It has been found that the addition of a weak chaotrope, for example betaine, to the elution buffer has an advantageous effect on the elution. When betaine is used in the elution buffer, the concentration may be around 3 M. Stronger chaotropes may be used in the elution buffer as well, be it in lower concentrations. Any chaotropic agent that is used to enhance the elution of the nucleic acid from the solid phase must be added at concentration that does not disturb any downstream use of the nucleic acid, for instance in nucleic acid amplification methods or direct hybridization methods. 
    
    
     BRIEF DESCRIPTION OF THE FIGURES 
     FIG.  1 : The ECL signals after nucleic acid isolation by the alternative method (alt.) and the Boom method, followed by NASBA amplification and ECL detection. In vitro transcribed HIV-RNA was spiked in plasma. 
     FIG.  2 : In the alternative isolation method different high salt solutions were analyzed. In vitro transcribed HIV-1 RNA was spiked in plasma and the different buffers in the wash steps were tested. Summarized are the RNA recoveries after quantitative amplification and ECL detection. The samples were tested in quadruplicate. 
     FIG.  3 : Analyses of the wash buffer at different pH and the elution buffer at different pH. RNA recoveries after quantitative amplification and detection by ECL. 
     FIG.  4 : Percentage RNA isolated with the new protocol with and without betaine, compared to the standard protocol Boom. The percentage RNA was determined against the 100% samples The experiments were performed in triplicate. 
    
    
     EXAMPLES 
     Preface 
     The following examples demonstrate the mechanism and utility of the present invention. They are not limiting and should not be considered as such. Standard isolations were performed according to protocol Y described in EP389063 and by Boom et al. (1990 , J. Clin. Microbiol . 28: 495-503), and is further referred to as the Boom protocol. 
     Analysis of the isolated nucleic acids was performed by several methods described in the examples. In case where the analysis is performed with the NASBA nucleic acid amplification method the following ingredients and conditions were used: 40 mM tris, pH 8.5, 70 mM KCl, 12 mM MgCl 2 , 5 mM DTT, 1 mM each dNTP, 2 mM rATP, 2 mM rCTP, 2 mM rUTP, 1.5 mM rGTP, 0.5 mM ITP, 0.2 μM each oligonucleotide, 375 mM sorbitol, 0.105 g/l BSA, 6.4 units AMV-RT, 32 units T7 RNA polymerase, 0.08 units  E. coli  RNase H and a specified amount of template (i.e. isolated nucleic acid) in 20 μl volume. The protocol that was used consisted of mixing the isolated nucleic acid with the ingredients described above except for the enzymes, heating to 65° C. for 5 minutes, cooling to 41° C., addition of enzymes and incubation at 41° for 90 minutes. 
     Amplifications with NASBA were done with control RNA&#39;s (internal standards, named Qa, Qb and Qc, respectively), with known concentrations, which were added before the amplification. Also a sample (called a 100% sample) was amplified with the same internal standards, without being subjected to nucleic acid isolation. This must represent the theoretical signal for a recovery in the isolation of 100%. The detection of the amplification products was done by electrochemiluminescense according to previously described protocols (B. van Gemen et al., 1994, A one-tube quantitative HIV-1 RNA NASBA nucleic acid amplification assay using electrochemiluminescent (ECL) labeled probes.  J. Virol. Methods . 49: 157-168). 
     Radioactive labeled RNA ( 32 P labeled RNA) was made by standard in vitro transcription protocols with incorporation of  32 P-ATP in the RNA. The different fractions of the isolation method used (see examples) were analyzed for the presence of  32 P-RNA in a liquid scintillation counter. 
     Example 1 
     In the standard Boom isolation, the nucleic acids are eluted from the solid phase in water or 1 mM tris. An alternative, new protocol was used, with surprising results (FIG. 
     1). The alternative protocol consisted of the following steps: 
     Binding of the nucleic acid to silica in the Boom lysis buffer. 
     Washing two times with high salt solution (5M NaSCN) 
     Washing two times with low salt solution (15 mM NaCl) elution with H 2 O 
     In a preliminary experiment (FIG. 1) this alternative protocol seemed to result in yields that are comparable with the standard Boom isolation protocol. In subsequent examples the protocol is worked out in more detail. 
     Example 2 
     Different solutions with high salt concentrations are analyzed in the aforementioned alternative protocol in the first washing steps. Isolations were performed with 10 5  molecules in vitro transcribed HIV-1 RNA spiked in plasma. After washing with the different salt solutions (see FIG. 2) and elution with H 2 O, amplification with internal standard RNA&#39;s (2×10 4  Qa and 5×10 3  Qb) was performed. The quantitative detection of amplicons was done by ECL, the results are depicted in FIG.  2 . 
     Washing with 2 and 5 M NaSCN is both possible, with the wash steps with 5 M NaSCN being a little better in terms of yield compared to the 2 M NaSCN wash steps. Also NaSCN seems to give more yield than NaCl in these high salt wash steps. 
     Example 3 
     To determine the optimal pH of the washing and elution buffer in the alternative isolation procedure, isolations with different pH of the low salt buffer and the elution buffer were performed. The washing buffers were 15 mM NaCl in 10 mM tris with different pH and the elution buffers were 10 mM tris with different pH. 
     To 3.6 ml lysis buffer 0.4 ml plasma, 3.2×10 6  molecules in vitro transcribed HIV-1 RNA and 800 μl silica were added. The silica was washed two times with 5 M NaSCN/10 mM tris, pH 7. The silica was aliquoted into 4 tubes and each tube was washed twice with a different pH wash buffer. Again the silica from each tube was aliquoted into 4 equal parts and incubated with elution buffer with different pH. From the results depicted in FIG. 3 it seemed that washing with 15 mM NaCl/10 mM tris at pH 6, 7 or 8 gave comparable results. The elution buffer can best have pH 8 or 9. 
     Example 4 
     To check the efficiency of the different steps in the alternative isolation protocol RNA was labeled with  32 P ATP and spiked in plasma. By labeling the RNA it can be followed perfectly throughout the procedure and can be measured in all the different steps of the isolation. 
     Purified,  32 P labeled in vitro transcribed HIV-1 RNA was spiked in plasma. Isolation was performed according to the alternative procedure described above with 5M NaSCN (2×), 15 mM NaCl/10 mM tris, pH 7 (2×) and elution with 10 mM tris, pH 8.5. From each step 50 μl was added to 3 ml scintillation fluid and counted in the scintillator. 
     From the results (table 1) it became clear that not all the labeled material was bound to the silica. Also in the first 15 mM NaCl/10 mM tris wash step much material was lost. Further, it appeared that not all the labeled material was eluted from the silica. 
     In comparable experiments with the Boom isolation it was also observed that not all the material was eluted from the silica. 
     
