Solutions for Oligonucleotides Synthesis

Liquid Reagents
from SAFC Supply Solutions ®

ProClin Preservatives
®

Mechanisms and Stability

for Diagnostics Reagents

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 Solutions for Oligonucleotides Synthesis
Liquid Reagents

Purity of Liquid Reagents to support

your overall synthesis performance
In solid-phase synthesis of oligonucleotides, liquid reagents are used in each
step of the synthesis cycle. Overall synthesis performance, and therefore total
product yield and purity of the crude oligonucleotide, is highly dependent on
the chemical purity of the monomers and the supporting liquid reagents.

SAFC Supply Solutions® has more than 25 already incorporated into the growing
years of manufacturing experience in DNA nucleic acid, prior to the addition of the
and RNA synthesis reagents. Our liquid next phosphoramidite. Removal of the DMT
reagents meet the most stringent quality allows the unprotected 5’hydroxyl moiety
specifications, making them ideal for use to react with a new phosphoramidite in a
in automated nucleic acid synthesis. Lot- subsequent extension reaction.
to-lot consistency is guaranteed for every
Wash solution containing anhydrous
product manufactured at SAFC Supply
acetonitrile (water content ≤30 ppm), is
Solutions ISO 9001 certified site and each
used as the overall wash solvent following
lot is quality-controlled to ensure optimum
each step in the synthesis cycle.
synthesis performance.
Activator solution containing powerful
Table 1. Liquid Reagent features and benefits
activators like 4,5-dicyanoimidazole (DCI)
Features Benefits or 5-(3,5-bis(trifluoromethyl) phenyl)-1H-
Products designed Constant high tetrazole (Activator 42) in acetonitrile are
for oligonucleotide synthesis performance mixed with solutions of phosphoramidites
synthesis
during the extension step. The activator
Liquid reagents offered Key oligonucleotide
in addition to amidites synthesis reagents reacts with the amidite group to form
and supports available in one shop a highly reactive intermediate. The
intermediate forms an internucleotide bond
Constant high Matching with high
control quality amidites and with the detritylated 5’hydroxyl group of the
support products growing oligonucleotide chain.

Broad range of Offering high flexibility Cap A solution containing acetic anhydride
packaging
and tetrahydrofurane (THF) is used
Customized Special requirements after the phosphoramidite reaction/
formulations and will be fulfilled
specifications coupling step. This solution aborts chains
bearing unreacted 5’hydroxyl groups
Technical expertise Supporting customized
solutions due to failure of reaction with activated
phosphoramidite (typically, 1 to 2%
New product Synthesis optimization of growing oligonucleotide chains in
development: and cost reduction
Activator® 42 each synthesis cycle). These unreacted
5’hydroxyl groups are capped with an

acetyl group, thus rendered unreactive for
Chemical composition and purpose subsequent synthesis steps. For synthesis
with Proligo® Reagents’ TAC-protected
Deblock solution containing trichloroacetic phosphoramidites, Fast Deprotection CAP A
acid (TCA) or dichloroacetic acid (DCA) in solution must be employed instead of Cap
dichloromethane or toluene removes the A solution.
dimethoxytrityl (DMT) protecting group
from the 5’hydroxyl moiety of nucleotides
2

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 The Oligonucleotide Synthesis Cycle
Fast Deprotection Cap A solution must be
used for synthesis with Proligo Reagents’
TAC-protected phosphoramidites. Fast
Deprotection Cap A solution, with tert-
butylphenoxyacetyl acetic anhydride
(TAC2O) in tetrahydrofuran is used in
place of Cap A solution to ensure that the
displacement of tert-butylphenoxyacetyl
(TAC) on guanine bases of the TAC-
protected phosphoramidites does not occur.
Cap B solution containing tetrahydrofurane
(THF) pyridine and N-methylimidazole (NMI),
is mixed in situ with Cap A solution during
the capping (acetylation) reaction. Pyridine
is applied as a mild base while NMI provides
a powerful acylation catalyst.
Oxidizer solution, containing
tetrahydrofurane (THF), pyridine, iodine and
water is applied to oxidize the chemically
unstable trivalent phosphorous triester
linkage formed in the coupling reaction to a
stable pentavalent phosphate triester. Iodine
functions as a mild oxidant while water
serves as an oxygen donor.
3
 Solutions for Oligonucleotides Synthesis
Liquid Reagents

