Reagents for Nucleic Acid Chemistry
Technical Note11/17/2019 2:11 pm

Published November 17, 2019

Our nucleotide synthesis is modeled to introduce technical & chemical optimization from start to finish. We achieve that by utilizing our precision arsenal of formulations to aid & improve very specific moments throughout our solid-phase production. Activation, sulfurizing, phosphorylating and capping reagents help add an extra layer of customization to every project we synthesize. NHS Esters enhance affinity and fluorescence and our mono-,di-, triphosphates offer more control to certain chemical reactions. 

See the full list of in-house Reagents used in our synthesis below:


Reagents for nucleic acid chemistry

A: Activation Reagents 
1 H -1,2,4-Triazole, (1,2,4-Triazole) 
1 H -Imidazole-4,5-dicarbonitrile, (Dicyanoimidazole (DCI)) 
5-Benzyl-thio-1-H-tetrazole (BMT) 
5-Ethyl-thio-1-H-tetrazole (ETT) 
Diisopropyl-ammonium-1 H -tetrazolide 
Dimethoxytrityl-Chloride; DMTr-Chloride 
Mesitylene Sulphonyl-3-Nitro-1,2,4-Triazole (MSNT)) 
Monoimethoxytrityl-Chloride; MMTr-Chloride 
Trimethoxytrityl-Chloride; TMTr-Chloride 
B: Beaucage Reagents &  Sufurizing reagents 
Phenylacetyl-Disulfide (PADS) 
Silanized Bottle (for Beaucage Reagent) 
DDTT ((Dimethylamino-methylidene)amino)-3 H -1,2,4-dithiazoline-3-thione / Sulfurizing Reagent 
3 H -1,2-Benzodithiol-3-one-1,1-dioxide/ Sulfurizing Reagent / Sulfurizing Reagent (Beaucage Reagent) 
C: Phosphorylating Reagents 
Dichloromethoxy-phosphite 
2-Cyanoethyl- N , N , N , N -teraisopropylphosphane 
Bis (diisopropylamino)-chlorophosphine 
Cyanoethyl-dichlorophosphite 
Diethoxy- N , N -diisopropyl-phosphoramidite 
Diethyl-phosphorochloride 
Ethylene-glycol-morpholino phosphoramidite 
Methoxy- N , N , N , N -tetraisopropylphosphane 
N , N -Diisopropylamino-Cyanoethyl phosphonamidic-chloride 
N , N -Diisopropylamino-methyl-phosphonamidic-chloride 
N , N -Diisopropyl-methoxy-phosphonamidic-Cl 
O -Chlorophenyl-phosphorodichloridate 
P -Ethoxy-Chloro-Reagent 
D: Nucleoside Synthesis Reagents 
4-Isopropyl-Phenoxy-Acetyl-Chloride 
Bis-Silyating Reagent 
E: Sugars, Purines & Pyrimidines 
1,3,5-Tri – O -acetyl-2-deoxy- β -L-ribose 
1,3,5-Tri– O -acetyl-2-deoxy- β -D-ribose 
1-Alpha-Chloro-3,5-ditoluoyl-2-deoxy- β -D-ribose 
1- O -Methyl-2,3,5-tri- O -benzoyl- β -D-ribose 
2,3,5- O -Tribenzoyl- β -D-Ribofuranosyl-1-Acetate 
2-Deoxy- β -D-ribose 
2-Deoxy- β -L-ribose 
6-Chloro-7-deaza-Guanine 
6-Chloro-7-deaza-Purine 
6-Chloro-Guanine 
6-Chloro-Purine

NHS ester/Monophosphate/Diphosphate: NHS esters

A: Fluorescein 
5-Fluorescein-Dipivalate-NHS Ester (5-FAM Dipivalate NHS Ester)\"
5-Fluorescein-NHS Ester(5-FAM NHS Ester)
6-Fluorescein-Dipivalate-NHS Ester (6-FAM Dipivalate NHS Ester)
6-Fluorescein-NHS Ester (6-FAM NHS Ester)
B: Biotin 
Biotin-Amido-Caproate- N -Hydroxy 
Biotin-Ester ( N -Hydroxysuccinimide) 
Biotin-X-Y-SSE (Biotinamidohexanoyl-amidobutanoyl Succinimidyl ester)

