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Regeneration of commercial nucleic acid The high surface density of the anion
groups on such chemically modified
extraction columns without the risk of silica resins makes the resins efficient
and highly selective for nucleic acids in
carryover contamination the presence of high salt concentration
and pH conditions. Commercial nucleic
Nagadenahalli B. Siddappa, Appukuttan Avinash, Mohanram acid extraction columns, therefore,
Venkatramanan, and Udaykumar Ranga ensure the highest level of nucleic acid
Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India recovery and purity with little technical
complication. Commercial nucleic
BioTechniques 42:186-192 (February 2007) acid extraction columns, however, are
doi 10.2144/000112327 expensive and are disposed of after a
single use. Considering the cost factor,
Nucleic acid extraction is a basic requirement in a molecular biology laboratory. In terms we set out to develop a procedure to
of purity and yield, commercial nucleic acid extraction columns are superior; however, they regenerate the commercial nucleic
are expensive. We report here an efficient strategy to regenerate diverse commercial col- acid extraction columns. We found that
umns for several rounds without altering the binding capacity of the columns or changing incubation of used commercial nucleic
the properties of the nucleic acids purified. Plasmids purified with regenerated columns were acid extraction columns in 1 M HCl for
functionally identical in super-coiled nature, restriction analysis, expression of the encoded 24 h can efficiently eliminate bound
reporter genes, or amplification of the viral RNA in real-time PCR. To ensure that the regen- DNA and regenerate them for a fresh
erated columns were free of the residual DNA, we used two different plasmids with different round of use. Applying this strategy,
drug-resistance markers. By colony plating and PCR amplification of the encoded genes, we the commercial nucleic acid extraction
show that the regeneration process is absolute. Using radiolabeled DNA, we demonstrate columns can be regenerated many
that DNA exposed to the regeneration reagent is fragmented to molecular weight below 36 times without a loss in the binding
bp. Our data collectively prove regeneration of the commercial columns without the concern capacity and, importantly, without the
of carryover contamination. A procedure to permit safe and efficient regeneration of the com- possibility of carryover contamination.
mercial columns is not only of great advantage to extend the lifetime of these columns but
also makes them commercially more affordable, especially in a resource-poor setting.
MATERIALS AND METHODS
mn
g plasmid DNA, consisting of 1 g
u m ed
rate
a
o lu
ilic
col rat
0.1 M HCl 1 M HCl
h c
n
reporter vector and 0.1 g pCMV--
ene
e
hs
gen
ca
s
s
Re g
si l i
Fre
M
Fre
0 5 min 1 h 4 24 48
Re
0 5 min 1 h 4 24 48
galactosidase expression vectorthe
latter included in all the transfections to
serve as an internal control for the trans-
fection efficiency. CEM-GFP cells were
electroporated using the Gene Pulser
II system (Bio-Rad Laboratories,
Hercules, CA, USA) at 240 V and 950 D E 40
F capacitance with a total of 5 g Fresh column 10 days 30 days
1 g cytomegalovirus (CMV)--galac- 10
A B C
Figure 2. Functional characterization of different plasmids extracted using regenerated columns. (A) Mammalian expression of alkaline phosphatase. HEK
293 cells were transiently transfected with pCMV-SEAP, and the levels of the alkaline phosphatase present in the spent media at three different time points were
determined. - Ve, cells transfected with an empty vector. (B) Virion production from mammalian cells. HEK 293 cells were transiently transfected with pINDIE,
a reference human immunodeficiency virus type 1 (HIV-1) subtype C molecular clone, and the amount of viral p24 antigen released into the culture medium was
quantified at three different time points using a commercial kit. (C) Tat transactivation assay. CEM-GFP cells, containing a reporter green fluorescent protein
(GFP) under the control of HIV-1 long terminal repeat (LTR), were electroporated with pCMV-Tat encoding the viral transactivator protein. Cells were fixed 72
h after transfection, and the expression of GFP was determined by flow cytometry (BD FACSCalibur; BD Biosciences, San Jose, CA, USA). The percentages
of cells positive for GFP expression are indicated. All the above experiments were repeated twice, and the data presented are from representative experiments.
(D) Evaluation of the column-extracted viral RNA in a real-time reverse transcription PCR (RT-PCR). Total RNA was extracted from the plasma samples of five
drug-nave HIV-1 seropositive donors (color-coded) using Qiagen columns, each in triplicate. The cycle threshold (CT) values have been illustrated in the table.
