What are phosphoramidites used for?

Phosphoramidites are activated monomers used in solid-phase DNA and RNA oligonucleotide synthesis.

What is the difference between DNA and RNA phosphoramidites?

RNA phosphoramidites include additional 2′-hydroxyl protecting groups, making them more sensitive to moisture and handling conditions.

Why is moisture control important for phosphoramidites?

Moisture can cause premature hydrolysis of phosphoramidites, reducing coupling efficiency and synthesis yield.

Can phosphoramidites be used for long oligonucleotide synthesis?

Yes, high-quality phosphoramidites are essential for achieving good yields in long and complex oligonucleotide sequences.

Are modified phosphoramidites available for custom oligos?

Modified and specialty phosphoramidites are commonly used to introduce functional groups or labels into oligonucleotides.

Phosphoramidites - RNA / BOC Sciences

5'-O-DMTr-5-trifluoroacetylaminomethyl-2'-O-TBDMS uridine 3'-CED phosphoramidite

Description: 5'-O-DMTr-5-trifluoroacetylaminomethyl-2'-O-TBDMS uridine 3'-CED phosphoramidite is a chemically modified phosphoramidite designed for oligonucleotide synthesis. Its structure features a 5'-dimethoxytrityl (DMTr) group for temporary protection during solid-phase synthesis, a 5-position trifluoroacetylaminomethyl group to introduce functionalized side chains, a 2'-O-tert-butyldimethylsilyl (TBDMS) group for ribose protection, and a 3'-cyanoethyl diisopropyl phosphoramidite for coupling. This compound is used in the synthesis of RNA oligonucleotides, enabling the incorporation of modified residues for structural, therapeutic, or biochemical applications, such as enhancing stability or introducing specific reactive functionalities.

CAT: BRP-02487

Molecular Formula: C48H63F3N5O10PSi

Molecular Weight: 986.11

Purity: ≥95%

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InChIKey: YWHOOIBNERVNIX-KMXDGGROSA-N

SMILES: COC(C=C1)=CC=C1C(C2=CC=C(OC)C=C2)(C3=CC=CC=C3)OC[C@H]4O[C@@H](N(C=C(CNC(C(F)(F)F)=O)C5=O)C(N5)=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]4OP(N(C(C)C)C(C)C)OCCC#N

IUPAC Name: (2R,3R,4R,5R)-2-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-4-((tert-butyldimethylsilyl)oxy)-5-(2,4-dioxo-5-((2,2,2-trifluoroacetamido)methyl)-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-3-yl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C48H63F3N5O10PSi/c1-31(2)56(32(3)4)67(63-27-15-26-52)65-40-39(30-62-47(34-16-13-12-14-17-34,35-18-22-37(60-8)23-19-35)36-20-24-38(61-9)25-21-36)64-43(41(40)66-68(10,11)46(5,6)7)55-29-33(42(57)54-45(55)59)28-53-44(58)48(49,50)51/h12-14,16-25,29,31-32,39-41,43H,15,27-28,30H2,1-11H3,(H,53,58)(H,54,57,59)/t39-,40-,41-,43-,67?/m1/s1

Synonyms: DMTr-2'-O-TBDMS-5-trifluoroacetylaminomethyl-rU-3'-CE-Phosphoramidite; 5'-DMT-2'-O-TBDMS-5-trifluoroacetylaminomethyl-rU Phosphoramidite; DMT-2'-O-TBDMS-5-trifluoroacetylaminomethyl-rU Phosphoramidite; 5'-O-(4,4-Dimethoxytrityl)-5-trifluoroacetylaminomethyl-2'-O-[(tert-butyl)dimethylsilyl]uridine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite; 2'-O-tert-Butyldimethylsilyl-5'-O-DMT-5-trifluoroacetylaminomethyl-uridine 3'-CE phosphoramidite; 5'-O-(4,4'-Dimethoxytrityl)-2'-O-(t-butyl-dimethylsilyl)-5-trifluoroacetylaminomethyl-uridine-3'-cyanoethyl Phosphoramidite

5'-O-DMTr-2'-O-(N-tri-fluoroacetylamino)ethyl-5-methyluridine 3'-CE-phosphoramidite

Description: 5'-O-DMTr-2'-O-(N-tri-fluoroacetylamino)ethyl-5-methyluridine 3'-CE-phosphoramidite is a modified phosphoramidite designed for oligonucleotide synthesis. The structure includes a 5-methyluridine base with a 2'-O-(N-tri-fluoroacetylamino)ethyl modification on the ribose, which enhances the molecule's stability and may influence its interaction with biological systems. The 5'-hydroxyl group is protected with a dimethoxytrityl (DMTr) group for efficient coupling during solid-phase synthesis, while the 3'-hydroxyl is protected with a cyanoethyl (CE) phosphoramidite group for coupling in the synthesis process. This modification improves the stability and specificity of the resulting oligonucleotides, making it suitable for use in RNA-based applications, including therapeutic and diagnostic purposes.

CAT: BRP-02490

CAS: 200423-98-9

Molecular Formula: C44H53F3N5O10P

Molecular Weight: 899.89

Purity: ≥95%

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InChIKey: KYHISSPNOZNEDF-AHGBXEAISA-N

SMILES: N#CCCOP(OC1C(OC(N2C=C(C(=O)NC2=O)C)C1OCCNC(=O)C(F)(F)F)COC(C=3C=CC=CC3)(C4=CC=C(OC)C=C4)C5=CC=C(OC)C=C5)N(C(C)C)C(C)C

IUPAC Name: (2R,3R,4R,5R)-2-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-(2-(2,2,2-trifluoroacetamido)ethoxy)tetrahydrofuran-3-yl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C44H53F3N5O10P/c1-28(2)52(29(3)4)63(60-24-11-22-48)62-37-36(61-40(51-26-30(5)39(53)50-42(51)55)38(37)58-25-23-49-41(54)44(45,46)47)27-59-43(31-12-9-8-10-13-31,32-14-18-34(56-6)19-15-32)33-16-20-35(57-7)21-17-33/h8-10,12-21,26,28-29,36-38,40H,11,23-25,27H2,1-7H3,(H,49,54)(H,50,53,55)/t36-,37-,38-,40-,63?/m1/s1