Monophosphates

A: Deoxy  N -Alkylated monophosphates 
N 1 -Methyl-deoxyadenosine-5’-monophosphate 
N 3 -Methyl-deoxycytidine-5’-monophosphate 
N 6 -Methyl-deoxyadenosine-5’-monophosphate 
B: Etheno deoxy & ribo monophosphates 
Etheno-deoxycytidine-5’-monophosphate 
Etheno-ribocytidine-5’-monophosphate 
C: 7-Deaza deoxymonophosphate 
7-Deaza-deoxyadenosine-5’-monophosphate 
D: 2’- O -Methyl-ribo monophosphates 
2’- O -Methyl-adenosine ( N 6 -Benzyl)-5’-monophosphate 
2’- O -Methyl-cytidine-5’-monophosphate 
2’- O -Methyl-guanosine-5’-monophosphate 
E:  β -L-ribo monophosphates 
β -L-Adenosine-5’-monophosphate sodium salt 
β -L-Uridine-5’-monophosphate sodium salt 
F: 3'-Substituted-ribo monophosphates 
3'-Amino-guanosine-5’-monophosphate 
3'-Methyl-guanosine-5’-monophosphate 
G: ribo monophosphate 
Thymidine-5’-monophosphate 
H: Iso ribo monophosphate 
Iso-guanosine ( N -iBu)-5’-monophosphate

Diphosphates 

A: 2'- O -Methyl ribo 3’,5’-diphosphates 
2'- O -Methyl-adenosine-3’,5’-diphosphate disodium salt 
2'- O -Methyl-cytidine-3’,5’-diphosphate disodium salt 
2'- O -Methyl-guanosine-3’,5’-diphosphate disodium salt 
2'- O -Methyl-uridine-3’,5’-diphosphate disodium salt 
B: Ribo U 5'-diphoosphates 
Uridine-5’-diphosphate 
Uridine-5’-diphosphate disodium salt 

Triphosphates

A: Etheno deoxy 5’-triphosphates 
Etheno-deoxyadenosine-5’-triphosphate disodium salt 
Etheno-deoxycytidine-5’-triphosphate disodium salt 
B: 7-Deaza-deoxy 5’-triphosphates 
7-Deaza-deoxyadenosine-5’-triphosphate disodium salt 
7-Deaza-deoxyguanosine-5’-triphosphate disodium salt 
C: Iso deoxy Triphosphate 
Iso-deoxyguanosine-5’-triphosphate disodium salt 
D: 7-Deaza-7-Propargylamine, dideoxy Triphosphates 
7-Deaza-7-propargylamine-2',3'-dideoxyadenosine-5’-triphosphate 
7-Deaza-7-propargylamine-2',3'-dideoxyadenosine-5’-triphosphate disodium salt 
7-Deaza-7-propargylamine-2',3'-dideoxyguanosine-5’-triphosphate disodium salt 
E: 5-Propargyl amine-2',3'-Dideoxy Triphosphates 
5-Propargylamine-2',3'-dideoxycytidine-5’-triphosphate 
5-Propargylamine-2',3'-dideoxycytidine-5’-triphosphate disodium salt 
5-Propargylamine-2',3'-dideoxyuridine-5’-triphosphate disodium salt 
F: 2',3'-Dideoxy G Triphosphate 
2',3'-Dideoxyguanosine-5’-triphosphate 
G: 2'- O -Methyl-ribo 5’-triphosphates 
2'- O -Methyl-adenosine-5’-triphosphate disodium salt 
2'- O -Methyl-cytidine-5’-triphosphate disodium salt 
2'- O -Methyl-guanosine-5’-triphosphate disodium salt 
2'- O -Methyl-uridine-5’-triphosphate disodium salt 
H: Ara-ribo Triphosphates 
Ara-adenosine-5’-triphosphate disodium salt 
Ara-cytidine-5’-triphosphate disodium salt 
Ara-guanosine-5’-triphosphate disodium salt 
Ara-uridine-5’-triphosphate disodium salt 
I: Ara-2'- O -Methyl-ribo Triphosphates 
Ara-(2'- O -Methyl)-adenosine-5’-triphosphate disodium salt 
Ara-(2'- O -Methyl)-cytidine-5’-triphosphate disodium salt 
Ara-(2'- O -Methyl)-guanosine-5’-triphosphate disodium salt 
Ara-(2'- O -Methyl)-uridine-5’-triphosphate disodium salt 
J: Iso ribo triphosphate 
Iso-Guanosine-5’-triphosphate disodium salt