The experiment was performed two times, and the data are from one representative experiment. Essentially identical results were obtained with RNA extraction
columns from a different vendor (Auprep; Life Technologies, Invitrogen; data not presented). RFU, relative fluorescence units; A, absorbance.
performed using a High-Capacity cDNA Analysis of the Fate of the DNA tated overnight at -20C by adding 2
Archive kit (Applied Biosystems, Foster Exposed to Acid volumes of ethanol in the presence of
City, CA, USA). The reaction volume of 2 M ammonium acetate, pH 4.8. DNA
50 L contained 25 L extracted RNA, A plasmid pC-LTR-SIE was pellet was dissolved in 50 L Tris
500 ng/mL random hexamers, 125 U linearized and labeled with [- EDTA (TE), pH 8.0, normalized for
32P]dCTP in a standard random labeling
SuperScript Reverse Transcriptase the radioactivity counts, and resolved
(Invitrogen), 2 L 25 dNTP mix, 5 reaction using the NEBlot kit (New on a gradient polyacrylamide gel (6%
L 10 reverse transcription buffer, and England BioLabs, Ipswich, MA, USA) 15%). The gel was wrapped in a plastic
1 L RNase inhibitor. After denatur- and purified on a G-50 Sephadex film, directly exposed to a phosphor
ation of the RNA for 5 min at 95C, column. Labeled DNA was mixed with imager plate, and analyzed on an FLA-
cDNA was synthesized at 37C for 2 h. the same but unlabeled plasmid DNA 5000 Phosphor Imager (Fuji, Osaka,
TaqMan PCR was performed using 5 at a 1:50 ratio for the assay. Six fresh Japan).
L reverse transcription mix as template spin columns were loaded each with
and a primer pair targeting a 133-bp 10 g pulsed DNA and exposed to 200
sequence in the HIV-1 subtype-C long L 1 M HCl in a plastic vial in a way RESULTS AND DISCUSSION
terminal repeat (LTR). A TaqMan probe that the membrane is immersed in the
covalently attached to Cy5 at the 5 acid. The column-bound DNA was Regeneration of the Commercial
end and BHQ3 at the 3 end was used for treated for different periods ranging Columns
the detection. The reverse transcription from 0 min to 24 h. At the end of the
PCR (RT-PCR) was performed on an incubation, equal volume of 1 M Tris Previously we reported a strategy for
iCycler real-time thermal cycler buffer, pH 11.5, was added to each small-scale plasmid DNA extraction
(Bio-Rad Laboratories), and the cycle column, mixed well, and the column using silica (8). Preparation of the
threshold (CT) values were calculated was spun at full speed to collect the silica required incubation of the resin
using iCycler IQ software (Bio-Rad sample in the lower chamber. DNA was at a low pH to destroy resin-associated
Laboratories). eluted from the columns and precipi- DNA. To see if silica used once can be
min
min
in
h
in 1 M HCl for 4 h and compared it
0m
4h
1h
M
24
30
10
with fresh resin for the extraction of
plasmid DNA. Fresh and treated silica
Number of Colonies
both isolated plasmid DNA at compa-
rable levels (Figure 1A), suggesting
that the DNA binding property of the
resin was not acid-labile. We next
extended this regeneration technique to
Qiagen-tip 20 columns and identified 36 bp
that these columns could be regen- 27 bp
erated in the same manner (Figure 20 bp
1B). Following this observation, we Pl at e : A mp Kan Amp Kan
set up several experiments to optimize 7 bp
regeneration of the commercial nucleic Column: Regenerated Reu s e d
acid extraction columns from different and Used
suppliers. For consistency, bacterial
cultures containing plasmid vectors
sed d
d U ate
were grown to large volumes, the B
an ener
ed
us
cells were harvested, resuspended in
g
Re
Re
Buffer P1 (Qiagen), and then stored
in multiple aliquots in a deep freezer. 400 bp
M 1 0 4 1 0 3 1 0 2 1 0 1 0 .5 - 1 0 4 1 0 3 1 0 4 1 0 3 Copy no.