Synonyms: 2'-O-Amino linker-5-methyl U CEP; Uridine, 5'-O-[bis(4-methoxyphenyl)phenylmethyl]-5-methyl-2'-O-[2-[(trifluoroacetyl)amino]ethyl]-, 3'-[2-cyanoethyl bis(1-methylethyl)phosphoramidite]; 5'-O-DMTr-2'-O-(N-tri-fluoroacetylamino)ethyl-5-MeU-3'-CE-Phosphoramidite; 5'-O-(4,4'-Dimethoxytrityl)-2'-O-(N-tri-fluoroacetylamino)ethyl-5-methyluridine-3'-[(2-cyanoethyl)-(N,N-diisopropropyl)]-Phosphoramidite; 2'-TFA-AE T amidite

Dimethyl P-[[[(2R,3S,4R,5R)-3-[[[bis(1-methylethyl)amino](2-cyanoethoxy)phosphino]oxy]-5-(3,4-dihydro-2,4-dioxo-1(2H)-pyrimidinyl)tetrahydro-4-methoxy-2-furanyl]oxy]methyl]phosphonate

Description: It is a modified phosphoramidite designed for medicinal chemistry purposes, likely targeting specific enzymes or pathways in nucleotide metabolism, cell signaling, or as a potential therapeutic agent for diseases where phosphorothioate or phosphonate derivatives play a key role in inhibition or modulation.

CAT: BRP-02493

CAS: 2197181-94-3

Molecular Formula: C21H36N4O10P2

Molecular Weight: 566.48

Purity: ≥95%

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InChIKey: CAAOTZQHIFLMLL-DPNUVZDTSA-N

SMILES: N#CCCOP(OC1C(OCP(=O)(OC)OC)OC(N2C=CC(=O)NC2=O)C1OC)N(C(C)C)C(C)C

IUPAC Name: 2-cyanoethyl ((2R,3S,4R,5R)-2-((dimethoxyphosphoryl)methoxy)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-methoxytetrahydrofuran-3-yl) diisopropylphosphoramidite

InChI: InChI=1S/C21H36N4O10P2/c1-14(2)25(15(3)4)36(33-12-8-10-22)35-18-17(29-5)19(24-11-9-16(26)23-21(24)27)34-20(18)32-13-37(28,30-6)31-7/h9,11,14-15,17-20H,8,12-13H2,1-7H3,(H,23,26,27)/t17-,18+,19-,20+,36?/m1/s1

Synonyms: MeMOP; Phosphonic acid, P-[[[(2R,3S,4R,5R)-3-[[[bis(1-methylethyl)amino](2-cyanoethoxy)phosphino]oxy]-5-(3,4-dihydro-2,4-dioxo-1(2H)-pyrimidinyl)tetrahydro-4-methoxy-2-furanyl]oxy]methyl]-, dimethyl ester

1-O-(4,4'-Dimethoxytrityl)-3-O-succinyl-1,3-propanediol

Description: 1-O-(4,4'-Dimethoxytrityl)-3-O-succinyl-1,3-propanediol is a bifunctional molecule commonly used as a linker or spacer in the synthesis of oligonucleotides. The 1-hydroxyl group is protected with a 4,4'-dimethoxytrityl (DMT) group, which serves as a temporary protecting group during solid-phase synthesis, enabling stepwise addition of nucleotides. The 3-hydroxyl group is modified with a succinyl moiety, introducing a carboxylic acid functionality that allows covalent attachment to solid supports, such as controlled-pore glass (CPG) or polymers. This compound is critical in oligonucleotide synthesis, ensuring efficient attachment and controlled chain elongation during automated synthesis processes.

CAT: BRP-02496

CAS: 110916-49-9

Molecular Formula: C28H30O7

Molecular Weight: 478.53

Purity: ≥97%

Appearance: White or off-white solid

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Storage: Store at RT

Density: 1.193±0.06 g/cm3

Boiling Point: 638.6±55.0 °C at 760 mmHg

InChIKey: FDXRQUXDYAHNQG-UHFFFAOYSA-N

SMILES: COC1=CC=C(C=C1)C(C2=CC=CC=C2)(C3=CC=C(C=C3)OC)OCCCOC(=O)CCC(=O)O

IUPAC Name: 4-[3-[bis(4-methoxyphenyl)-phenylmethoxy]propoxy]-4-oxobutanoic acid

InChI: InChI=1S/C28H30O7/c1-32-24-13-9-22(10-14-24)28(21-7-4-3-5-8-21,23-11-15-25(33-2)16-12-23)35-20-6-19-34-27(31)18-17-26(29)30/h3-5,7-16H,6,17-20H2,1-2H3,(H,29,30)

Synonyms: Butanedioic acid, 1-[3-[bis(4-methoxyphenyl)phenylmethoxy]propyl] ester; 1-[3-[Bis(4-methoxyphenyl)phenylmethoxy]propyl] butanedioate; Butanedioic acid, mono[3-[bis(4-methoxyphenyl)phenylmethoxy]propyl] ester

GalNAc-EDTAECA-PEG2 Phosphoramidite

Description: It is a new diamine-scaffold-based phosphoramidite in the N-acetylgalactosamine (GalNAc)-siRNA conjugate that enhances siRNA delivery efficiency, particularly for liver targeting. It demonstrates superior silencing activity compared to the standard GalNAc L96 due to the incorporation of a PS-linkage at the 3' end, which increases resistance to nuclease degradation and prolongs gene silencing effects. This innovative structure provides a promising strategy for RNA-based therapeutics, especially in the treatment of undruggable diseases.

