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

3'-DMT-2'-OMe-G(iBu)-CE Reverse

Description: 3'-DMT-2'-OMe-G(iBu)-CE Reverse is a specialized nucleotide compound used in oligonucleotide synthesis. It consists of a 2'-O-methyl modification and a 3'-DMT protecting group to ensure stability during synthesis. Additionally, the guanosine base is modified with an isobutyryl (ibu) group. The 5'-CED phosphoramidite functionality allows for controlled addition to oligonucleotide chains, providing precision in molecular biology research for tailored oligonucleotide design and synthesis.

CAT: BRP-00428

CAS: 2721427-31-0

Molecular Formula: C45H56N7O9P

Molecular Weight: 869.96

Purity: ≥98% by HPLC

Appearance: White to off-white powder

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Storage: Store at -20 °C

InChIKey: ZRRIKKNCSIFYAP-MLLDKZSOSA-N

CanonicalSMILES: N#CCCOP(OCC1OC(N2C=NC=3C(=O)N=C(NC(=O)C(C)C)NC32)C(OC)C1OC(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: ((2R,3R,4R,5R)-3-(bis(4-methoxyphenyl)(phenyl)methoxy)-5-(2-isobutyramido-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-methoxytetrahydrofuran-2-yl)methyl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C45H56N7O9P/c1-28(2)41(53)49-44-48-40-37(42(54)50-44)47-27-51(40)43-39(57-9)38(36(60-43)26-59-62(58-25-13-24-46)52(29(3)4)30(5)6)61-45(31-14-11-10-12-15-31,32-16-20-34(55-7)21-17-32)33-18-22-35(56-8)23-19-33/h10-12,14-23,27-30,36,38-39,43H,13,25-26H2,1-9H3,(H2,48,49,50,53,54)/t36-,38-,39-,43-,62?/m1/s1

Synonyms: 3'-O-DMTr-2'-O-Me-G(iBu)-5'-CE-Phosphoramidite; 2'-O-Methyl-3'-DMT Guanosine (n-ibu) 5'-CED phosphoramidite

3'-DMT-2'-OMe-C(Ac)-CE Reverse

Description: 3'-DMT-2'-OMe-C(Ac)-CE Reverse is a specialized nucleotide compound used in oligonucleotide synthesis. It features a 2'-O-methyl modification and a 3'-DMT protecting group to ensure stability during synthesis. Additionally, the cytidine base is modified with an acetyl (N-Ac) group. The 5'-CED phosphoramidite functionality enables controlled addition to oligonucleotide chains, providing precision in molecular biology research for customized oligonucleotide design and synthesis.

CAT: BRP-00429

Molecular Formula: C42H52N5O9P

Molecular Weight: 801.88

Purity: ≥98% by HPLC

Appearance: White to off-white powder

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Storage: Store at -20 °C

InChIKey: ZAQGXRDUFSXSGR-UAQIPLLRSA-N

IUPAC Name: ((2R,3R,4R,5R)-5-(4-acetamido-2-oxopyrimidin-1(2H)-yl)-3-(bis(4-methoxyphenyl)(phenyl)methoxy)-4-methoxytetrahydrofuran-2-yl)methyl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C42H52N5O9P/c1-28(2)47(29(3)4)57(53-26-12-24-43)54-27-36-38(39(52-8)40(55-36)46-25-23-37(44-30(5)48)45-41(46)49)56-42(31-13-10-9-11-14-31,32-15-19-34(50-6)20-16-32)33-17-21-35(51-7)22-18-33/h9-11,13-23,25,28-29,36,38-40H,12,26-27H2,1-8H3,(H,44,45,48,49)/t36-,38-,39-,40-,57?/m1/s1

Synonyms: 3'-O-DMTr-2'-O-Me-C(Ac)-5'-CE-Phosphoramidite; 2'-O-Methyl-3'-DMT Cytidine (N-Ac) 5'-CED phosphoramidite

3'-O-DMTr-2'-O-Me-rU-5'-CE-Phosphoramidite

Description: 3'-O-DMTr-2'-O-Me-rU-5'-CE-Phosphoramidite is a specialized nucleotide used in oligonucleotide synthesis. It contains a 3'-dimethoxytrityl (DMTr) protecting group on the 3' hydroxyl, a methyl (Me) modification at the 2' position of the ribose sugar with uracil (U) as the base, and a 5'-cyanoethyl (CE) phosphoramidite functionality for controlled addition during synthesis. This compound facilitates stable and precise synthesis of customized oligonucleotides for molecular biology research applications.