       
         
               
             
               
               
             
               
               
               
               
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 Analyses of the wash steps in the alternative isolation. Percentage 
               
               
                 RNA in each wash step for six different samples. 
               
             
          
           
               
                   
                 Sample 
               
             
          
           
               
                 Wash step of the isolation 
                 1 
                 2 
                 3 
                 4 
                 5 
                 6 
               
               
                   
               
               
                 Lysis 
                 56%  
                 60%  
                 51%  
                 52%  
                 48%  
                 45%  
               
               
                 5M NaSCN 
                 1% 
                 1% 
                 1% 
                 1% 
                 1% 
                 1% 
               
               
                 5M NaSCN 
                 0% 
                 0% 
                 0% 
                 0% 
                 0% 
                 0% 
               
               
                 15 mM NaCl/10 mM Tris 
                 28%  
                 24%  
                 33%  
                 29%  
                 33%  
                 36%  
               
               
                 15 mM NaCl/10 mM Tris 
                 0% 
                 0% 
                 2% 
                 1% 
                 3% 
                 4% 
               
               
                 10 mM tris pH = 8.5 
                 5% 
                 5% 
                 5% 
                 5% 
                 5% 
                 5% 
               
               
                 silica 
                 10%  
                 10%  
                 9% 
                 11%  
                 10%  
                 10%  
               
               
                   
               
             
          
         
       
     
     Example 5 
     In the following example next to the introduction of the 70% ethanol wash step a comparison was made between washing with 5M NaSCN and 5M NaCl. All samples were tested in duplicate. Again, purified,  32 P labeled in vitro transcribed HIV-1 RNA was spiked in plasma and used as input for the isolation. In the isolation, washing was done with either 5M NaSCN or 5M NaCl followed by two times washing with 70% ethanol and two times with 15 mM NaCl/10 mM tris, pH 6.5. Elution was done with 10 mM tris, pH 8.5. 
     