A broad range of packaging

Flexible packaging options are available operations that can accommodate

to meet most synthesizer requirements, small-scale bottles to 1,400 L returnable
including ABI® 394, ABI® 3900, ExpediteTM, containers.
ÄKTATM and Mermade. As a single source
Our worldwide distribution network offers
supplier, SAFC Supply Solutions’ Hamburg
advantages of dedicated airfreight space,
(Germany) and Sheboygan, Wisconsin
expertise in chemical transport regulations
manufacturing sites can liquid fill and blend
and local delivery knowledge.
material in and have complete packaging

Table 2. Worldwide Packaging Options

Bottles
Description Height Diameter Capacity Total Capacity Material Closure
100 mL Septum 95 mm 51 mm 100 mL 120 mL amber glass septum
4 oz 22-400 Bottle 112 mm 48,5 mm 120 mL 125 mL amber glass screw cap 22-400
8 oz 24-400 Bottle 137 mm 60 mm 200 mL 240 mL amber glass screw cap 24-400
8 oz 28-400 Bottle 137 mm 60 mm 200 mL 240 mL amber glass screw cap 28-400
16 oz 28-400 Bottle 170 mm 72 mm 450 mL 480 mL amber glass screw cap 28-400
32 oz 28-400 Bottle 210 mm 94 mm 900 mL 960 mL amber glass screw cap 28-400
2 L 38-430 Bottle 310 mm 135 mm 2L 2.5 L amber glass screw cap 38-430
2.5 L GL 45 Bottle 296 mm 135 mm 2.5 L 2750 mL amber glass screw cap GL 45
4 L 38-430 Bottle 353 mm 161 mm 4L 4300 mL amber glass screw cap 38-430
1 L GL 45 Bottle 212 mm 101 mm 1000 mL 1158 mL amber glass screw cap GL 45

100 mL Septum 4 oz 22-400 Bottle 8 oz 24-400 Bottle 8 oz 28-400 Bottle 16 oz 28-400 Bottle

32 oz 28-400 Bottle 2 L 38-430 Bottle 2.5 L GL 45 Bottle 4 L 38-430 Bottle 1 L GL 45 Bottle

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Table 3. Liquid Reagent Packaging
Drums
Total Wall Operating Approval
Description Capacity Weight Height Diameter Material Closure
Capacity Thickness Pressure Number
18 L Returnable Stainless steel drum 18 L 20 L 6,6 kg 442 mm 278 mm 1.5 mm V2A 1.4301 Screw cap DIN 11851 0.5 bar 1A1/
Drum 18 L with Dip Tube SS304 PTFE R52x1/6” X2,0/900
25 L Drum, Composite drum sheet 25 L 30 L 3.4 kg 560 mm 280 mm 0.5 mm PE-HD A BCS 56x4 (1x) 1A1/
Disposal steel/PE X1,6/250
25 L Returnable Stainless Steel Drum 25 L 30 L 10 kg 400 mm 380 mm 1.5 1.4301 3A Coding 0.5 bar 1A1/
Drum with Dip Tube MAV Micro Matic Valve X2,3/900
45 L Returnable Stainless steel drum 45 L 50 L 11 kg 600 mm 363 mm 1.5 mm V2A 1.4301 Screw cap DIN 11851 0.5 bar 1A1/
Drum 45 L with Dip Tube SS304 PTFE R52x1/6” X2,3/900