CAT: BRP-00430

CAS: 2721427-32-1

Molecular Formula: C40H49N4O9P

Molecular Weight: 760.82

Purity: ≥98% by HPLC

Appearance: White to off-white powder

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Storage: Store at -20 °C

InChIKey: ATKRAEVWEXDALJ-XKZJCBTISA-N

CanonicalSMILES: N#CCCOP(OCC1OC(N2C=CC(=O)NC2=O)C(OC)C1OC(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)-3-(bis(4-methoxyphenyl)(phenyl)methoxy)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-methoxytetrahydrofuran-2-yl)methyl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C40H49N4O9P/c1-27(2)44(28(3)4)54(50-25-11-23-41)51-26-34-36(37(49-7)38(52-34)43-24-22-35(45)42-39(43)46)53-40(29-12-9-8-10-13-29,30-14-18-32(47-5)19-15-30)31-16-20-33(48-6)21-17-31/h8-10,12-22,24,27-28,34,36-38H,11,25-26H2,1-7H3,(H,42,45,46)/t34-,36-,37-,38-,54?/m1/s1

Synonyms: 3'-DMT-2'-OMe-U-CE Reverse; 2'-O-Methyl-3'-DMT Uridine 5'-CED phosphoramidite

UNA-C(Ac)-CE Phosphoramidite

Description: UNA-C(Ac)-CE Phosphoramidite is a compound employed in the chemical synthesis of nucleic acids, specifically in RNA synthesis. It features a UNA (Unlocked Nucleic Acid) modification, denoted by "UNA," which alters the structure and properties of the nucleotide. The "C(Ac)" indicates the nucleotide base cytosine (C) with an acetyl (Ac) group attached, potentially impacting base pairing and stability. Additionally, "CE" denotes cyanoethyl, a protecting group for the phosphate moiety, and "Phosphoramidite" refers to the reactive form of the nucleotide used in automated oligonucleotide synthesis. This compound facilitates controlled addition of modified nucleotides during RNA synthesis for various research and biotechnological applications.

CAT: BRP-00431

CAS: 1120329-56-7

Molecular Formula: C48H56N5O10P

Molecular Weight: 893.96

Purity: ≥98% by HPLC

Appearance: White to off-white powder

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Storage: Store at -20 °C

InChIKey: UMUWXRLDMCRCFS-GXOVKUNTSA-N

CanonicalSMILES: CC(C)N(C(C)C)P(OCCC#N)OCC(COC(C1=CC=CC=C1)(C2=CC=C(C=C2)OC)C3=CC=C(C=C3)OC)OC(COC(=O)C4=CC=CC=C4)N5C=CC(=NC5=O)NC(=O)C

IUPAC Name: [(2R)-2-(4-acetamido-2-oxopyrimidin-1-yl)-2-[(2R)-1-[bis(4-methoxyphenyl)-phenylmethoxy]-3-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxypropan-2-yl]oxyethyl] benzoate

InChI: InChI=1S/C48H56N5O10P/c1-34(2)53(35(3)4)64(61-30-14-28-49)62-32-43(63-45(33-59-46(55)37-15-10-8-11-16-37)52-29-27-44(50-36(5)54)51-47(52)56)31-60-48(38-17-12-9-13-18-38,39-19-23-41(57-6)24-20-39)40-21-25-42(58-7)26-22-40/h8-13,15-27,29,34-35,43,45H,14,30-33H2,1-7H3,(H,50,51,54,56)/t43-,45-,64?/m1/s1