       
         
               
             
               
               
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 Analyses of the wash steps in the new isolation procedure. Percentage 
               
               
                 RNA in each wash step for two different samples in two different 
               
               
                 methods. A) for washing with 5 M NaSCN and B) for washing 
               
               
                 with 5 M NaCl. 
               
             
          
           
               
                   
                 Sample 
                   
               
             
          
           
               
                   
                 Wash buffer 
                 A1 
                 A2 
                 B1 
                 B2 
               
               
                   
                   
               
               
                   
                 Lysis-buffer 
                 48%  
                 60%  
                 39%  
                 38%  
               
               
                   
                 5 M NaSCN 
                 0% 
                 0% 
               
               
                   
                 5 M NaCl 
                   
                   
                 2% 
                 2% 
               
               
                   
                 Ethanol 70% 
                 0% 
                 0% 
                 0% 
                 0% 
               
               
                   
                 Ethanol 70% 
                 0% 
                 0% 
                 0% 
                 0% 
               
               
                   
                 15 mM NaCl/10 mM Tris 
                 4% 
                 5% 
                 2% 
                 0% 
               
               
                   
                 15 mM NaCl/10 mM Tris 
                 0% 
                 0% 
                 0% 
                 0% 
               
               
                   
                 10 mM Tris 
                 4% 
                 2% 
                 9% 
                 12%  
               
               
                   
                 Silica-pellet 
                 44%  
                 25%  
                 36%  
                 37%  
               
               
                   
                   
               
             
          
         
       
     
     Analysis of the results (table 2) revealed a slight loss of material in the wash step with 5M NaCl and no loss of material with 5M NaSCN and with 70% ethanol. In the first wash with 15 mM NaCl/10 mM tris pH 6.5 about 4% of the material was lost in all cases. A better elution was obtained by washing with 5M NaCl and less material was lost in the 15 mM NaCl/10 mM tris, pH 6.5. 
     Example 6 
     In the standard isolation procedure according to “Boom” elution of the nucleic acid from the silica is done with either H 2 O or 1 mM tris, pH=8.5. Elution with different concentrations of NaCl were tested in H 2 O, 1 mM tris (pH=8.5). and 10 mM tris, pH 8.5. For each buffer 18 samples were isolated with 2×10 5  molecules in vitro transcribed HIV-1 RNA and two no template samples from plasma. Elution with different NaCl concentrations were tested in triplicate. After the isolation the samples were quantified by NASBA amplification with internal standard RNA&#39;s (10 4  Qa and 10 3  Qb). 
     
       
         
               
             
               
               
               
               
               
               
             
               
               
               
               
               
               
               
               
               
               
               
               
             
           
               
                 TABLE 3 
               
               
                   
               
             
             
               
                 The percentage nucleic acid recovery after standard Boom isolation with 
               
               
                 different amounts of salt in the elution buffer. Elution was performed with different NaCl 
               
               
                 concentrations in water, 1 mM Tris (pH = 8.5) and 10 mM Tris (pH = 8.5). The conditions 
               
               
                 were tested in triplicate. 
               
             
          
           
               
                 Concentration 
                   
                   
                   
                   
                 10 mM 
               
               
                 NaCl in the 
                 Water 
                   
                 1 mM TRIS pH 8.5 
                   
                 TRIS pH 8.5 
               
             
          
           
               
                 elution buffer 
                 1 
                 2 
                 3 
                   
                 1 
                 2 
                 3 
                   
                 1 
                 2 
                 3 
               
               
                   
               
               
                  0 mM NaCl 
                 78%  
                 150%  
                 69%  
                   
                 9% 
                 16%  
                 9% 
                   
                 11% 
                 30% 
                 17% 
               
               
                  2 mM NaCl 
                 1% 
                 2% 
                 2% 
                   
                 0% 
                 15%  
                 22%  
                   
                 15% 
                 22% 
                 12% 
               
               
                  4 mM NaCl 
                 1% 
                 0% 
                 1% 
                   
                 0% 
                 0% 
                 4% 
                   
                 56% 
                 11% 
                 16% 
               
               
                  6 mM NaCl 
                 0% 
                 0% 
                 0% 
                   
                 0% 
                 0% 
                 16%  
                   
                 40% 
                 49% 
                 18% 
               
               
                  8 mM NaCl 
                 1% 
                 1% 
                 0% 
                   
                 0% 
                 3% 
                 0% 
                   
                 54% 
                 35% 
                 66% 
               
               
                 10 mM NaCl 
                 1% 
                 0% 
                 2% 
                   
                 0% 
                 0% 
                 1% 
                   
                  0% 
                 43% 
                 79% 
               
               
                   