Aliquots were removed as required and 300 bp
Tat PCR (AmpR)
used for various experiments described 200 bp
below. 400 bp
p24 PCR (KanR)
300 bp
To identify the optimal concentration 200 bp
of HCl and the time of incubation
Figure 3. Regenerated columns do not carry over DNA to subsequent cycles of purification. (A)
needed to regenerate the columns, Regeneration process destroys the residual DNA. Two sets of columns were differentially treated to
we loaded several fresh columns with leave the contaminating plasmid (pCMV-p24-KanR) on one of the sets. A second plasmid (pCMV-Tat-
plasmid DNA. Columns with DNA AmpR) was extracted using both the sets, and transformed bacteria were seeded on LB agar plates sup-
bound on them were incubated in 0.1 plemented with ampicillin or kanamycin. The number of colonies developed on the plates was manually
determined. This experiment was repeated three times, and the data presented are from one representa-
or 1.0 M HCl for different periods; the tive experiment. The data are presented as mean of triplicate assays 1 sd (B) PCR-mediated detection
bound DNA was eluted with Buffer of the contaminating plasmid DNA. Plasmid preparations extracted above were diluted to defined copy
QF, and the DNA was resolved on numbers in the presence of carrier DNA and used as a template in a nested PCR for the detection of
a 1% agarose gel. Incubation of the Tat and p24 targets encoded by the AmpR and KanR plasmids, respectively (right panels). For positive
columns in 0.1 M HCl required 48 standards, the plasmids were subjected to a serial 10-fold dilution in the presence of carrier DNA to con-
tain defined number of copies as shown (left panels). M, DNA molecular weight standards (GeneRuler
h to completely eliminate the bound 100-bp DNA ladder; Fermentas), and the standard sizes are indicated. (C) Acid-treated DNA is degraded
plasmid DNA from the columns, on the column to low molecular weight fragments. Isotopically labeled plasmid DNA was loaded to the
whereas no plasmid DNA was found on columns and exposed to 1 M HCl for different periods as shown. Eluted DNA normalized for the radio-
the columns after 4 h incubation in 1 M activity counts was subjected to electrophoresis on a 6%15% gradient polyacrylamide gel and analyzed
by phosphor imager scanning. The experiment was repeated several times, and the data presented are
HCl (Figure 1C). Prolonged exposure representative of one such experiment. Oligonucleotides of known molecular size were end-labeled with
of the columns to 1 M HCl for 0, 10, [-32P]dATP and used as molecular weight standards as shown.
and 30 days or longer did not alter the
DNA binding capacity of the columns,
suggesting that the active groups on ation protocol to diverse columns from Nucleic Acids Purified with
the resin surface are quite stable to Qiagen that use different strategies Regenerated Columns Are
acid exposure (Figure 1D). As illus- of plasmid purification, spin versus Functionally Competent
trated, the columns can be regenerated gravity separation, or different scales of
many times without a reduction in the DNA yield (data not presented), as well We observed comparable expression
binding capacity (Figure 1E). In our as columns from different manufac- levels of different mammalian genes
experience, most of the columns could turers (Figure 1F). Additionally, we from plasmids prepared using fresh
be regenerated up to 20 times. DNA tested columns intended for genomic columns or columns regenerated for
eluted from each round was resolved DNA isolation (data not presented), five rounds (Figure 2). A plasmid
on a 1% agarose gel to confirm the extraction of DNA from agarose vector pCMV-SEAP, encoding SEAP
supercoiled nature of the plasmid gels (data not presented), and RNA under the control of a CMV promoter,
(Figure 1E, middle panel) and compa- extraction (see section entitled Nucleic expressed comparable levels of SEAP
rable expression levels of the encoded Acids Purified with Regenerated when the plasmid was isolated with
enhanced GFP (EGFP) (Figure 1E, Columns Are Functionally Competent) fresh or regenerated columns (Figure
bottom panel). We applied the regener- and obtained similar results. 2A). Identical results were obtained
190 BioTechniques www.biotechniques.com Vol. 42 No. 2 2007
Short Technical Reports
with a GFP expression vector, pCMV- PCR amplification in the subsequent described in the Materials and Methods
EGFP (Figure 1E, bottom panel). The experiments. section. We observed a progressive
plasmid pINDIE harbors a full-length Six fresh Qiagen-tip 20 columns were degradation of the DNA with prolonged
molecular clone of HIV-1. HEK 293 loaded with a plasmid DNA containing exposure to HCl (Figure 3C). At zero
cells transfected with pINDIE secreted the kanamycin-resistance gene (pCMV- time point, most of the DNA remained
comparable levels of the viral core p24-KanR). After washing, the columns in the well, and DNA that entered the
antigen p24 into the medium at 24, were eluted only once, thus leaving a gel developed a smear in the lane. DNA
48, and 72 h (Figure 2B). CEM-GFP significant quantity of the residual KanR exposed to acid for periods as short
cells electroporated with pCMV-Tat, plasmid on the columns, which was as 60 min readily entered the gel and
prepared using fresh and regenerated expected to be approximately 56 g or migrated below the 36-bp marker. After
columns, induced comparable levels of 20% of the overall binding capacity of 24 h, nearly all the DNA moved into the
GFP expression as determined by flow the column (see Figure 1D). Three of the gel and was predominantly reduced to a
cytometry (Figure 2C). six columns were incubated in 1 M HCl size below 36 bp. The data presented in
We also regenerated commercial for 4 h to strip the residual DNA. The Figure 3 collectively proved that DNA
nucleic acid extraction columns for total other three columns were incubated in exposed to 1 M HCl was efficiently
RNA extraction from human plasma Buffer QC and were expected to contain destroyed, and the columns regenerated
samples and evaluated the RNA quality residual plasmid DNA that should be thus were safe for reuse without a risk
in a real-time RT-PCR targeting the carried over to the next round of purifi- of carryover contamination.