Synonyms: (2R)-2-(4-Acetamido-2-oxopyrimidin-1(2H)-yl)-2-(((2R)-1-(bis(4-methoxyphenyl)(phenyl)methoxy)-3-(((2-cyanoethoxy)(diisopropylamino)phosphino)oxy)propan-2-yl)oxy)ethyl benzoate; Phosphoramidous acid, N,N-bis(1-methylethyl)-, (2R)-2-[(1R)-1-[4-(acetylamino)-2-oxo-1(2H)-pyrimidinyl]-2-(benzoyloxy)ethoxy]-3-[bis(4-methoxyphenyl)phenylmethoxy]propyl 2-cyanoethyl ester; (2R)-2-[(1R)-1-[4-(Acetylamino)-2-oxo-1(2H)-pyrimidinyl]-2-(benzoyloxy)ethoxy]-3-[bis(4-methoxyphenyl)phenylmethoxy]propyl 2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite

UNA-U-CE Phosphoramidite

Description: UNA-U-CE Phosphoramidite is a compound utilized in nucleic acid synthesis, particularly in RNA synthesis. It consists of UNA (Unlocked Nucleic Acid), denoted by "UNA," which modifies the nucleotide structure and properties. The "U" signifies uridine as the base, and "CE" indicates cyanoethyl, a protecting group for the phosphate moiety. "Phosphoramidite" refers to the reactive form of the nucleotide used in automated oligonucleotide synthesis. This compound enables controlled addition of modified uridine nucleotides during RNA synthesis for various research and biotechnological applications.

CAT: BRP-00432

CAS: 1120329-48-7

Molecular Formula: C46H53N4O10P

Molecular Weight: 852.91

Purity: ≥98% by HPLC

Appearance: White to off-white powder

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Storage: Store at -20 °C

InChIKey: MHRGEJFLFYZLJI-LZOZAVILSA-N

CanonicalSMILES: CC(C)N(C(C)C)P(OCCC#N)OCC(COC(C1=CC=CC=C1)(C2=CC=C(C=C2)OC)C3=CC=C(C=C3)OC)OC(COC(=O)C4=CC=CC=C4)N5C=CC(=O)NC5=O

IUPAC Name: [(2R)-2-[(2R)-1-[bis(4-methoxyphenyl)-phenylmethoxy]-3-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxypropan-2-yl]oxy-2-(2,4-dioxopyrimidin-1-yl)ethyl] benzoate

InChI: InChI=1S/C46H53N4O10P/c1-33(2)50(34(3)4)61(58-29-13-27-47)59-31-41(60-43(49-28-26-42(51)48-45(49)53)32-56-44(52)35-14-9-7-10-15-35)30-57-46(36-16-11-8-12-17-36,37-18-22-39(54-5)23-19-37)38-20-24-40(55-6)25-21-38/h7-12,14-26,28,33-34,41,43H,13,29-32H2,1-6H3,(H,48,51,53)/t41-,43-,61?/m1/s1

Synonyms: 5'-(4,4'-dimethoxytrityl)-2'-benzoyl-2',3'-seco-uridine-3'-cyanoethyl Phosphoramidite; Phosphoramidous acid, N,N-bis(1-methylethyl)-, (2R)-2-[(1R)-2-(benzoyloxy)-1-(3,4-dihydro-2,4-dioxo-1(2H)-pyrimidinyl)ethoxy]-3-[bis(4-methoxyphenyl)phenylmethoxy]propyl 2-cyanoethyl ester; 5'-DMTr-2'-Bz-3'-O-CEP-UNA-U; 5'-(4,4'-dimethoxytrityl)-2'-benzoyl-2',3'-seco-uridine-3'-[(2-cyanoethyl)-(N,N-diisopropyl)] Phosphoramidite; (2R)-2-[(1R)-2-(Benzoyloxy)-1-(3,4-dihydro-2,4-dioxo-1(2H)-pyrimidinyl)ethoxy]-3-[bis(4-methoxyphenyl)phenylmethoxy]propyl 2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite

Morpholino G(PhAc) subunit

Description: The Morpholino G(PhAc) subunit is a component used in the synthesis of morpholino oligomers, synthetic analogs of nucleic acids. It features a morpholine ring structure as the backbone, with a guanine base modified by a phenylacetyl group (PhAc). This modification enhances the binding affinity of the oligomers to complementary RNA or DNA targets. The Morpholino G(PhAc) subunit is utilized in molecular biology and biotechnology for applications such as gene knockdown experiments, antisense therapy, and the study of gene function.