               
             
          
         
       
     
     The results are summarized in table 3. The presence of NaCl in the elution with water interferes very strong with the elution of the RNA, no RNA was detected after amplification. In the elution with 1 mM tris only 4 mM NaCl is tolerated. In contrast, the effect of NaCl (up to 10 mM) in 10 mM tris with pH 8.5 seems to be minimal. 
     Example 7 
     To make a statistical assessment concerning the “quality” of the isolation a comparison of the efficiency of the new isolation protocol vs. the Boom protocol was made using 20 samples. For each sample 2×10 5  copies in vitro transcribed HIV-1 RNA were spiked in plasma. Elution was performed in 100 μl H 2 O in the standard Boom protocol. After binding of the RNA to the silica, the new protocol existed of washings with 5M NaSCN, 5M NaCl, 70% ethanol (2×), 15 mM NaCl/10 mM tris pH=6.5 (2×) and elution in 10 mM tris, pH 8.5. After the isolation a quantitative NASBA amplification was performed by adding 10 4  Qa and 10 5  Qb RNA molecules as internal standards. 
     
       
         
               
             
               
               
               
             
           
               
                 TABLE 4 
               
             
             
               
                   
               
               
                 The statistical figures of the isolation of 20 samples with the Boom 
               
               
                 method and the protocol Z. 
               
               
                 (avg = average; std = standard deviation; cv = variation coefficient) 
               
             
          
           
               
                 Definition/method 
                 BOOM 
                 New protocol 
               
               
                   
               
               
                 avg 
                 42,4 
                 18,1 
               
               
                 std 
                 18,5 
                  8,9 
               
               
                 cv 
                   44% 
                   49% 
               
               
                   
               
             
          
         
       
     
     From these results the yield of the isolation according Boom appeared to be better (avg. 42%) compared to the protocol Z yield (avg. 18%). 
     Example 8 
     The new protocol could become much better with a more efficient elution. For the investigation of improved elution in the new protocol purified,  32 P labeled in vitro transcribed HIV-1 RNA was spiked in plasma. Isolation was performed according the above outlined new protocol (but with only one 15 mM NaCl/10 mM tris washing) and different solutions were tested in the elution step. Analyzed were 10 mM tris elution (pH=9) with the addition of 10 or 100 mM NaSCN or 100 or 3000 mM N,N,N trimethylglycine (betaine). Also the effect of an extra washing step with 15 mM NaCl/10 mM tris, pH 6.5 just prior to elution was investigated. 
     The elution was improved (table 5) by addition of 100 mM NaSCN or 3 M betaïne to the elution buffer. 
     
       
         
               
             
               
               
             
               
               
               
               
               
               
               
             
           
               
                 TABLE 5 
               
             
             
               
                   
               
               
                 Analyses of different elution buffers in the alternative isolation. Depicted 
               
               
                 in the table is the percentage RNA measured in each fraction. 
               
             
          
           
               
                   
                 Sample 
               
             
          
           
               
                 Wash buffer 
                 1 
                 2 
                 3 
                 4 
                 5 
                 6 
               
               
                   
               
               
                 Lysis buffer 
                 4% 
                 6% 
                 7% 
                 4% 
                 5% 
                 4% 
               
               
                 5M NaSCN 
                 1% 
                 1% 
                 1% 
                 1% 
                 1% 
                 1% 
               
               
                 5M NaCl 
                 0% 
                 0% 
                 0% 
                 0% 
                 0% 
                 0% 
               
               
                 Ethanol 70% 
                 0% 
                 0% 
                 0% 
                 0% 
                 0% 
                 0% 
               
               
                 Ethanol 70% 
                 0% 
                 0% 
                 0% 
                 0% 
                 0% 
                 0% 
               
               
                  15 mM NaCl/10 mM Tris 
                 4% 
                 4% 
                 8% 
                 6% 
                 12%  
                 9% 
               
               
                  15 mM NaCl/10 mM Tris 
                 0% 
               
               
                  10 mM Tris 
                 4% 
               
               
                  10 mM NaSCN/10 mM Tris 
                   
                 0% 
               
               
                 100 mM NaSCN/10 mM Tris 
                   
                   
                 57%  
               
               
                 100 mM betaine/10 mM Tris 
                   
                   
                   