45 L Returnable Stainless Steel Drum 45 L 50 L 12 kg 600 mm 263 mm 1.5 mm 1.4301 4F Coding 0.5 bar 1A1/
Drum with Dip Tube MAV Micro Matic Valve X2,3/900
180 L Drum, Composite drum sheet 180 L 200 L 21 kg 884 mm 585 mm 1 mm PE-HD BCS 56x4 (2x) 1A1/
Disposal steel/PE X1,3/250
200 L Returnable Stainless steel drum 200 L 225 L 43 kg 970 mm 600 mm 2 mm 1.4301 On Demand 0.5 bar 1A1W/
Drum, Level 200 L with level sensor X2,0/900
Sensor and Dip Tube
200 L Returnable Stainless steel drum 200 L 225 L 43 kg 970 mm 600 mm 2 mm 1.4301 Screw cap DIN 11851 0.5 bar 1A1W/
Drum, Standard 200 L with Dip Tube PTFE R52x1/6” X2,0/900
Returnable 1400 L Stainless Steel IBC 1400 L 1500 L 247 kg 1960 mm 1200 mm 1.4301 On demand 0.5 bar 31A/Y
Container 1400 L with Dip Tube

18 L Returnable Drum 25 L Drum, Disposal 25 L Returnable Drum 45 L Returnable Drum 45 L Returnable Drum

180 L Drum, Disposal 200 L Returnable 200 L Returnable Returnable 1400 L

Drum, Level Sensor Drum, Standard Container

5
 Solutions for Oligonucleotides Synthesis
Liquid Reagents
Table 4. Liquid Reagent Packaging
Additional Drum Options (US market only)
Total Wall Operating Approval
Description Capacity Weight Height Diameter Material Closure
Capacity Thickness Pressure Number
20 L Pure-Pac II 20 L 22 L 8 kg 20 inches 11 inches 1.5 mm SS304 MAV Micro Matic 0.34 bar 1A1/
Valve - Simriz 485 X2.3/900
50 L Pure-Pac II 50 L 55 L 15 kg 23 inches 16 inches 1.5 mm SS304 MAV Micro Matic 0.34 bar 1A1/
Valve - Simriz 485 X2.0/600
200 L Pure-Pac II 200 L 220 L 47 kg 38 inches 24 inches 2 mm SS304 MAV Micro Matic 0.34 bar 1A1/
Valve - Simriz 485 X2.0/600
200 L Pure-Pac 200 L 220 L 47 kg 38 inches 24 inches 2 mm SS304 MAV Micro Matic 0.34 bar 1A1/
II, level sensor Valve - Simriz 485 X2.0/600

For your custom packaging requirements, including

technical and product specifications, please contact your
sales representative to inquire. Some packaging options
may not be available in your region.

Custom Blending Solutions to speed up your processes

For special requirements on formulations, Six additional production plants support

specifications and packaging, our manufact- the Sheboygan and Hamburg facilities
with custom blending and risk mitigation
uring sites offer custom blending services:
for all projects.
• Batch sizes from 100 L up to 4000 L
All inquiries are evaluated by a Project
• A wide variety of high purity solvents, Management Group that selects the most
including flammable solvents handling appropriate manufacturing site and follows
up on customer projects.
• Raw materials supplier qualification
process in alignment with customer
expectations

• Specifications and Quality Control

according to customer requirements

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Table 5. Liquid Reagent Formulations

Reagent Description Packaging Available

Formulation Specifications Product Number Unit Bottle Type
Amidite Diluent & ACN Water Content L010010-06 6 x 100 mL 100 mL septum
Acetonitrile ≤ 30ppm
or ≤10ppm also
available *
nD20 = 1,342-1,346 L010200-04 4x 2L 2 L 38/430

App. of Sol. = clear L010250-04 4 x 2.5 L 2.5 L GL45

L010400-04 4x4L 4 L 38/430

L011800-01 1 x 18 L 18 L Returnable
Drum
L014500-01 1 x 45 L 45 L Returnable
Drum
L014500-C01-01 1 x 45 L 45 L Returnable
Drum
L0120000-01 1 x 200 L 200 L Returnable
Drum 2” Level
Sensor
L0120000-C01-01 1 x 200 L 200L Returnable
Dru m 2”
Standard
L0114000-01* 1 x 1400 L Returnable 1400L
Container
L810045-06 6 x 450 mL 16 oz 28/400
(450 mL) for PE
8900/Polygen
TFA Deblock Toluene Toluene/TFA Water Content L0202502-04 4 x 2.5 L 2.5 L GL45
≤ 200 ppm
100/1 TFA Content =
10.3-12.5 g/l
v/w App. of Sol. = clear

