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Abstract
Keywords: SOURCEk 15Q; RESOURCEk Q; Polymer matrices; Anion exchange chromatography; HPLC;
Oligonucleotide; Scale-up
1. Introduction
0165-022X/$ - see front matter D 2005 Elsevier B.V. All rights reserved.
doi:10.1016/j.jbbm.2005.08.004
J. Shanagar / J. Biochem. Biophys. Methods 64 (2005) 216–225 217
first introduced by Letsinger [7], in an analogous fashion with MerrifeldsT work on peptides [8].
With the use of ÄKTAk oligopilot DNA/RNA Synthesizer, SONs can be produced with high
coupling efficiency [9]. However, the product obtained contains many impurities and short
failure sequences. Since highly pure SONs are a prerequisite for therapeutic and other
applications, purification is required.
Most purification procedures are based on either reversed phase chromatography (RPC) [10–
13] or anion exchange chromatography (AEC) [14,15].
AEC is an attractive technique for the purification of synthetic oligonucleotides because the
separation is performed in aqueous conditions without the use of high cost eluents, at low to
moderate operating pressures. Furthermore, during the purification process, it is of vital
importance to avoid aggregation of self-complementary or GC-rich oligonucleotides [10]. It is,
therefore, preferred to perform the purification in mild alkaline conditions. Attempt to optimize
separation of oligonucleotides and DNA using computer simulations modeling methods has
been reported [16]. The modeling based optimization method offers a more effective manner to
predict the elution behaviour and also offers significant time and cost saving over trial-and-error
approaches [16].
SOURCEk 15Q (GE Healthcare) is a polymer-based anion exchanger consisting of 15 Am
monosized beads. This anion exchanger has several advantages, such as a wide operating pH-
range, low back-pressure and the good recovery making the medium ideal for use in process-
scale purification of oligonucleotides [15]. Furthermore, the high pH stability of SOURCE 15Q
allows purification of oligonucleotides under denaturing conditions at pH 12. It is thus possible
to capture and purify oligonucleotides directly from the crude ammonia solution obtained after
cleavage of the oligonucleotide from the synthesis support.
The objective of this work is to develop a single-step chromatographic protocol for
purification of oligonucleotides with high purity and recovery using SOURCE 15Q medium. It
is also aimed to show the successful scalability of the developed method from a small lab-scale
to a preparative scale for purification of large amount of oligonucleotides.
The oligonucleotide with a sequence of 5V-ATA CCG ATT AAG CGA AGT TT-3V used in
this study was synthesized with an ÄKTA oligopilot DNA/RNA Synthesizer (GE Healthcare)
using its trityl-off mode [6,9]. Purity of the full-length oligonucleotide product (FLP) in the
crude reaction mixture was 68% after cleavage from the synthesis support. This sample was
applied directly onto the anion exchanger columns without any pretreatment.
All runs were done with columns packed with SOURCE 15Q, using ÄKTAexplorerk 10,
ÄKTAexplorer 100 or ÄKTApilotk systems (GE Healthcare). The ÄKTAexplorer systems were
comprised of a model P-900 HPLC pump, a model UV-900 monitor, a model pH/C-900 pH/
conductivity monitor and UNICORNk software system control. The column effluent from
ÄKTAexplorer systems was fractionated using a Frac-950 Fraction Collector (GE Healthcare)
although the effluent from ÄKTApilot system was collected manually. The volume of each
fraction collected in all the preparative purification experiments was 0.5 column volume (CV).
218 J. Shanagar / J. Biochem. Biophys. Methods 64 (2005) 216–225
The chromatographic conditions are described in Section 3.1 and in the legend for each
respective Figure.
The SOURCE 15Q stationary phases used for the purification of oligonucleotide were
obtained from GE Healthcare in prepacked analytical columns (RESOURCE Q and SOURCE Q
PE 4.6/100) and in bulk packs. For scale-up studies, the SOURCE 15Q bulk medium was
packed in Tricornk (i.d. 10 mm), FineLINEk Pilot 35 (i.d. 35 mm), and FineLINE 70 (i.d. 70
mm) columns from GE Healthcare. Details on packing of the columns are described in the next
section). For desalting of the purified material, a HiPrepk 26/10 Desalting Column (GE
Healthcare) was used. All other chemicals used in these studies were of analytical grade and
were purchased from Merck (Darmstadt, Germany).