CAT: BRP-00433

CAS: 1044241-74-8

Molecular Formula: C39H39ClN7O5P

Molecular Weight: 752.20

Purity: ≥98% by HPLC

Appearance: White to off-white powder

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Storage: Store at -20 °C

Density: 1.37±0.1 g/cm3

InChIKey: NURVOJDGJURYKG-BFXPVMCSSA-N

CanonicalSMILES: O=C1N=C(NC(=O)CC=2C=CC=CC2)NC3=C1N=CN3C4OC(COP(=O)(Cl)N(C)C)CN(C4)C(C=5C=CC=CC5)(C=6C=CC=CC6)C=7C=CC=CC7

IUPAC Name: ((2S,6R)-6-(6-oxo-2-(2-phenylacetamido)-1,6-dihydro-9H-purin-9-yl)-4-tritylmorpholin-2-yl)methyl dimethylphosphoramidochloridate

InChI: InChI=1S/C39H39ClN7O5P/c1-45(2)53(40,50)51-26-32-24-46(39(29-17-9-4-10-18-29,30-19-11-5-12-20-30)31-21-13-6-14-22-31)25-34(52-32)47-27-41-35-36(47)43-38(44-37(35)49)42-33(48)23-28-15-7-3-8-16-28/h3-22,27,32,34H,23-26H2,1-2H3,(H2,42,43,44,48,49)/t32-,34+,53?/m0/s1

Synonyms: Phosphoramidochloridic acid, N,N-dimethyl-, [(2S,6R)-6-[1,6-dihydro-6-oxo-2-[(2-phenylacetyl)amino]-9H-purin-9-yl]-4-(triphenylmethyl)-2-morpholinyl]methyl ester; [(2S,6R)-6-[1,6-Dihydro-6-oxo-2-[(2-phenylacetyl)amino]-9H-purin-9-yl]-4-(triphenylmethyl)-2-morpholinyl]methyl N,N-dimethylphosphoramidochloridate; (2S,6R)-6-(6-oxo-2-(2-phenylacetamido)-1H-purin-9(6H)-yl)-4-tritylmorpholin-2-yl)methyl dimethylphosphoramidochloridate

XIMA Phosphoramidite II

Description: XIMA Phosphoramidite II is a chemical compound used in oligonucleotide synthesis, particularly in the field of molecular biology and biotechnology. It is a type of phosphoramidite reagent that enables the efficient and precise incorporation of nucleotides during the synthesis of DNA and RNA oligonucleotides. XIMA Phosphoramidite II is valued for its high coupling efficiency and stability, making it a reliable choice for the synthesis of oligonucleotides for various applications, including gene synthesis, PCR primers, and nucleic acid aptamers.

CAT: BRP-00473

Molecular Formula: C84H89Cl2N4O14P

Molecular Weight: 1480.52

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InChIKey: RTFBWGDBWIXUCV-PHEZNKQISA-N

IUPAC Name: 6-((6-((2S,4R)-2-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-4-(((2-cyanoethoxy)(diisopropylamino)phosphaneyl)oxy)pyrrolidin-1-yl)-6-oxohexyl)carbamoyl)-4,7-dichloro-3-oxo-2',7'-diphenyl-3H-spiro[isobenzofuran-1,9'-xanthene]-3',6'-diyl bis(2,2-dimethylpropanoate)

InChI: InChI=1S/C84H89Cl2N4O14P/c1-52(2)90(53(3)4)105(99-43-25-41-87)104-62-44-59(51-98-83(56-30-21-15-22-31-56,57-33-37-60(96-11)38-34-57)58-35-39-61(97-12)40-36-58)89(50-62)73(91)32-23-16-24-42-88-77(92)65-47-68(85)74-75(76(65)86)84(103-78(74)93)66-45-63(54-26-17-13-18-27-54)69(101-79(94)81(5,6)7)48-71(66)100-72-49-70(102-80(95)82(8,9)10)64(46-67(72)84)55-28-19-14-20-29-55/h13-15,17-22,26-31,33-40,45-49,52-53,59,62H,16,23-25,32,42-44,50-51H2,1-12H3,(H,88,92)/t59-,62+,105?/m0/s1