DCA Deblock DCM/DCA Water Content L020251-04 4 x 2.5 L 2.5 L GL45

≤ 200 ppm
97/3 DCA Content =
42.2-51.6 g/l
v/v App. of Sol. = clear

TCA Deblock DCM/TCA Water Content L020250-04 4 x 2.5 L 2,5 L GL45

≤ 200 ppm
100/3 TCA Content = L020400-04 4x4L 4 L 38/430
28-32 g/l
v/w App. of Sol. = clear L022500-01 1 x 25 L 25 L Drum,
Disposal
L320045-01 1 x 450 mL 16 oz 28/400
(450 mL)
L820090-06 6 x 900 mL 32 oz 28/400
(900 mL) for PE
8900/Polygen
Activator 42 0.1M ACN/Activator42 Water Content L0302502-04 4 x 2.5 L 2,5 L GL45
≤ 30ppm
100/3 Act. 42 Content = L3300182-06 6 x 180 mL 8 oz 24/400
28-31 g/l (200 mL) for ABI
v/w App. of Sol. = clear L8300202-06 6 x 200 mL 8 oz 28/400
(200 mL) for PE
8900/Polygen

L8300452-06 6 x 450 mL 16 oz 28/400

(450 mL)

7
 Solutions for Oligonucleotides Synthesis
Liquid Reagents
Table 6. Liquid Reagent Formulations

Reagent Description Packaging Available

Formulation Specifications Product Number Unit Bottle Type
Activator 42 0.25 M ACN/Activator42 Water Content L0302512-04 4 x 2.5 L 2.5 L GL45
≤ 30 ppm
100/7 Act. 42 Content = L8300212-06 6 x 200 mL 8 oz 28/400
70-77 g/l (200 mL) for PE
8900/Polygen
v/w App. of Sol. = clear L8300462-06 6 x 450 mL 16 oz 28/400
(450 mL)
ETT Activator 0.25M ACN/ETT Water Content L0302501-04 4 x 2.5 L 2.5 L GL45
≤ 30 ppm
100/3 ETT Content = L0302001-04 4x2L 2 L 38/430
32-35 g/l
v/w App. of Sol. = clear L8300201-06 6 x 200 mL 8 oz 28/400
(200 mL) for PE
8900/Polygen
L8300451-06 6 x 450 mL 16 oz 28/400
(450 mL)
DCI Activator 0.25M ACN/DCI Water Content L080250-04 4 x 2.5 L 2,5 L GL45
≤ 30 ppm
100/3 DCI Content=29-32 g/l L080400-04 4x4L 4 L 38/430
v/w App. of Sol. = clear L082500-01 1 x 25 L 25 L Returnable
Drum
L380018-06 6 x 180 mL 8 oz 24/400
(200 mL) for ABI
L880020-06 6 x 200 mL 8 oz 28/400
(200 mL)
L880045-06 6 x 450 mL 16 oz 28/400
(450 mL)
Cap A THF/Ac2O Ac2O Content = L040250-01 1 x 2.5 L 2.5 L GL45
88.7-108.4 g/l
90.9/9.1 App. of Sol. = clear L040250-04 4 x 2.5 L 2.5 L GL45
v/v L040400-01 1x4L 4 L 38/430
L040400-04 4x4L 4 L 38/430
L040200-04 4x2L 2 L 38/430
L840020-06 6 x 200 mL 8 oz 28/400
(200 mL) for PE
8900/Polygen
L840045-06 6 x 450 mL 16 oz 28/400
(450 mL)
Cap A for ABI THF/Lutidine/Ac2O Ac2O Content = L040251-01 1 x 2.5 L 2.5 L GL45
instruments 97.0-119.0 g/l
80/10/10 App. of Sol. = clear, L340018-06 6 x 180 mL 8 oz 24/400
colorless to brownish (200 mL)
solution
v/v/v L340045-06 6 x 450 mL 16 oz 28/400
(450 mL)
Cap B THF/Py/NMI Water Content L050250-01 1 x 2.5 L 2.5 L GL45
≤ 200 ppm
80/10/10 Formulation (GC) L050250-04 4 x 2.5 L 2.5 L GL45
conforms
v/v/v App. of Sol. = clear L050400-01 1x4L 4 L 38/430
L050400-04 4x4L 4 L 38/430
L050200-04 4x2L 2 L 38/430
L850020-06 6 x 200 mL 8 oz 28/400
(200 mL) for PE
8900/Polygen
L850045-06 6 x 450 mL 16 oz 28/400
(450 mL) for PE
8900/Polygen
8