The oligonucleotide was detected by monitoring UV absorbance at 260 nm. The fractions
were diluted properly to obtain absorbance into the linear response range. The mass estimates of
the oligonucleotide was calculated from spectrophotometric absorbance measurements at 260
nm. The measured optical density (OD)/ml was converted into mg/ml values by using the factor
of 1 OD = 0.033 mg oligonucleotide.
J. Shanagar / J. Biochem. Biophys. Methods 64 (2005) 216–225 219
Analyses of the collected fractions (from the purification experiments) and the crude
oligonucleotide material were performed by anion exchange HPLC on a non-porous medium
(DNAPack PA-100 analytical column [4/250 mm]) from Dionex Corporation, Sunnyvale, CA,
USA) and/or by capillary electrophoresis [19].
The anion exchange HPLC analysis was conducted on Hewlett-Packard (Palo Alto, CA,
USA) Model 1100 liquid chromatography fitted with the DNAPac column, thermostatted to 25
8C and operated at a flow rate of 480 cm/h. The column was equilibrated with 5 column volumes
(CVs) of the equilibration buffer of 90% A and 10% B (A = 0.001 M Tris containing 0.01 M
NaClO4; pH 9.3 and B = 0.001 M Tris containing 0.3 M NaClO4; pH 9.3). Twenty-five
microliters of each fraction was injected into the column and eluted with a 7.6 CVs linear
gradient from 10% to 70% B. The column effluent was monitored at 260 nm.
All capillary electrophoresis experiments were performed using a 20 cm (effective length 18
cm) 50 Am i.d. capillary. The capillary was treated with PlusOnek Bind-Silane (GE
Healthcare) and filled with polyacrylamide cyclodextrin gel. Buffer was consisted of 0.1 M Tris-
0.25 M boric acid, pH 8.5, containing 7 M urea. Injection was made at 1 kV for 5 s. Analysis
was performed at 1.5 kV for 30 min.
3. Results
Method scouting was first carried out using a small sample load (10 Ag crude oligonucleotide)
on a 1 ml RESOURCEk Q column (GE Healthcare), which has a bed height of 30 mm. The
column was equilibrated with solution A (0.01 M NaOH, pH 12). Elution of the sample was
performed with gradient formed with solutions A and B (0.01 M NaOH, pH 12 containing 2 M
NaCl). Different start conditions and elution profiles, which made up of steps and linear
gradients were tested to optimize the purification. Both the start conditions and slope of the
gradient were varied until an acceptable resolution was achieved. The optimal condition was
found to be a 40 CVs linear gradient from 15% to 35% B. This corresponded to 0.30 to 0.70 M
NaCl in a 0.01 M NaOH solution, pH 12 (see Fig. 1a–b). To further optimise the method, the bed
height was increased to 100 mm using a SOURCE Q PE 4.6/100 column. Except for the change
in bed height, all chromatographic conditions were kept the same as in the 30 mm bed height
column. Fig. 1C shows the resulting chromatogram where resolution has been further improved.
Fractions from each experiment were collected and the fractions of interest were analysed on the
DNAPac PA-100 analytical column to determine the purity. Fig. 1d shows a purity of 99%
achieved with SOURCE Q PE 4.6/100 column.