Solvents/Reagents-DNA Synthesis 

A: PolyPlex Oligo-Synthesizer 
Acetonitrile Anhydrous (Phosphoramidite Diluent & Washings), PolyPlex Oligonucleotide Synthesizer 
Acetonitrile Wash Grade,PolyPlex Oligonucleotide Synthesizer 
Activation Reagent (0.25M 4,5-Dicyanoimidazole/Acetonitrile), PolyPlex Oligonucleotide Synthesizer 
Activation Reagent (0.25M 5-Ethylthio Tetrazole/Acetonitrile), PolyPlex Oligonucleotide Synthesizer 
Activation Reagent (0.45M 5-Ethylthio Tetrazole/Acetonitrile), PolyPlex Oligonucleotide Synthesizer 
Activation Reagent (BMT Solution) (0.3M Benzylthio Tetrazole/Acetonitrile) PolyPlex Oligonucleotide Synthesizer 
AMA Reagent, PolyPlex Oligonucleotide Synthesizer 
CAP A (Acetic Anhydride/Pyridine/THF),PolyPlex Oligonucleotide Synthesizer 
CAP B (10%  N -Methylimidazole/THF),PolyPlex Oligonucleotide Synthesizer 
CAP B (16%  N -Methylimidazole/THF), PolyPlex Oligonucleotide Synthesizer 
DDTT Solution 1 [0.05M] (Sulfurizing Reagent), PolyPlex Oligonucleotide Synthesizer 
DDTT Solution 1 [0.10M] (Sulfurizing Reagent), PolyPlex Oligonucleotide Synthesizer 
DMTr Removal Reagent (3% Dichloracetic Acid/Dichloromethane), PolyPlex Oligonucleotide Synthesizer 
DMTr Removal Reagent (3% Trichloracetic Acid/Dichloromethane), PolyPlex Oligonucleotide Synthesizer 
Oxidation Solution (0.02M Iodine/Pyridine/H2O/THF), PolyPlex Oligonucleotide Synthesizer 
Oxidation Solution (0.1M Iodine/Pyridine/H2O/THF), PolyPlex Oligonucleotide Synthesizer 
Silanized Bottles for Beaucage Reagent, PolyPlex Oligonucleotide Synthesizer 
Sulfurizing Reagent (Beaucage Reagent) for Introduction of Phosphorothioate (S-oligonucleotide), PolyPlex Oligonucleotide Synthesizer 
Thiophenol/Triethylamine/Dioxane, PolyPlex Oligonucleotide Synthesizer 
B: MerMade Oligo-Synthesizer 
Acetonitrile Anhydrous (Phosphoramidite Diluent & Washings), MerMade Oligonucleotide Synthesizer 
Acetonitrile Wash Grade, MerMade Oligonucleotide Synthesizer 
Activation Reagent (0.25M 4,5-Dicyanoimidazole/Acetonitrile), MerMade Oligonucleotide Synthesizer 
Activation Reagent (0.25M 5-Ethylthio Tetrazole/Acetonitrile), MerMade Oligonucleotide Synthesizer 
Activation Reagent (0.45M 5-Ethylthio Tetrazole/Acetonitrile), MerMade Oligonucleotide Synthesizer 
Activation Reagent (BMT Solution) (0.3M Benzylthio Tetrazole/Acetonitrile) MerMade Oligonucleotide Synthesizer 
AMA Reagent, MerMade Oligonucleotide Synthesizer 
CAP A (Acetic Anhydride/Pyridine/THF),MerMade Oligonucleotide Synthesizer 
CAP B (10%  N -Methylimidazole/THF), MerMade Oligonucleotide Synthesizer 
CAP B (16%  N -Methylimidazole/THF), MerMade Oligonucleotide Synthesizer 
DDTT Solution 1 [0.05M] (Sulfurizing Reagent), MerMade   Oligonucleotide Synthesizer 
DDTT Solution 1 [0.10M] (Sulfurizing Reagent), MerMade   Oligonucleotide Synthesizer 
DMTr Removal Reagent (2.5% Dichloracetic Acid/Dichloromethane), MerMade Oligonucleotide Synthesizer 
DMTr Removal Reagent (3% Trichloracetic Acid/Dichloromethane), MerMade Oligonucleotide Synthesizer 
Oxidation Solution (0.02M Iodine/Pyridine/H2O/THF), MerMade Oligonucleotide Synthesizer 