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Table 7. Liquid Reagent Formulations

Reagent Description Packaging Available

Formulation Specifications Product Number Unit Bottle Type
Cap B for ABI THF/NMI Water Content L050251-01 1 x 2.5 L 2.5 L GL45
instruments ≤ 200 ppm
84/16 Formulation (GC) L350018-06 6 x 180 mL 8 oz 24/400
conforms (200 mL)
v/v App. of Sol. = clear L350045-06 6 x 450 mL 16 oz 28/400
(450 mL)
Fast Deprotection Cap A THF/Tac2O Tac2O Content = L070250-01 1 x 2.5 L 2.5 L GL45
45-55 g/l
100/5 App. of Sol. = clear L070400-01 1x4L 4 L 38/430
v/w L370018-06 6 x 180 mL 8 oz 24/400
(200 mL) for ABI
L370045-06 6 x 450 mL 16 oz 28/400
(450 mL)
L870020-06 6 x 200 mL 8 oz 28/400
(200 mL) PE
8900/Polygen
Oxidizer 0.02M THF/H2O/Py/Iodine Iodine Content = 3.9- L060250-04 4 x 2.5 L 2.5 L GL45
4.7 g/l
90.54/9.05/0.41/0.43 App. of Sol. = brownish L060400-04 4x4L 4 L 38/430
v/v/v/w L060200-04 4x2L 2 L 38/430

L860021-06 6 x 200 mL 8 oz 24/400

(200 mL) for ABI
L860020-06 6 x 200 mL 8 oz 28/400
(200 mL) for PE
8900/Polygen
L860045-06 6 x 450 mL 16 oz 28/400
(450 mL) for PE
8900/Polygen
Oxidizer 0.1M for ABI THF/H2O/Py/Iodine Iodine Content = L060251-04 4 x 2.5 L 2.5L GL45
instruments 22.9-27.9 g/l
77/2/21/2.54 App. of Sol. = L360020-06 6 x 200 mL 8 oz 24/400
brownish (200 mL)
v/v/v/w L360045-06 6 x 450 mL 16 oz 28/400
(450 mL)
Oxidizer 0.02M for ABI THF/H2O/Py/Iodine Iodine Content = L060252-04 4 x 2.5 L 2.5 L GL45
3900 instruments 5.4-6.6 g/l
66/12/22/0.6 App. of Sol. = L260045-06 6 x 450 mL 16 oz 28/400
brownish (450 mL)
v/v/v/w