To determine the binding capacity for the oligonucleotide, a frontal analysis experiment was
carried out on the RESOURCE Q column. The column was equilibrated with 5 CVs of 0.01 M
NaOH solution. The crude oligonucleotide sample was diluted to a concentration of 1.5 mg/ml
with the same equilibration solution and was applied continuously into the column at a flow rate
of 360 cm/h until the column was saturated. Thus, the effluent UV absorbance at 300 nm was
similar to that of the applied sample. Fig. 2 shows the resulting breakthrough curve. From this
220 J. Shanagar / J. Biochem. Biophys. Methods 64 (2005) 216–225
a b
mAU mAU
RESOURCE Q 1 ml RESOURCE Q 1 ml
150 0-50% B in 30 cv 150 15-35% B in 40 cv
100 100
50 50
0 0
0.0 5.0 10.0 15.0 20.0 25.0 30.0 min 0.0 10.0 20.0 30.0 40.0 50.0 min
c d
mAU SOURCE Q PE 4.6/100
15-35% B in 40 cv
mAU
150 DNAPac PA-100
(4/250) analytical
column
15.0
100
10.0
50
5.0
0.0
0
0.0 10.0 20.0 30.0 40.0 50.0 60.0 70.0 min 8.0 9.0 10.0 11.0 12.0 13.0 14.0 min
Fig. 1. a–c. Effect of gradient shape and slope on the resolution of oligonucleotide. Sample: Crude oligonucleotide 20-
mer (10 Ag). Flow rate: 360 cm/h. Solution A: 0.01 M NaOH, pH 12. Solution B: 0.01 M NaOH + 2 M NaCl, pH 12. a)
Column: RESOURCE Q 1ml. Gradient,: 0–50% B in 30 column volumes. b) Column: RESOURCE Q 1ml. Gradient:
15–35% B in 40 column volumes. c) Column: SOURCE Q PE 4.6/100. Gradient: 15–35% B in 40 column volumes.
Fig. 1d. Analysis of a fraction collected from the main peak in Fig. 1c on the DNAPac PA-100 (4/250) analytical column.
Column: DNAPac PA-100 (4/250). Flow rate: 480 cm/h. Volume injected: 25 Al. Buffer A: 0.001M Tris + 0.01M NaClO4.
Buffer B: 0.001M Tris + 0.3 M NaClO4.Gradient: 10–70% B, 7.6 CVs.
curve, the capacity of the SOURCE Q media was calculated to be 30 mg oligonucleotide /ml
medium.
The SOURCE Q PE 4.6/100 column was used in a small lab-scale preparative purification of
the oligonucleotide. Since the result from frontal analysis measurement showed that capacity of
the medium was 30 mg oligonucleotide/ml, it was decided to load the medium with the
J. Shanagar / J. Biochem. Biophys. Methods 64 (2005) 216–225 221
mAU
800
600
400
200
Fig. 2. Breakthrough curve for the crude 20-mer oligonucleotide. Column: RESOURCE Q 1 ml (6.4[ i.d]. 30 mm).
Flow rate: 360 cm/h. Sample: 20-mer oligonucleotide (1.5 mg/ml in 0.01M NaOH, pH 12). Detection: UV-300 nm.
3.4. Scale-up
A 5-, 58- and 230-fold scale-up was performed by increasing the column diameter while
keeping other parameters such as linear flow rate, sample load/ml medium and column bed
height constant.
A Tricorn column (10 mm inner diameter), a FineLINE Pilot 35 column (35 mm inner
diameter) and a FineLINE 70 column (70 mm inner diameter) were packed with 7.85, 96 and
385 ml of SOURCE 15Q media, respectively and used for the scale-up experiments.
Fig. 3 shows the scale-up results of the purification of the 20-mer oligonucleotide from a
sample load of 18 mg/ml medium. When the protocol was scaled-up 5-fold, 141 mg crude
material was processed giving a yield of 70 mg. The 58-fold scale-up was performed using the
same method but on ÄKTAexplorer 100 system. From 1 825 mg crude sample a product yield of
980 mg was obtained. At the final scale using ÄKTApilot system, 7.0 g of crude material was
purified in one run resulting in a yield of 4.1 g product. This corresponds to a 230-fold scale-up
from the small laboratory scale. The final yield and the purities are shown in Table 1. These
results correspond well to the result achieved with the small lab-scale column (1.66 ml
prepacked SOURCE Q PE 4.6/100) and clearly demonstrate the scalability of the method. The
cycle time was 110 min, which corresponds to a purification capacity of about 90 g crude
oligonucleotide material per 24 h using a FineLINE 70 column.