Oxidation Solution (0.1M Iodine/Pyridine/H2O/THF), MerMade Oligonucleotide Synthesizer 
Silanized Bottles for Beaucage Reagent, MerMade Oligonucleotide Synthesizer 
Sulfurizing Reagent (Beaucage Reagent) for Introduction of Phosphorothioate (S-oligonucleotide), MerMade Oligonucleotide Synthesizer 
Thiophenol/Triethylamine/Dioxane, MerMade Oligonucleotide Synthesizer 
C: Expedite Oligo-Synthesizer 
Acetonitrile Anhydrous (Phosphoramidite Diluent & Washings), Expedite Oligonucleotide Synthesizer 
Acetonitrile Wash Grade, Expedite Oligonucleotide Synthesizer 
Activation Reagent (0.25M 4,5-Dicyanoimidazole/Acetonitrile), Expedite Oligonucleotide Synthesizer 
Activation Reagent (0.25M 5-Ethylthio Tetrazole/Acetonitrile), Expedite Oligonucleotide Synthesizer 
Activation Reagent (0.45M 5-Ethylthio Tetrazole/Acetonitrile), Expedite Oligonucleotide Synthesizer 
Activation Reagent (BMT Solution) (0.3M Benzylthio Tetrazole/Acetonitrile) Expedite Oligonucleotide Synthesizer 
AMA Reagent, Expedite Oligonucleotide Synthesizer 
CAP A (Acetic Anhydride/Pyridine/THF), Expedite Oligonucleotide Synthesizer 
CAP B (10%  N -Methylimidazole/THF), Expedite Oligonucleotide Synthesizer 
CAP B (16%  N -Methylimidazole/THF), Expedite Oligonucleotide Synthesizer 
DMTr Removal Reagent (2.5% Dichloracetic Acid/Dichloromethane), Expedite Oligonucleotide Synthesizer 
DMTr Removal Reagent (3% Trichloracetic Acid/Dichloromethane), Expedite Oligonucleotide Synthesizer 
Oxidation Solution (0.02M Iodine/Pyridine/H2O/THF), Expedite Oligonucleotide Synthesizer 
Oxidation Solution (0.1M Iodine/Pyridine/H2O/THF), Expedite Oligonucleotide Synthesizer 
Silanized Bottles for Beaucage Reagent, Expedite Oligonucleotide Synthesizer 
Sulfurizing Reagent (Beaucage Reagent) for Introduction of Phosphorothioate (S-oligonucleotide), Expedite Oligonucleotide Synthesizer 
Thiophenol/Triethylamine/Dioxane, Expedite Oligonucleotide Synthesizer 
D: Expedite Oligo-Synthesizer 
Activator (Benzyl thio tetrazole; 0.2M in acetonitrile) Akta Oligonucleotide Synthesizer 
Cap A ( N -Methyl imidazole; 20% in Acetonitrile) Akta Oligonucleotide Synthesizer 
Cap B1 (Acetic Anhydride; 40% (v:v) in Acetonitrile) Akta Oligonucleotide Synthesizer 
Cap B2 (Symmetrical Collidine; 60% (v:v) in Acetonitrile, Akta Oligonucleotide Synthesizer 
Deblock (3% DCA in Toluene) Akta Oligonucleotide Synthesizer 
Oxidizer 4 Liter 50 mM Iodine in 10% Water/Pyridine) Akta Oligonucleotide Synthesizer 
E: ABI 3900 Oligo-Synthesizer 
Acetonitrile Anhydrous (Phosphoramidite Diluent & Washings), ABI 3900 Oligonucleotide Synthesizer 
Acetonitrile Wash Grade, ABI 3900 Oligonucleotide Synthesizer 
Activation Reagent (0.25M 4,5-Dicyanoimidazole/Acetonitrile), ABI 3900 Oligonucleotide Synthesizer 
Activation Reagent (0.25M 5-Ethylthio Tetrazole/Acetonitrile) 
Activation Reagent (0.45M 5-Ethylthio Tetrazole/Acetonitrile), ABI 3900 Oligonucleotide Synthesizer 
Activation Reagent (BMT Solution) (0.3M Benzylthio Tetrazole/Acetonitrile) 
AMA Reagent, ABI 3900 Oligonucleotide Synthesizer 