CAT: BRP-02497

CAS: 2766336-04-1

Molecular Formula: C90H150N13O42P

Molecular Weight: 2117.19

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Boiling Point: 1645.5±65.0 °C at 760 mmHg

InChIKey: SPYSMTSEACHRCL-MWVAOEIWSA-N

SMILES: N#CCCOP(OCCOCCN(CC(=O)NCCNC(=O)CCOCCOCCOC1OC(COC(=O)C)C(OC(=O)C)C(OC(=O)C)C1NC(=O)C)CCN(CC(=O)NCCNC(=O)CCOCCOCCOC2OC(COC(=O)C)C(OC(=O)C)C(OC(=O)C)C2NC(=O)C)CC(=O)NCCNC(=O)CCOCCOCCOC3OC(COC(=O)C)C(OC(=O)C)C(OC(=O)C)C3NC(=O)C)N(C(C)C)C(C)C

InChI: InChI=1S/C90H150N13O42P/c1-56(2)103(57(3)4)146(135-31-17-21-91)136-49-45-125-35-30-101(50-76(119)95-25-22-92-73(116)18-32-122-36-39-126-42-46-129-88-79(98-58(5)104)85(140-67(14)113)82(137-64(11)110)70(143-88)53-132-61(8)107)28-29-102(51-77(120)96-26-23-93-74(117)19-33-123-37-40-127-43-47-130-89-80(99-59(6)105)86(141-68(15)114)83(138-65(12)111)71(144-89)54-133-62(9)108)52-78(121)97-27-24-94-75(118)20-34-124-38-41-128-44-48-131-90-81(100-60(7)106)87(142-69(16)115)84(139-66(13)112)72(145-90)55-134-63(10)109/h56-57,70-72,79-90H,17-20,22-55H2,1-16H3,(H,92,116)(H,93,117)(H,94,118)(H,95,119)(H,96,120)(H,97,121)(H,98,104)(H,99,105)(H,100,106)/t70-,71-,72-,79-,80-,81-,82+,83+,84+,85-,86-,87-,88-,89-,90-,146?/m1/s1

Synonyms: GalNAc-EDT-(2-AECA)-PEG2 Phosphoramidite; Peracetylated-TG1 phosphoramidite; Tri-TG1(OAc)3 phosphoramidite; Tri-Gal(OAc)3 TG1 phosphoramidite

GalNAc-EDTAECA-PEG2-DMT

Description: It is a new diamine-scaffold structure that plays a significant role in enhancing the delivery and effectiveness of GalNAc-siRNA conjugated. It is often designed to improve the binding affinity of the siRNA to specific receptors, such as the asialoglycoprotein receptor (ASGPR) on hepatocytes (liver cells). By reinforcing the interaction between the conjugated siRNA and its target receptor, it ensures more efficient uptake of the siRNA into liver cells, which is pivotal for achieving therapeutic levels of gene silencing. Moreover, it may also include stabilizing modifications that protect the siRNA against degradation by nucleases, thus prolonging its half-life in circulation. Overall, it significantly contributes to the overall effectiveness of siRNA therapeutics by optimizing delivery to targeted tissues and enhancing their stability.

CAT: BRP-02498

Molecular Formula: C106H158N12O46

Molecular Weight: 2336.47

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InChIKey: XTXPAJCTQLIALI-PNRPZMGPSA-N

SMILES: O=C(CCOCCOCCO[C@H]1[C@H](NC(C)=O)[C@@H](OC(C)=O)[C@@H](OC(C)=O)[C@@H](COC(C)=O)O1)NCCNC(CN(CC(NCCNC(CCOCCOCCO[C@H]2[C@H](NC(C)=O)[C@@H](OC(C)=O)[C@@H](OC(C)=O)[C@@H](COC(C)=O)O2)=O)=O)CCN(CC(NCCNC(CCOCCOCCO[C@@H]3O[C@@H]([C@@H]([C@@H]([C@H]3NC(C)=O)OC(C)=O)OC(C)=O)COC(C)=O)=O)=O)CCOCCOC(NCC(O)COC(C4=CC=CC=C4)(C5=CC=C(OC)C=C5)C6=CC=C(OC)C=C6)=O)=O

InChI: InChI=1S/C106H158N12O46/c1-66(119)114-93-99(159-75(10)128)96(156-72(7)125)84(63-152-69(4)122)162-102(93)148-54-50-145-47-44-141-40-28-87(132)107-31-34-110-90(135)59-117(39-43-144-53-57-151-105(138)113-58-81(131)62-155-106(78-18-16-15-17-19-78,79-20-24-82(139-13)25-21-79)80-22-26-83(140-14)27-23-80)37-38-118(60-91(136)111-35-32-108-88(133)29-41-142-45-48-146-51-55-149-103-94(115-67(2)120)100(160-76(11)129)97(157-73(8)126)85(163-103)64-153-70(5)123)61-92(137)112-36-33-109-89(134)30-42-143-46-49-147-52-56-150-104-95(116-68(3)121)101(161-77(12)130)98(158-74(9)127)86(164-104)65-154-71(6)124/h15-27,81,84-86,93-104,131H,28-65H2,1-14H3,(H,107,132)(H,108,133)(H,109,134)(H,110,135)(H,111,136)(H,112,137)(H,113,138)(H,114,119)(H,115,120)(H,116,121)/t81?,84-,85-,86-,93-,94-,95-,96+,97+,98+,99-,100-,101-,102-,103-,104-/m1/s1

Synonyms: GalNAc-EDT-(2-AECA)-PEG2-DMT; Peracetylated-TG2-DMT; Tri-TG2(OAc)3-DMT; Tri-Gal(OAc)3 TG1-DMT

GalNAc-EDTAECA-PEG2-DMT-Suc

Description: It is a new diamine-scaffold structure that is designed to enhance the pharmacokinetic profiles of GalNAc-siRNA conjugated by providing increased metabolic stability. It often incorporates modifications that protect the siRNA from exonuclease degradation, which extends its half-life in circulation and improves its therapeutic efficacy. By ensuring more prolonged availability in the bloodstream, it contributes to the sustained release of siRNA at the target site, facilitating more effective gene silencing. Furthermore, it may also aid in optimizing the specificity and efficiency of liver-targeted delivery, making it valuable for the development of RNA-based therapeutics.