Synonyms: SIMA phosphoramidite, 6-isomer hydroxyprolinol

5'-Aquafluor 593 CE Phosphoramidite

Description: Aquafluor 593 is a highly fluorescent molecule with maximum absorption at 593 nm and maximum emission at 613 nm, with a quantum yield of 0.6. The fluorescence of Aquafluor 593 is very little affected by pH, with only a few percent variation in the pH range of 5-8. Moreover, when heated from 20°C to 95°C, the fluorescence only decreased by about 30%.

CAT: BRP-00476

CAS: 2378004-16-9

Molecular Formula: C57H78F3N6O8P2+

Molecular Weight: 1094.23

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InChIKey: MMNHPDDWLXVTRC-UHFFFAOYSA-O

CanonicalSMILES: N#CCCOP(OCCCCCCOP(=O)(OCCCCNC(=O)C(F)(F)F)C=1C=CC(C(=O)N(CC)CC)=C(C1)C=2C=3C=C4C5=C(C3[O+]=C6C2C=C7C8=C6CCCN8CCC7)CCCN5CCC4)N(C(C)C)C(C)C

InChI: InChI=1S/C57H77F3N6O8P2/c1-7-63(8-2)55(67)44-25-24-43(76(69,73-35-14-11-27-62-56(68)57(58,59)60)72-34-13-10-9-12-32-70-75(71-33-19-26-61)66(39(3)4)40(5)6)38-47(44)50-48-36-41-20-15-28-64-30-17-22-45(51(41)64)53(48)74-54-46-23-18-31-65-29-16-21-42(52(46)65)37-49(50)54/h24-25,36-40H,7-23,27-35H2,1-6H3/p+1

Synonyms: 5'-AquaPhluor 593; 1H,5H,11H,15H-Xantheno[2,3,4-ij:5,6,7-i'j']diquinolizin-18-ium, 9-[5-[10-[bis(1-methylethyl)amino]-13-cyano-1-oxido-1-[4-[(2,2,2-trifluoroacetyl)amino]butoxy]-2,9,11-trioxa-1,10-diphosphatridec-1-yl]-2-[(diethylamino)carbonyl]phenyl]-2,3,6,7,12,13,16,17-octahydro-; 9-[5-[10-[Bis(1-methylethyl)amino]-13-cyano-1-oxido-1-[4-[(2,2,2-trifluoroacetyl)amino]butoxy]-2,9,11-trioxa-1,10-diphosphatridec-1-yl]-2-[(diethylamino)carbonyl]phenyl]-2,3,6,7,12,13,16,17-octahydro-1H,5H,11H,15H-xantheno[2,3,4-ij:5,6,7-i'j']diquinolizin-18-ium

Related CAS: 2378004-17-0 (hexafluorophosphate)

Quassar 670 Phosphoramidite

Description: Quasar 670 Phosphoramidite is a specialized chemical used in oligonucleotide synthesis for molecular biology and biotechnology applications. It is a type of phosphoramidite reagent designed to incorporate the Quasar 670 fluorescent dye into synthetic oligonucleotides. This dye is part of the Quasar series of fluorescent dyes, known for their high brightness and photostability. Quasar 670 Phosphoramidite enables the synthesis of labeled oligonucleotides for various applications such as fluorescence in situ hybridization (FISH), real-time PCR, and nucleic acid detection assays. Its incorporation allows researchers to visualize and track nucleic acids in biological samples with high sensitivity and specificity.