The purity of the oligonucleotide purified by analytical anion exchange chromatography and
capillary electrophoresis was greater than 97% at all scales used. Fig. 4 shows an example of
analysis by capillary electrophoresis of the crude oligonucleotide and the pooled fractions from
the separation of the 20-mer oligonucleotide, shown in Fig. 3c.
a b
222
mAU
2500
2000
mAU
1500 2500
2000
1000
500 I II
500 I II
0 0
0.0 10.0 20.0 30.0 40.0 50.0 60.0 70.0 80.0 min 0.0 10.0 20.0 30.0 40.0 50.0 60.0 70.0 80.0 min
c d
mAU
mAU
3000
2500 4000
2000 3000
1500
2000
1000
1000
500
I II I II
0 0
0.0 10.0 20.0 30.0 40.0 50.0 60.0 70.0 80.0 min 0.0 10.0 20.0 30.0 40.0 50.0 60.0 70.0 min
Fig. 3. Scale-up of the optimised purification method for 20-mer oligonucleotide using 1.66, 7.85, 96 and 385 ml columns packed with SOURCE 15Q. Sample: Crude
oligonucleotide 20-mer. Flow rate: 360 cm/h. Solution A: 0.01 M NaOH, pH 12. Solution B: 0.01 M NaOH, pH 12 + 2 M NaCl. Gradient: 15–35% B in 40 column volumes.
a) Column: SOURCE Q PE 4.6/100 (1.66 ml). Sample load: 30 mg. b) Column: Tricorn (10/100 mm) packed with SOURCE 15Q (7.85 ml). Sample load: 141 mg. c) Column:
FineLINE Pilot 35 (35/100 mm) packed with SOURCE 15Q (96 ml). Sample load: 1825 mg. d) Column: FineLINE 70 (70/100 mm) packed with SOURCE 15Q (385 ml). Sample
load: 7000 mg.
J. Shanagar / J. Biochem. Biophys. Methods 64 (2005) 216–225 223
Table 1
Comparison of yield and purity at different scales
Sample Yield Recovery Purity
load (mg) (mg) (%) (%)
Small lab-scale (SOURCE Q PE 4.6 / 100 mm) 30 17 83 97
5-fold scale-up (SOURCE 15Q [10 / 100 mm]) 141 70 73 97
58-fold scale-up FineLINE Pilot 35 (SOURCE 15Q [35 / 100 mm]) 1825 980 80 97
230-fold scale-up FineLINE 70 (SOURCE 15Q [70 / 100 mm]) 7000 4067 85 97
After purification of the 20-mer oligonucleotide by AEC, the purified material contained a
high concentration of salt. The salt was removed from the purified 20-mer by a desalting
method using Milli-Qk ultrapure water (Milliporek Corporation, Billerica, USA) as eluent. A
a b
mAU mAU
2.5 2.5
1.5 1.5
1.0 1.0
0.5 0.5
0 0
0 5 10 15 min 0 5 10 15 min
c
mAU
2.5
Pool II
2.0
1.5
1.0
0.5
0
0 10 20 min
Fig. 4. Analysis by capillary electrophoresis from the separation of the 20-mer oligonucleotide shown in Fig. 3c.
Capillary: 50 Am 18 cm filled with polyacrylamide cyclodextrin gel. Buffer: 0.1 M Tris, 0.25 M borate/7 M urea.
Running conditions: 1.5 kV/30 min. Sample application: 1 kV/5 s. a) Crude material. b) The eluted failure sequences
(pool I in Fig. 3c). c) The purified 20-mer oligonucleotide (pool II in Fig. 3c).
224 J. Shanagar / J. Biochem. Biophys. Methods 64 (2005) 216–225
mAU
2500
2000
1500
1000
500
0
0.0 10.0 20.0 30.0 40.0 50.0 60.0 70.0 ml
Fig. 5. The elution profile of oligonucleotide desalting. Column: HiPrep 26/10 Desalting. Flow rate: 60 cm/h. Eluent:
Water. Sample: 15 ml purified 20-mer oligonucleotide. Detection: UV at 260 nm (—) and conductivity measurement (–).
HiPrep 26/10 desalting column was employed for desalting 15 ml of the purified 20-mer
oligonucleotide per run. The oligonucleotide was detected by monitoring UV absorbance at
260 nm and the salt by conductivity measurements. The recovery from the desalting was 98%
(see Fig. 5).
4. Discussion
Acknowledgments
The author is grateful to Israel Solomon for performing some chromatographic optimisation
experiments. Dr Akos Vegvari, BMC, University of Uppsala, is sincerely appreciated for the
HPCE analyses.
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