CAT: BRP-02499

Molecular Formula: C110H162N12O49

Molecular Weight: 2436.54

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InChIKey: JACYEVOOTPTQAH-BSHJQCNLSA-N

SMILES: O=C(CCOCCOCCO[C@H]1[C@H](NC(C)=O)[C@@H](OC(C)=O)[C@@H](OC(C)=O)[C@@H](COC(C)=O)O1)NCCNC(CN(CC(NCCNC(CCOCCOCCO[C@H]2[C@H](NC(C)=O)[C@@H](OC(C)=O)[C@@H](OC(C)=O)[C@@H](COC(C)=O)O2)=O)=O)CCN(CC(NCCNC(CCOCCOCCO[C@@H]3O[C@@H]([C@@H]([C@@H]([C@H]3NC(C)=O)OC(C)=O)OC(C)=O)COC(C)=O)=O)=O)CCOCCOC(NCC(OC(CCC(O)=O)=O)COC(C4=CC=CC=C4)(C5=CC=C(OC)C=C5)C6=CC=C(OC)C=C6)=O)=O

IUPAC Name: 1-(((2R,3R,4R,5R,6R)-3-acetamido-4,5-diacetoxy-6-(acetoxymethyl)tetrahydro-2H-pyran-2-yl)oxy)-16,19-bis(15-(((2R,3R,4R,5R,6R)-3-acetamido-4,5-diacetoxy-6-(acetoxymethyl)tetrahydro-2H-pyran-2-yl)oxy)-2,7-dioxo-10,13-dioxa-3,6-diazapentadecyl)-29-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-9,14,26,31-tetraoxo-3,6,22,25,30-pentaoxa-10,13,16,19,27-pentaazatetratriacontan-34-oic acid

InChI: InChI=1S/C110H162N12O49/c1-68(123)118-97-103(165-77(10)132)100(162-74(7)129)86(65-158-71(4)126)169-106(97)154-56-52-151-49-46-147-42-30-89(135)111-33-36-114-92(138)61-121(41-45-150-55-59-157-109(144)117-60-85(168-96(143)29-28-95(141)142)64-161-110(80-18-16-15-17-19-80,81-20-24-83(145-13)25-21-81)82-22-26-84(146-14)27-23-82)39-40-122(62-93(139)115-37-34-112-90(136)31-43-148-47-50-152-53-57-155-107-98(119-69(2)124)104(166-78(11)133)101(163-75(8)130)87(170-107)66-159-72(5)127)63-94(140)116-38-35-113-91(137)32-44-149-48-51-153-54-58-156-108-99(120-70(3)125)105(167-79(12)134)102(164-76(9)131)88(171-108)67-160-73(6)128/h15-27,85-88,97-108H,28-67H2,1-14H3,(H,111,135)(H,112,136)(H,113,137)(H,114,138)(H,115,139)(H,116,140)(H,117,144)(H,118,123)(H,119,124)(H,120,125)(H,141,142)/t85?,86-,87-,88-,97-,98-,99-,100+,101+,102+,103-,104-,105-,106-,107-,108-/m1/s1

Synonyms: GalNAc-EDT-(2-AECA)-PEG2-DMT-Suc; Peracetylated-TG2-DMT-Suc; Tri-TG2(OAc)3-DMT-Suc; Tri-Gal(OAc)3 TG1-DMT-Suc

GalNAc-EDTAECA-PEG2-OH

Description: It is a trivalent GalNAc precursor based on a diamine core, which serves as a crucial building block in the synthesis of GalNAc-siRNA conjugated. Its primary function is to facilitate the creation of ligands that can be efficiently attached to either the 5'-end or 3'-end of the sense strand of the oligonucleotide. By providing a versatile scaffold, it enables the development of siRNA molecules with enhanced liver-targeting capabilities due to the strong interactions of GalNAc with the asialoglycoprotein receptor (ASGPR). This targeted delivery is essential for improving the therapeutic efficacy of siRNA by promoting greater cellular uptake and allowing for effective silencing of the intended RNA targets.

CAT: BRP-02501

CAS: 2766335-88-8

Molecular Formula: C81H133N11O41

Molecular Weight: 1916.98

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Density: 1.344±0.10 g/cm3

Boiling Point: 1624.6±65.0 °C at 760 mmHg

InChIKey: ZMJAUJSGNNBXPE-LGAHQTLJSA-N

SMILES: O=C(OCC1OC(OCCOCCOCCC(=O)NCCNC(=O)CN(CC(=O)NCCNC(=O)CCOCCOCCOC2OC(COC(=O)C)C(OC(=O)C)C(OC(=O)C)C2NC(=O)C)CCN(CC(=O)NCCNC(=O)CCOCCOCCOC3OC(COC(=O)C)C(OC(=O)C)C(OC(=O)C)C3NC(=O)C)CCOCCO)C(NC(=O)C)C(OC(=O)C)C1OC(=O)C)C

InChI: InChI=1S/C81H133N11O41/c1-49(94)88-70-76(128-58(10)103)73(125-55(7)100)61(46-122-52(4)97)131-79(70)119-40-37-116-34-31-112-26-13-64(106)82-16-19-85-67(109)43-91(24-29-115-30-25-93)22-23-92(44-68(110)86-20-17-83-65(107)14-27-113-32-35-117-38-41-120-80-71(89-50(2)95)77(129-59(11)104)74(126-56(8)101)62(132-80)47-123-53(5)98)45-69(111)87-21-18-84-66(108)15-28-114-33-36-118-39-42-121-81-72(90-51(3)96)78(130-60(12)105)75(127-57(9)102)63(133-81)48-124-54(6)99/h61-63,70-81,93H,13-48H2,1-12H3,(H,82,106)(H,83,107)(H,84,108)(H,85,109)(H,86,110)(H,87,111)(H,88,94)(H,89,95)(H,90,96)/t61-,62-,63-,70-,71-,72-,73+,74+,75+,76-,77-,78-,79-,80-,81-/m1/s1