CAT: BRP-00478

Molecular Formula: C48H69F6N5O3P2

Molecular Weight: 940.05

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InChIKey: LSSOBLPIXZOCPG-UHFFFAOYSA-O

IUPAC Name: 2-(5-(1-(6-((4-(((2-cyanoethoxy)(diisopropylamino)phosphaneyl)oxy)cyclohexyl)amino)-6-oxohexyl)-3,3-dimethylindolin-2-ylidene)penta-1,3-dien-1-yl)-1-ethyl-3,3-dimethyl-3H-indol-1-ium;hexafluorophosphate

InChI: InChI=1S/C48H68N5O3P.F6P/c1-10-51-42-24-18-16-22-40(42)47(6,7)44(51)26-13-11-14-27-45-48(8,9)41-23-17-19-25-43(41)52(45)34-20-12-15-28-46(54)50-38-29-31-39(32-30-38)56-57(55-35-21-33-49)53(36(2)3)37(4)5;1-7(2,3,4,5)6/h11,13-14,16-19,22-27,36-39H,10,12,15,20-21,28-32,34-35H2,1-9H3;/q;-1/p+1

DusQ 1 phosphoramidite

Description: DusQ 1 phosphoramidite is a true dark quencher with broad absorption curve which covers the visible spectrum with maximum in green to yellow region. It is used for the synthesis of dual labeled oligonucleotide probes for qPCR bearing 5'-quencher DusQ 1 and other FRET applications for multiplexing assays.

CAT: BRP-00479

CAS: 374591-94-3

Molecular Formula: C55H63N8O8P

Molecular Weight: 995.11

Purity: ≥95%

Appearance: Black Powder

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InChIKey: GQGUDTGZCZTGBR-UHFFFAOYSA-N

Solubility: Soluble in acetonitrile

CanonicalSMILES: N#CCCOP(OCCN(C1=CC=C(N=NC2=CC(=C(N=NC3=CC=C(C=C3N(=O)=O)C)C=C2OC)C)C=C1)CCOC(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: 2-((2-(bis(4-methoxyphenyl)(phenyl)methoxy)ethyl)(4-((2-methoxy-5-methyl-4-((4-methyl-2-nitrophenyl)diazenyl)phenyl)diazenyl)phenyl)amino)ethyl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C55H63N8O8P/c1-39(2)62(40(3)4)72(70-33-13-30-56)71-35-32-61(31-34-69-55(43-14-11-10-12-15-43,44-17-25-48(66-7)26-18-44)45-19-27-49(67-8)28-20-45)47-23-21-46(22-24-47)57-60-52-37-42(6)51(38-54(52)68-9)59-58-50-29-16-41(5)36-53(50)63(64)65/h10-12,14-29,36-40H,13,31-35H2,1-9H3

Synonyms: Phosphoramidous acid, bis(1-methylethyl)-, 2-[[2-[bis(4-methoxyphenyl)phenylmethoxy]ethyl][4-[[2-methoxy-5-methyl-4-[(4-methyl-2-nitrophenyl)azo]phenyl]azo]phenyl]amino]ethyl 2-cyanoethyl ester (9CI)

DusQ 2 phosphoramidite

Description: DusQ 2 is a dark quenched dye used in the synthesis of double-labeled oligonucleotide probes for qPCR with a 5' quench agent. This quencher is ideal for HEX, JOE, ROX, Cyanine5 and other dyes that have emission spectra in the orange and red parts of the spectrum.

CAT: BRP-00480

CAS: 374591-98-7

Molecular Formula: C54H61N8O9P

Molecular Weight: 997.09

Purity: NMR 1H, 31P, HPLC-MS (95%)

Appearance: Dark colored solid

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Storage: Storage: 12 months after receival at -20 °C in the Dark. Transportation: at room temperature for up to 3 weeks. Avoid prolonged exposure to light. Desiccate.