CAP A (Acetic Anhydride/Pyridine/THF), ABI 3900 Oligonucleotide Synthesizer 
CAP B (10%  N -Methylimidazole/THF), ABI 3900 Oligonucleotide Synthesizer 
CAP B (16%  N -Methylimidazole/THF), ABI 3900 Oligonucleotide Synthesizer 
DDTT Solution 1 [0.05M] (Sulfurizing Reagent), ABI 3900 Oligonucleotide Synthesizer 
DDTT Solution 1 [0.10M] (Sulfurizing Reagent), ABI 3900 Oligonucleotide Synthesizer 
DMT Removal Reagent (3% Dichloracetic Acid/Dichloromethane), ABI 3900 Oligonucleotide Synthesizer 
DMT Removal Reagent (3% Trichloracetic Acid/Dichloromethane) 
Oxidation Solution (0.02M Iodine/Pyridine/H2O/THF), ABI 3900 Oligonucleotide Synthesizer 
Oxidation Solution (0.1M Iodine/Pyridine/H2O/THF), ABI 3900 Oligonucleotide Synthesizer 
Silanized Bottles for Beaucage Reagent, ABI 3900 Oligonucleotide Synthesizer 
Sulfurizing Reagent (Beaucage Reagent) for Introduction of Phosphorothioate (S-oligonucleotide), ABI 3900 Oligonucleotide Synthesizer 
Thiophenol/Triethylamine/Dioxane, ABI 3900 Oligonucleotide Synthesizer 
F: ABI Oligo-Synthesizer 
Acetonitrile Anhydrous (Phosphoramidite Diluent & Washings), ABI Oligonucleotide Synthesizer 
Acetonitrile Wash Grade, ABI Oligonucleotide Synthesizer 
Activation Reagent ((0.25M 5-Ethylthio Tetrazole/Acetonitrile), ABI Oligonucleotide Synthesizer 
Activation Reagent (0.25M 4,5-Dicyanoimidazole/Acetonitrile), ABI Oligonucleotide Synthesizer 
Activation Reagent (0.45M 5-Ethylthio Tetrazole/Acetonitrile), ABI Oligonucleotide Synthesizer 
Activation Reagent (BMT Solution) (0.3M Benzylthio Tetrazole/Acetonitrile), ABI Oligonucleotide Synthesizer 
AMA Reagent, ABI Oligonucleotide Synthesizer 
CAP A (Acetic Anhydride/Pyridine/THF), ABI Oligonucleotide Synthesizer 
CAP B (10% N-Methylimidazole/THF), ABI Oligonucleotide Synthesizer 
CAP B (16% N-Methylimidazole/THF), ABI Oligonucleotide Synthesizer 
DMT Removal Reagent  (3% Dichloracetic Acid/Dichloromethane), ABI Oligonucleotide Synthesizer 
DMT Removal Reagent (3% Trichloracetic Acid/Dichloromethane), ABI Oligonucleotide Synthesizer 
Oxidation Solution (0.02M Iodine/Pyridine/H2O/THF), ABI Oligonucleotide Synthesizer 
Oxidation Solution (0.1M Iodine/Pyridine/H2O/THF), ABI   Oligonucleotide Synthesizer 
Silanized Bottles for Beaucage Reagent, ABI Oligonucleotide Synthesizer 
Sulfurizing Reagent (Beaucage Reagent) for Introduction of Phosphorothioate (S-oligonucleotide), ABI Oligonucleotide Synthesizer 
Thiophenol/Triethylamine/Dioxane, ABI Oligonucleotide Synthesizer 
G: Solvents/Reagents For  H -phosphonate Chemistry 
Acetonitrile/Pyridine (50:50), Anhydrous (Diluent for Monomers) 
Acetonitrile/Pyridine (95:5), Anhydrous (Diluent for Activator) 
Acetonitrile/Pyridine (wash solvent) 
Activator for monomers and Capping Reagent (Adamantane catbonyl chloride) 
Capping for ABI Synthesizers (Isopropyl Phosphite/Acetonitrile/Pyridine) 
Dipentaflurophenyl Carbonate (Reagent for H-phosphonate) 
Oxidation Solution 1 (Iodine in Pyridine/H2O/THF) 
Oxidation Solution 2  (THF/H2O/TEA) 
H: Deprotection solution for DNA Synthesis 
Ammonia Free Oligo Deprotection Solution 
Deprotection solution for Levulinyl