                 1% 
               
               
                 3M betaine/10 mM Tris 
                   
                   
                   
                   
                 62%  
               
               
                 Elution buffer 
                   
                   
                   
                   
                   
                 6% 
               
               
                 Silica-pellet 
                 86%  
                 88%  
                 25%  
                 87%  
                 19%  
                 79%  
               
               
                   
               
             
          
         
       
     
     Example 9 
     To analyze the relative improvement of the new protocol by the addition of betaine to the elution buffer, isolation experiments were performed according to the new protocol, with or without betaïne in the elution buffer. As a control also three samples were isolated according to the standard Boom protocol. For each sample 2×10 5  molecules in vitro transcribed HIV-1 RNA were spiked in plasma. The Boom protocol was performed with elution in 100 μl H2O. After binding of the RNA to the silica, the new protocol existed of washings with 5M NaSCN, 5M NaCl, 70% ethanol (2×), 15 mM NaCl/10 mM tris, pH 6.5 and elution with 3M betaïne in 10 mM tris, pH 8.5. After the isolation a quantitative amplification was performed by adding 10 4  Qa and 5×10 3  Qb RNA molecules as internal standards. 
     From these results (FIG. 4) it was obvious that the addition of betaïne in the isolation improved the elution in the new protocol. The new protocol was as efficient as the standard Boom protocol. 
     Example 10 
     To be able to make a statistical evaluation and comparison between new protocol and the standard Boom protocol, 10 samples were analyzed by each protocol. For each example 2×10 5  molecules in vitro transcribed HIV-1 RNA were spiked in plasma. The Boom protocol was performed with elution in 100 μl H 2 O. After binding of the RNA to the silica, the new protocol existed of washings with 5M NaSCN, 5M NaCl, 70% ethanol (2×), 15 mM NaCl/10 mM tris, pH 0.5 and elution with 3M betaine in 10 mM tris, pH 8.5. After the isolation a quantitative amplification was performed by adding 10 4  Qa and 5×10 3  Qb RNA molecules as internal standards. The results are summarized in table 6 and table 7. By statistical calculations the two methods proof to be identical in performance. 
     
       
         
               
             
               
               
               
               
               
               
               
               
             
           
               
                 TABLE 6 
               
             
             
               
                   
               
               
                 ECL counts for the RNA&#39;s after the NASBA amplification and the average 
               
               
                 of these signals. The in vitro transcribed HIV-1 RNA is denoted as wt in this table. 
               
             
          
           
               
                   
                   
                   
                   
                 new 
                   
                   
                   
               
               
                 Boom: 
                 Q A   
                 Q B   
                 wt 
                 protocol: 
                 Q A   
                 Q B   
                 wt 
               
               
                   
               
               
                 1 
                 797839 
                 873594 
                 366947 
                 1 
                 669353 
                 971196 
                 349116 
               
               
                 2 
                 849519 
                 883281 
                 190842 
                 2 
                 723736 
                 838659 
                 302830 
               
               
                 3 
                 865491 
                 842505 
                 264414 
                 3 
                 756767 
                 841488 
                 264288 
               
               
                 4 
                 738739 
                 974851 
                 381059 
                 4 
                 737875 
                 906776 
                 276051 
               
               
                 5 
                 891318 
                 963281 
                  87410 
                 5 
                 791250 
                 859990 
                 247159 
               
               
                 6 
                 841075 
                 863602 
                 279727 
                 6 
                 755119 
                 979499 
                 238056 
               
               
                 7 
                 780242 
                 803434 
                 226597 
                 7 
                 683193 
                 890830 
                 297602 
               
               
                 8 
                 715077 
                 890399 
                 371066 
                 8 
                 836213 
                 807986 
                  96754 
               
               
                   
                   
                   
                   
                 9 
                 739428 
                 730010 
                 236861 
               
               
                 average 
                 809913 
                 886868 
                 271008 
                 average 
                 743659 
                 869604 
                 256524 
               
               
                   
               
             
          
         
       
     
     
       
         
               
             
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 7 
               
             
             
               
                   
               
               
                 Average the ECL signals of the internal standards and of the wt (HIV-1) 
               
               
                 RNA. Also is determined the standard deviation (std) of the RNA recovery 
               
               
                 and the variation coefficient. The ratio of the average ECL signal of the 
               
               
                 methods is also depicted in this table 
               
             
          
           
               
                   
                 Boom: 
                 new protocol: 
                 Ratio: 
               