Synonyms: GalNAc-EDTAECA-PEG1-CH2CH2OH; GalNAc-EDT-(2-AECA)-PEG2-OH; Peracetylated-TG1; Tri-TG1(OAc)3; Tri-Gal(OAc)3 TG1

2'-TC-G(iBu) Phosphoramidite

Description: 2'-TC-G(Ibu) Phosphoramidite is a modified phosphoramidite featuring a TC modification on the ribose sugar and a guanine base that is protected with an isobutyryl (Ibu) group at the exocyclic amine. The 2'-thio modification enhances the stability and resistance of the resulting oligonucleotides to nuclease degradation, improving their overall chemical stability. The isobutyryl protection on the guanine base ensures selective incorporation and prevents unwanted side reactions during the synthesis process. The 3'-cyanoethyl (CE) phosphoramidite group facilitates efficient addition of this modified nucleoside into oligonucleotides. This phosphoramidite is particularly useful for synthesizing oligonucleotides with enhanced stability, making it valuable for therapeutic applications, including antisense oligonucleotides and other RNA-based therapies.

CAT: BRP-02502

CAS: 1219089-77-6

Molecular Formula: C49H61N8O11PS2

Molecular Weight: 1033.17

Purity: ≥98%

Appearance: White to light yellow to light orange solid

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Storage: Store at -20 °C

InChIKey: LXUNLMGCWYNULU-NWGULGMGSA-N

Solubility: Soluble in Acetonitrile:Toluene (1:1)

SMILES: CC(C)C(=O)NC1=NC2=C(C(=O)N1)N=CN2[C@H]3[C@@H]([C@@H]([C@H](O3)COC(C4=CC=CC=C4)(C5=CC=C(C=C5)OC)C6=CC=C(C=C6)OC)OP(N(C(C)C)C(C)C)OCCC#N)OC(=S)N7CCS(=O)(=O)CC7

IUPAC Name: O-[(2R,3R,4R,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxy-2-[2-(2-methylpropanoylamino)-6-oxo-1H-purin-9-yl]oxolan-3-yl] 1,1-dioxo-1,4-thiazinane-4-carbothioate

InChI: InChI=1S/C49H61N8O11PS2/c1-31(2)44(58)53-47-52-43-40(45(59)54-47)51-30-56(43)46-42(67-48(70)55-24-27-71(60,61)28-25-55)41(68-69(65-26-12-23-50)57(32(3)4)33(5)6)39(66-46)29-64-49(34-13-10-9-11-14-34,35-15-19-37(62-7)20-16-35)36-17-21-38(63-8)22-18-36/h9-11,13-22,30-33,39,41-42,46H,12,24-29H2,1-8H3,(H2,52,53,54,58,59)/t39-,41-,42-,46-,69?/m1/s1

Synonyms: N2-Isobutyryl-O5'-(4,4'-dimethoxytrityl)-O2'-(1,1-dioxothiomorpholine-4-thiocarbonyl)guanosine O3'-(O-(2-cyanoethyl)-N,N-diisopropylphosphoramidite); DMT-2'O-TC-rG(iBu) Phosphoramidite; Guanosine, 5'-O-[bis(4-methoxyphenyl)phenylmethyl]-N-(2-methyl-1-oxopropyl)-, 3'-[2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite] 2'-(1,1-dioxido-4-thiomorpholinecarbothioate); DMT-2'-O-TC-rG(ibu) Phosphoramidite

NED CE Phosphoramidite

Description: NED CE Phosphoramidite is a fluorescent phosphoramidite derivative designed for site-specific incorporation of the NED dye (a proprietary xanthene-based fluorophore) into oligonucleotides during solid-phase synthesis. NED emits in the yellow-orange spectrum with an excitation maximum at 546 nm and emission at 575 nm, making it suitable for multiplex PCR, fragment analysis, and genetic typing applications. The phosphoramidite chemistry ensures efficient coupling in automated synthesizers, while the CE (cyanoethyl) protecting group on the phosphate enhances stability during synthesis.

CAT: BRP-02657

Molecular Formula: C50H56CI3FN3O10P

Molecular Weight: 1015.33

Purity: ≥97%

Appearance: Off-white solid

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Synonyms: NED Phosphoramidite

PET CE Phosphoramidite

Description: PET CE Phosphoramidite is a fluorescent phosphoramidite derivative designed for site-specific incorporation of the PET dye (a proprietary xanthene-based fluorophore) into oligonucleotides during solid-phase synthesis. The PET dye emits in the red-orange spectrum, making it suitable for multiplex PCR, fragment analysis, and genetic typing applications. The phosphoramidite chemistry ensures efficient coupling in automated synthesizers, while the CE (cyanoethyl) protecting group on the phosphate enhances stability during synthesis.

CAT: BRP-02658

Molecular Formula: C54H60CI2N3O10P

Molecular Weight: 1012.96

Purity: ≥97%

Appearance: Off-white solid

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Synonyms: PET Phosphoramidite

CAL Fluor Red 635 CE Phosphoramidite

Description: CAL Fluor Red 635 Phosphoramidite is a xanthene-based fluorescent phosphoramidite derivative designed for site-specific incorporation of the CAL Fluor Red 635 dye into oligonucleotides during solid-phase synthesis. With an excitation maximum at 616 nm and emission at 637 nm, it serves as a cost-effective alternative to LC Red 640, enabling applications in real-time PCR (qPCR), molecular beacons, and Scorpions primers.