ACN Based Liquid Reagents

Cap A ACN ACN/Ac2O Ac2O Content = LB40250-01 1 x 2.5 L 2.5 L GL45
88.7-108.4 g/l
90.9/9.1 App. of Sol. = clear

v/v

Cap B ACN ACN/Py/NMI Water Content LB50250-01 1 x 2.5 L 2.5 L GL45

≤ 100 ppm
80/10/10 Formulation (GC)
conforms
v/v/v App. of Sol. = clear

Cap 1 in ACN ACN/Lutidine/NMI Water Content LR40250-01 1 x 2.5 L 2.5 L GL45

≤ 200 ppm
80/10/10 Formulation (GC)
conforms
v/v/v App. of Sol. = clear

9
 Solutions for Oligonucleotides Synthesis
Liquid Reagents

Table 8. Liquid Reagent Formulations

Reagent Description Packaging Available

Formulation Specifications Product Number Unit Bottle Type
Fast Deprotection Cap 2 Tac2O/ACN Tac2O Content = LR50250-01 1 x 2.5 L 2.5 L GL45
in ACN 45-55g/l
100/5 App. of Sol. = clear
v/w
Oxidizer in ACN ACN/H2O/Py/Iodine Iodine Content = 3.9- LR60250-04 4 x 2.5 L 2.5 L GL45
4.7 g/l
90.54/9.05/0.41/0.43
v/v/v/w

ÄKTA Solution
DCA Deblock (Toluene) DCA/Toluene Water Content L520251-04 4 x 2.5 L 2.5 L GL45
≤ 200 ppm
97/3 DCA Content =
42.2-51.6
v/v App. of Sol. = clear
BTT Activator 0.3 M ACN/BTT Water Content L580250-04 4 x 2.5 L 2.5 L GL45
2.5 L, ÄKTA ≤ 30 ppm
100/6 BTT Content =
51.9-63.4
v/w App. of Sol. = clear
Cap A for Äkta and ACN/NMI Water Content L540250-01 1 x 2.5 L 2.5 L GL45
Oligo Pilot ≤ 100 ppm
80/20 Formulation (GC)
conforms
v/v App. of Sol. = clear
Cap B1 for Äkta and ACN/Ac2O Formulation (GC) L550250-01 1 x 1.25 L 2.5 L GL45
Oligo Pilot conforms
60/40 App. of Sol. = clear
v/v
Cap B2 for Äkta and ACN/Py Water Content L550251-01 1 x 1.25 L 2.5 L GL45
Oligo Pilot ≤ 200 ppm
40/60 Formulation (GC)
conforms
v/v App. of Sol. = clear
Oxidizer 0,05M for Äkta Iodine/Py/H2O Iodine Content = L560250-04 4 x 2.5 L 2.5 L GL45
and Oligo Pilot 11.4-14.0 g/l
0,05M/90/10 App. of Sol. = clear
m/v/v

10

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Quality Control Quality Assurance

SAFC has rigorous QC protocol for every
product produced to identify purity levels
against set specifications, including custom
QC testing. State-of-the-art analytical
methods include:
• RP & SAX HPLC
• LC-MS
• NMR (31P, 1H, 13C, 19F)
• Nucleic acid synthesis test
• FT-IR
• Titration & “Wet Chemistry”
• UV/VIS
• Karl Fischer water analysis
• Mercury porosimetry
As a trusted partner to the oligonucleotide
market, SAFC assists its customers in
new product development. We know that
developing materials includes having insight
to their quality requirements. As a result,
our company culture fosters continuous
process improvement and employs quality
systems to provide complete traceability
on all our raw materials, processes and
procedures. We serve customers conducting
audits with complete documentation and
files; our quality assurance department
routinely accepts requests for documentation,
including Certificates of Origin. Our Hamburg
facility was one of the first in the industry to
be ISO 9001 certified (1993), and we have
synthesized amidites and liquid reagents
under ISO9000:2000 since then.

Abbreviations

ACN Acetonitrile

DCM Dichloromethane

TCA Trichloroacetic Acid

TFA Trifluoroacetic Acid

DCA Dichloroacetic Acid

THF Tetrahydrofurane

Ac2O Acetic Acid Anhydride

Py Pyridine

NMI N-Methylimidazole

Tac2O tert. Butylphenoxyacetyl Acetic Acid Anhydride

DCI 4,5-Dicyanoimidazole

ETT 5-Ethylthio-1H-tetrazole

11
 Solutions for Oligonucleotides Synthesis
Liquid Reagents
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