               
                   
                   
               
             
          
           
               
                   
                 Q A : 
                 809913 
                 743659 
                 1,09:1 
               
               
                   
                 Q B : 
                 886868 
                 869604 
                 1,02:1 
               
               
                   
                 wt: 
                 271008 
                 256524 
                 1,06:1 
               
               
                   
                 % RNA isolated: 
                 33% 
                 32% 
               
               
                   
                 std 
                 12,12 
                 8,37 
               
               
                   
                 cv 
                 0,37 
                 0,26 
               
               
                   
                   
               
             
          
         
       
     
     Example 11 
     The same example as described above was performed with in vitro transcribed HCV RNA spiked in whole blood. For each sample 5.9×10 5  molecules HCV RNA were spiked in whole blood. The standard Boom protocol was performed with elution in 100 μl H 2 O. After binding of the RNA to the silica, the new protocol existed of washings with 5M NaSCN, 5M NaCl, 70% ethanol (2×), 15 mM NaCl/10 mM tris, pH 6.5 and elution with 3M betaïne in 10 mM tris, pH 8.5. After the isolation a quantitative amplification was performed by adding 10 4  Qe and 5×10 3  Qf RNA molecules as internal standards. 
     The results are shown in tables 8 and 9. Statistical calculations revealed that both methods proof to be identical 
     
       
         
               
             
               
               
               
               
               
               
               
               
             
           
               
                 TABLE 8 
               
             
             
               
                   
               
               
                 ECL counts for the RNA&#39;s after the NASBA amplification and the average 
               
               
                 of these signals. The in vitro transcribed HCV RNA is denoted as wt in this table. 
               
             
          
           
               
                   
                   
                   
                   
                 new 
                   
                   
                   
               
               
                 Boom: 
                 Q E   
                 Q F   
                 wt 
                 protocol: 
                 Q E   
                 Q F   
                 wt 
               
               
                   
               
               
                 1 
                 27486 
                 19826 
                 25112 
                 1 
                 102509 
                 52062 
                 27491 
               
               
                 2 
                 31549 
                 19906 
                 29220 
                 2 
                 189642 
                 70934 
                 79123 
               
               
                 3 
                 32152 
                 24979 
                 34910 
                 3 
                 114150 
                 50641 
                 39092 
               
               
                 4 
                 32416 
                 26361 
                 35251 
                 4 
                  89838 
                 108772  
                 63296 
               
               
                 5 
                 39094 
                 31323 
                 38752 
                 5 
                 128956 
                 60813 
                 52171 
               
               
                 6 
                 42471 
                 31955 
                 40001 
                 6 
                 114181 
                 43156 
                 92707 
               
               
                 7 
                 47300 
                 33755 
                 42681 
                 7 
                 183674 
                 61813 
                 71924 
               
               
                 8 
                 48125 
                 46406 
                 52939 
                 8 
                  18322 
                 57185 
                 38332 
               
               
                 9 
                 50074 
                 47738 
                 64116 
                 9 
                 176058 
                 82952 
                 18480 
               
               
                 10  
                 52082 
                 47813 
                   
                 10  
                 212759 
                 24901 
               
               
                 11  
                 54879 
                 51822 
                   
                 11  
                 183631 
                 56489 
               
               
                 average 
                 41603 
                 34717 
                 40331 
                 average 
                 137611 
                 60883 
                 53624 
               
               
                   
               
             
          
         
       
     
     
       
         
               
             
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 9 
               
             
             
               
                   
               
               
                 Average the ECL signals of the internal standards and of the wt (HCV) 
               
               
                 RNA. Also is determined the standard deviation (std) of the RNA recovery 
               
               
                 and the variation coefficient. The ratio of the average ECL signal of the 
               
               
                 methods is also depicted in this table. 
               
             
          
           
               
                   
                 Boom: 
                 new protocol: 
                 Ratio: 
               
               
                   
                   
               
             
          
           
               
                   
                 Q E : 
                 41603 
                 137611 
                 1:3,31 
               
               
                   
                 Q F : 
                 34717 
                 60883 
                 1:1,75 
               
               
                   
                 wt: 
                 40331 
                 53624 
                 1:1,33 
               
               
                   
                 % RNA isolated: 
                 8% 
                 5,67% 
               
               
                   
                 std 
                 2,49 
                 3,30 
               
               
                   
                 cv 
                 0,31 
                 0,58