CAT: BRP-02659

CAS: 1206197-75-2

Molecular Formula: C50H63Cl2F6N5O4P2

Molecular Weight: 1044.92

Purity: ≥97%

Appearance: Violet solid

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InChIKey: AIASBRLHSJHOFE-UHFFFAOYSA-N

SMILES: N#CCCOP(N(C(C)C)C(C)C)OC1CCN(C(C2=CC(Cl)=C(Cl)C=C2C(C3=C4C=C(N5CC)C(C(C)=CC5(C)C)=C3)=C6C=C(C(C=C6O4)=[N+]7CC)C(C)=CC7(C)C)=O)CC1.F[P-](F)(F)(F)(F)F

IUPAC Name: 6-(4,5-dichloro-2-(4-(((2-cyanoethoxy)(diisopropylamino)phosphaneyl)oxy)piperidine-1-carbonyl)phenyl)-1,11-diethyl-2,2,4,8,10,10-hexamethyl-10,11-dihydro-2H-pyrano[3,2-g:5,6-g']diquinolin-1-ium;hexafluorophosphate

InChI: InChI=1S/C50H63Cl2N5O4P.F6P/c1-13-55-43-26-45-39(22-35(43)32(7)28-49(55,9)10)47(40-23-36-33(8)29-50(11,12)56(14-2)44(36)27-46(40)60-45)37-24-41(51)42(52)25-38(37)48(58)54-19-16-34(17-20-54)61-62(59-21-15-18-53)57(30(3)4)31(5)6;1-7(2,3,4,5)6/h22-31,34H,13-17,19-21H2,1-12H3;/q+1;-1

Synonyms: CAL Fluor Red 635 Phosphoramidite; CAL Fluor Red 635 Amidite; Pyrano[3,2-g:5,6-g']diquinolin-13-ium, 6-[2-[[4-[[[bis(1-methylethyl)amino](2-cyanoethoxy)phosphino]oxy]-1-piperidinyl]carbonyl]-4,5-dichlorophenyl]-1,11-diethyl-1,2,10,11-tetrahydro-2,2,4,8,10,10-hexamethyl-, hexafluorophosphate(1-) (1:1)

Related CAS: 1206197-74-1 (free base)

ZEN CE Phosphoramidite

Description: ZEN CE Phosphoramidite is a dual-quenching phosphoramidite reagent designed for solid-phase oligonucleotide synthesis, enabling site-specific incorporation of the ZEN quencher moiety into DNA or RNA strands. The ZEN quencher is a non-fluorescent dark quencher that efficiently quenches fluorescence through resonance energy transfer (FRET) when in proximity to a compatible fluorophore, making it ideal for molecular beacon probes, real-time PCR assays, and other applications requiring precise fluorescence modulation.

CAT: BRP-02660

Molecular Formula: C50H55N6O7P

Molecular Weight: 883.00

Purity: ≥97%

Appearance: Black solid

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Synonyms: ZEN Phosphoramidite

Endo BCN-PEG3 CE Phosphoramidite

Description: Endo BCN-PEG3 CE Phosphoramidite is a phosphoramidite reagent designed for solid-phase oligonucleotide synthesis, enabling site-specific incorporation of an endo-bicyclononyne (BCN) group functionalized with a PEG3 spacer into DNA or RNA strands. The BCN moiety facilitates copper-free click chemistry reactions, specifically strain-promoted alkyne-azide cycloaddition (SPAAC) with azide-containing molecules or inverse electron demand Diels-Alder (IEDDA) reactions with tetrazines, allowing post-synthetic conjugation to labels, surfaces, or biomolecules. The PEG3 linker enhances water solubility and biocompatibility, reducing non-specific interactions and improving the stability of the conjugated oligonucleotides.

CAT: BRP-02668

Molecular Formula: C28H48N3O7P

Molecular Weight: 569.68

Purity: ≥95%

Appearance: Slight yellow oily matter

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InChIKey: BUMXYCDWEZVUQG-UWZSUSAUSA-N

SMILES: CC(N(P(OCCC#N)OCCOCCOCCOCCNC(OC[C@@H]1[C@]2([H])CCC#CCC[C@@]21[H])=O)C(C)C)C

IUPAC Name: ((1R,8S,9s)-bicyclo[6.1.0]non-4-yn-9-yl)methyl (2-(2-(2-(2-(((2-cyanoethoxy)(diisopropylamino)phosphaneyl)oxy)ethoxy)ethoxy)ethoxy)ethyl)carbamate

InChI: InChI=1S/C28H48N3O7P/c1-23(2)31(24(3)4)39(37-14-9-12-29)38-21-20-35-19-18-34-17-16-33-15-13-30-28(32)36-22-27-25-10-7-5-6-8-11-26(25)27/h23-27H,7-11,13-22H2,1-4H3,(H,30,32)/t25-,26+,27-,39?

Synonyms: Endo BCN-PEG3 Phosphoramidite

Amino-Modifier C3 CE Phosphoramidite

Description: Amino-Modifier C3 CE Phosphoramidite is a reagent used in automated oligonucleotide synthesis to introduce an amino group at the 5' end of nucleic acids. This modification is achieved through a phosphoramidite linkage and is useful for creating modified oligonucleotides with enhanced properties. The C3 spacer allows for a three-carbon interval between the amino group and the nucleic acid backbone, providing a suitable distance for subsequent conjugation with various molecules. This reagent is commonly used in applications such as drug discovery, gene synthesis, and molecular diagnostics.

CAT: BRP-02669

CAS: 258343-51-0

Molecular Formula: C35H43F3N3O6P

Molecular Weight: 689.71

Purity: ≥97%

Appearance: Colourless oily matter

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Boiling Point: 693.5±55.0 °C at 760 mmHg

InChIKey: HISMCSMWIYBWHF-UHFFFAOYSA-N

SMILES: CC(C)N(C(C)C)P(OCCC#N)OC(CNC(=O)C(F)(F)F)COC(C1=CC=CC=C1)(C2=CC=C(C=C2)OC)C3=CC=C(C=C3)OC

IUPAC Name: N-[3-[bis(4-methoxyphenyl)-phenylmethoxy]-2-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxypropyl]-2,2,2-trifluoroacetamide

InChI: InChI=1S/C35H43F3N3O6P/c1-25(2)41(26(3)4)48(46-22-10-21-39)47-32(23-40-33(42)35(36,37)38)24-45-34(27-11-8-7-9-12-27,28-13-17-30(43-5)18-14-28)29-15-19-31(44-6)20-16-29/h7-9,11-20,25-26,32H,10,22-24H2,1-6H3,(H,40,42)

Synonyms: Amino-Modifier C3 Phosphoramidite; Phosphoramidous acid, bis(1-methylethyl)-, 1-[[bis(4-methoxyphenyl)phenylmethoxy]methyl]-2-[(trifluoroacetyl)amino]ethyl 2-cyanoethyl ester; 1-(Bis(4-methoxyphenyl)(phenyl)methoxy)-3-(2,2,2-trifluoroacetamido)propan-2-yl (2-cyanoethyl) diisopropylphosphoramidite

HPro CE Phosphoramidite

Description: HPro CE Phosphoramidite is a specialized phosphoramidite reagent designed for solid-phase oligonucleotide synthesis, enabling site-specific incorporation of the HPro modifier into DNA or RNA strands. It is particularly useful for introducing functional groups or labels into oligonucleotides, facilitating applications in molecular diagnostics, therapeutics, or research tools requiring post-synthetic modifications.