HIV-1 promoter sequence. Total RNA cation. After the incubation, both sets of In summary, we identified an
was extracted from 150-L plasma of the columns were washed and loaded efficient, simple, and inexpensive
each of five individual HIV-1 seropos- with a second plasmid containing the procedure to regenerate commercial
itive donors using commercial nucleic ampicillin-resistance gene (pCMV- nucleic acid extraction columns.
acid extraction columns supplied by Tat-AmpR). Bound plasmid was eluted Commercial kits supply limited
two different manufacturers. RNA from the columns, and competent E. volume of the buffers required for
extracted with fresh or regenerated coli cells were transformed and seeded column regeneration. However, the
columns amplified the target sequence on agarose plates supplemented with composition of the buffers is provided
in a manner indistinguishable from ampicillin or kanamycin. The number of in several technical brochures, and a
each other (Figure 2D). We did not see colonies developed on the plates after a laboratory with adequate molecular
large differences in viral titers among 16 h incubation was determined. AmpR biology expertise should be able to
the individual donors tested, probably plasmid extracted using the regenerated make its own reagents. We routinely
as all the donors were drug-nave and column contained approximately 400 store the columns in 1 M HCl, as this
asymptomatic. However, the CT values colonies on the ampicillin plate and procedure not only regenerates the
of the samples of the highest and lowest absolutely no colonies on the kanamycin columns but also prevents microbial
titer differed by 4.5 cycles, suggesting plate (Figure 3A). In contrast, plasmid growth. A procedure to permit safe and
a 20- to 25-fold difference in viral load DNA extracted using the contaminated efficient regeneration of the commercial
between these donors. columns contained approximately 300 columns makes them commercially
and 20 colonies on plates supplemented more affordable, especially in a
Acid-Treated DNA Is Degraded with ampicillin and kanamycin, respec- resource-poor setting.
tively. To validate this finding, we used
to Small Fragments and Cannot
PCR to detect the presence of residual
Function as a Template DNA in the plasmid preparation. We ACKNOWLEDGMENTS
The most serious concern with the optimized PCRs for Tat (AmpR, 240 bp) A number of reagents used in this
reuse of the disposable columns is the and p24 (KanR, 330 bp) to detect target study were obtained through the AIDS
possibility of nucleic acid carryover genes on respective plasmids. Both the Research and Reference Reagent
from one preparation to the next. Even PCRs were sensitive enough to detect a Program, Division of Acquired
the minutest quantity of nucleic acid single copy of the template (Figure 3B, Immunodeficiency Syndrome (AIDS),
carryover between samples could have left panels). The Tat PCR successfully National Institute of Allergy and
serious consequences for subsequent amplified the target DNA from both Infectious Diseases (NIAID), and
molecular manipulations. Therefore, the plasmid preparations as expected National Institutes of Health (NIH),
it is critical to ensure that the columns (Figure 3B, top panel). In contrast, p24 USA. U.R. acknowledges financial
are absolutely free of residual DNA PCR-amplified only the DNA isolated support from The Department of
after regeneration. We devised a series with the reused, but not the regenerated Science and Technology, government
of experiments to detect residual DNA columns (Figure 3B, lower panel). of India (grant no. VII-PRDSF/105/05-
on the columns after regeneration. We Furthermore, we examined the fate of 06/TDT). N.B.S. is a recipient of the
selected a pair of vectors containing the DNA exposed to 1 M HCl while Council for Scientific and Industrial
two different drug markers, ampicillin bound on the column. Radioactively Research (CSIR) fellowship from the
and kanamycin, for differential labeled DNA bound on the columns was government of India.
colony plating and two different gene exposed to 1 M HCl for different time
sequences, p24 and Tat, for differential periods, recovered, and analyzed as