CAT: BRP-02671

CAS: 1445145-68-5

Molecular Formula: C37H45F3N3O6P

Molecular Weight: 715.75

Purity: ≥97%

Appearance: Off-white solid

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Boiling Point: 712.9±60.0 °C at 760 mmHg

InChIKey: JKBXEFCHTNRDHZ-IGCNUVEYSA-N

SMILES: N#CCCOP(OC1CN(C(=O)C(F)(F)F)C(COC(C=2C=CC=CC2)(C3=CC=C(OC)C=C3)C4=CC=C(OC)C=C4)C1)N(C(C)C)C(C)C

IUPAC Name: (3R,5S)-5-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-1-(2,2,2-trifluoroacetyl)pyrrolidin-3-yl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C37H45F3N3O6P/c1-26(2)43(27(3)4)50(48-22-10-21-41)49-34-23-31(42(24-34)35(44)37(38,39)40)25-47-36(28-11-8-7-9-12-28,29-13-17-32(45-5)18-14-29)30-15-19-33(46-6)20-16-30/h7-9,11-20,26-27,31,34H,10,22-25H2,1-6H3/t31-,34+,50?/m0/s1

Synonyms: HPro Phosphoramidite; (3R,5S)-5-[[Bis(4-methoxyphenyl)phenylmethoxy]methyl]-1-(2,2,2-trifluoroacetyl)-3-pyrrolidinyl 2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite; Phosphoramidous acid, N,N-bis(1-methylethyl)-, (3R,5S)-5-[[bis(4-methoxyphenyl)phenylmethoxy]methyl]-1-(2,2,2-trifluoroacetyl)-3-pyrrolidinyl 2-cyanoethyl ester

Spermine CE Phosphoramidite (unprotected)

Description: Spermine CE Phosphoramidite (unprotected) is a specialized phosphoramidite reagent designed for solid-phase oligonucleotide synthesis, enabling site-specific incorporation of spermine moieties into DNA or RNA strands. This reagent facilitates the creation of Zip Nucleic Acids (ZNAs), where the cationic spermine groups reduce electrostatic repulsion between the oligonucleotide and its target, significantly enhancing binding affinity and stability of the duplex. ZNAs are widely used in applications such as multiplex PCR, RT-qPCR, microRNA detection, and antisense/antigene therapies due to their improved hybridization kinetics and cellular uptake.

CAT: BRP-02674

CAS: 1969276-81-0

Molecular Formula: C48H77N6O5P

Molecular Weight: 849.14

Purity: ≥97%

Appearance: Colourless oily matter

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Boiling Point: 840.0±65.0 °C at 760 mmHg

InChIKey: YMDADIHGMHJYIE-UHFFFAOYSA-N

SMILES: N#CCCOP(OCCCCNCCCNCCCCNCCCNCCCCOC(C=1C=CC=CC1)(C2=CC=C(OC)C=C2)C3=CC=C(OC)C=C3)N(C(C)C)C(C)C

IUPAC Name: 1,1-bis(4-methoxyphenyl)-1-phenyl-2-oxa-7,11,16,20-tetraazatetracosan-24-yl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C48H77N6O5P/c1-41(2)54(42(3)4)60(59-40-16-29-49)58-39-15-13-33-53-37-18-35-51-31-11-10-30-50-34-17-36-52-32-12-14-38-57-48(43-19-8-7-9-20-43,44-21-25-46(55-5)26-22-44)45-23-27-47(56-6)28-24-45/h7-9,19-28,41-42,50-53H,10-18,30-40H2,1-6H3

Synonyms: Spermine Phosphoramidite (unprotected); Phosphoramidous acid, N,N-bis(1-methylethyl)-, 24,24-bis(4-methoxyphenyl)-24-phenyl-23-oxa-5,9,14,18-tetraazatetracos-1-yl 2-cyanoethyl ester; Spermine CE Phosphoramidite

Related CAS: 1969276-82-1 (tetra-TFA salt) ; 942054-48-0 (Spermine Phosphoramidite (NTFA-protected))

DNP CE Phosphoramidite

Description: DNP CE Phosphoramidite is a modified phosphoramidite reagent designed for solid-phase oligonucleotide synthesis, enabling site-specific incorporation of a dinitrophenyl (DNP) group into DNA or RNA strands. The DNP moiety serves as a versatile chemical handle for post-synthetic conjugation or detection, facilitating applications such as hapten labeling for immunoassays, molecular diagnostics, or affinity purification.

CAT: BRP-02675

CAS: 136949-85-4

Molecular Formula: C21H34N5O6P

Molecular Weight: 483.51

Purity: ≥97%

Appearance: Brown oily matter

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Boiling Point: 568.0±50.0 °C at 760 mmHg

InChIKey: FSQUUZFFAJZEPM-UHFFFAOYSA-N

SMILES: N#CCCOP(OCCCCCCNC1=CC=C(C=C1N(=O)=O)N(=O)=O)N(C(C)C)C(C)C

IUPAC Name: 2-cyanoethyl (6-((2,4-dinitrophenyl)amino)hexyl) diisopropylphosphoramidite

InChI: InChI=1S/C21H34N5O6P/c1-17(2)24(18(3)4)33(32-15-9-12-22)31-14-8-6-5-7-13-23-20-11-10-19(25(27)28)16-21(20)26(29)30/h10-11,16-18,23H,5-9,13-15H2,1-4H3

Synonyms: DNP Phosphoramidite; Phosphoramidous acid, bis(1-methylethyl)-, 2-cyanoethyl 6-[(2,4-dinitrophenyl)amino]hexyl ester

Desthiobiotin(N-BB) TEG CE Phosphoramidite

Description: Desthiobiotin(N-BB) TEG CE Phosphoramidite is a modified phosphoramidite reagent designed for solid-phase oligonucleotide synthesis, enabling site-specific incorporation of a desthiobiotin label with a triethylene glycol (TEG) spacer into DNA or RNA strands. The desthiobiotin moiety, a biotin derivative, binds to streptavidin with lower affinity (2×10^-9 M) compared to biotin (4×10^-14 M), allowing reversible capture and elution of labeled oligonucleotides under mild conditions (e.g., 95 °C in water or via biotin displacement). The TEG spacer provides a 15-atom linker to minimize steric hindrance, enhancing accessibility for streptavidin binding and facilitating applications in affinity purification, molecular diagnostics, and hybridization assays.

CAT: BRP-02676

Molecular Formula: C63H90N5O12P

Molecular Weight: 1140.41

Purity: ≥95%

Appearance: Off-white solid

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InChIKey: GUHQVSVLGODZAZ-WHJDPYJGSA-N

SMILES: [H][C@]([C@@](CCCCCC(NCCCOCCOCCOCCOCC(COC(C1=CC=C(C=C1)OC)(C2=CC=CC=C2)C3=CC=C(C=C3)OC)OP(N(C(C)C)C(C)C)OCCC#N)=O)(NC4=O)[H])(N4C(C5=CC=C(C(C)(C)C)C=C5)=O)C

IUPAC Name: 25-((4R,5S)-1-(4-(tert-butyl)benzoyl)-5-methyl-2-oxoimidazolidin-4-yl)-1,1-bis(4-methoxyphenyl)-20-oxo-1-phenyl-2,6,9,12,15-pentaoxa-19-azapentacosan-4-yl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C63H90N5O12P/c1-47(2)68(48(3)4)81(79-38-17-35-64)80-57(46-78-63(52-19-13-11-14-20-52,53-27-31-55(72-9)32-28-53)54-29-33-56(73-10)34-30-54)45-77-44-43-76-42-41-75-40-39-74-37-18-36-65-59(69)22-16-12-15-21-58-49(5)67(61(71)66-58)60(70)50-23-25-51(26-24-50)62(6,7)8/h11,13-14,19-20,23-34,47-49,57-58H,12,15-18,21-22,36-46H2,1-10H3,(H,65,69)(H,66,71)/t49-,57?,58+,81?/m0/s1

Synonyms: Desthiobiotin(N-BB) TEG Phosphoramidite

Biotin(N-BB) TEG CE Phosphoramidite

Description: Biotin(N-BB) TEG CE Phosphoramidite is a modified phosphoramidite reagent designed for solid-phase oligonucleotide synthesis, enabling site-specific incorporation of a biotin label with a triethylene glycol (TEG) spacer into DNA or RNA strands. The reagent features a tert-butylbenzoyl (N-BB) protecting group on the biotin moiety to enhance solubility and prevent side reactions during synthesis. The TEG spacer provides a 15-atom linker between the biotin and the oligonucleotide, reducing steric hindrance and improving accessibility for binding to streptavidin or avidin in downstream applications. It is typically used to introduce biotin at the 5'-end or internally within an oligonucleotide sequence, facilitating applications such as molecular diagnostics, affinity purification, and hybridization assays.

CAT: BRP-02677

CAS: 1799331-53-5

Molecular Formula: C63H88N5O12PS

Molecular Weight: 1170.45

Purity: ≥95%

Appearance: Off-white solid

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InChIKey: ZJLRGMPCKKAODT-QBULNJHFSA-N

SMILES: N#CCCOP(OC(COCCOCCOCCOCCCNC(=O)CCCCC1SCC2N(C(=O)NC12)C(=O)C3=CC=C(C=C3)C(C)(C)C)COC(C=4C=CC=CC4)(C5=CC=C(OC)C=C5)C6=CC=C(OC)C=C6)N(C(C)C)C(C)C

IUPAC Name: 24-((3aS,4S,6aR)-1-(4-(tert-butyl)benzoyl)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)-1,1-bis(4-methoxyphenyl)-20-oxo-1-phenyl-2,6,9,12,15-pentaoxa-19-azatetracosan-4-yl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C63H88N5O12PS/c1-46(2)68(47(3)4)81(79-36-15-33-64)80-55(44-78-63(50-17-11-10-12-18-50,51-25-29-53(72-8)30-26-51)52-27-31-54(73-9)32-28-52)43-77-42-41-76-40-39-75-38-37-74-35-16-34-65-58(69)20-14-13-19-57-59-56(45-82-57)67(61(71)66-59)60(70)48-21-23-49(24-22-48)62(5,6)7/h10-12,17-18,21-32,46-47,55-57,59H,13-16,19-20,34-45H2,1-9H3,(H,65,69)(H,66,71)/t55?,56-,57-,59-,81?/m0/s1

Synonyms: Biotin(N-BB) TEG Phosphoramidite; Phosphoramidous acid, N,N-bis(1-methylethyl)-, 1-[[bis(4-methoxyphenyl)phenylmethoxy]methyl]-21-[(3aS,4S,6aR)-1-[4-(1,1-dimethylethyl)benzoyl]hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl]-17-oxo-3,6,9,12-tetraoxa-16-azaheneicos-1-yl 2-cyanoethyl ester; 1-[[Bis(4-methoxyphenyl)phenylmethoxy]methyl]-21-[(3aS,4S,6aR)-1-[4-(1,1-dimethylethyl)benzoyl]hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl]-17-oxo-3,6,9,12-tetraoxa-16-azaheneicos-1-yl 2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite; Biotin (BB) TEG CE Phosphoramidite; Biotin (BB)-TEG CEP; Biotin (BB) TEG amidite