InChIKey: GISIZSAJGDUWFU-UHFFFAOYSA-N

CanonicalSMILES: CC(C)N(C(C)C)P(OCCC#N)OCCN(CCOC(C1=CC=CC=C1)(C2=CC=C(C=C2)OC)C3=CC=C(C=C3)OC)C4=CC=C(C=C4)N=NC5=CC(=C(C=C5OC)N=NC6=CC=C(C=C6)[N+](=O)[O-])OC

IUPAC Name: 3-[2-[N-[2-[bis(4-methoxyphenyl)-phenylmethoxy]ethyl]-4-[[2,5-dimethoxy-4-[(4-nitrophenyl)diazenyl]phenyl]diazenyl]anilino]ethoxy-[di(propan-2-yl)amino]phosphanyl]oxypropanenitrile

InChI: InChI=1S/C54H61N8O9P/c1-39(2)61(40(3)4)72(70-34-12-31-55)71-36-33-60(32-35-69-54(41-13-10-9-11-14-41,42-15-27-48(65-5)28-16-42)43-17-29-49(66-6)30-18-43)46-23-19-44(20-24-46)56-58-50-37-53(68-8)51(38-52(50)67-7)59-57-45-21-25-47(26-22-45)62(63)64/h9-11,13-30,37-40H,12,32-36H2,1-8H3

Synonyms: HCQ-2 Phosphoramidite; DusQ2 phosphoramidite; Phosphoramidous acid, bis(1-methylethyl)-, 2-[[2-[bis(4-methoxyphenyl)phenylmethoxy]ethyl][4-[[2,5-dimethoxy-4-[(4-nitrophenyl)azo]phenyl]azo]phenyl]amino]ethyl 2-cyanoethyl ester; BHQ-2 Phosphoramidite; 4'-(4-Nitro-phenyldiazo)-2'-methoxy-5'-methoxy-azobenzene-4''-(N-2-4,4'-dimethoxytrityl(oxyethyl))-N-ethyl-2-cyanoethyl-(N,N-diisopropyl)-phosphoramidite

5'-Amino-Modifier C3 PDA

Description: 5'-Amino-Modifier C3 PDA is a biomedical research reagent used for oligonucleotide and DNA modification. Its versatility is manifested in facilitating the linking of a variety of molecules, such as antibodies and fluorescent dyes, enabling diagnostic and therapeutic interventions.

CAT: BRP-00481

Molecular Formula: C21H33N4O4P

Molecular Weight: 436.49

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InChIKey: OZSWCSLCEAQVDE-UHFFFAOYSA-N

CanonicalSMILES: CC(N(C(C)C)P(OCCCNC(C1=C(C(NC)=O)C=CC=C1)=O)OCCC#N)C

IUPAC Name: 2-cyanoethyl (3-(2-(methylcarbamoyl)benzamido)propyl) diisopropylphosphoramidite

InChI: InChI=1S/C21H33N4O4P/c1-16(2)25(17(3)4)30(28-14-8-12-22)29-15-9-13-24-21(27)19-11-7-6-10-18(19)20(26)23-5/h6-7,10-11,16-17H,8-9,13-15H2,1-5H3,(H,23,26)(H,24,27)

5'-Amino-Modifier C6 PDA

Description: 5'-Amino-Modifier C6 PDA is a chemical reagent used in oligonucleotide synthesis for molecular biology and biotechnology applications. It is a modification reagent designed to introduce an amino group at the 5' end of synthetic oligonucleotides. This amino group enables further conjugation with various molecules, such as fluorescent dyes, biotin, or other chemical groups, allowing for labeling or functionalization of the oligonucleotides. The C6 designation refers to the presence of a carbon chain spacer (hexyl linker) between the amino group and the phosphate group of the oligonucleotide backbone. This modification is particularly useful for applications such as PCR, sequencing, hybridization assays, and probe-based detection methods.

CAT: BRP-00482

CAS: 1445745-26-5

Molecular Formula: C24H39N4O4P

Molecular Weight: 478.57

Appearance: Light-yellow oily matter

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InChIKey: MXRKQHDWLCHOMH-UHFFFAOYSA-N

CanonicalSMILES: CC(C)N(C(C)C)P(OCCCCCCNC(=O)C1=CC=CC=C1C(=O)NC)OCCC#N

IUPAC Name: 2-N-[6-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyhexyl]-1-N-methylbenzene-1,2-dicarboxamide

InChI: InChI=1S/C24H39N4O4P/c1-19(2)28(20(3)4)33(32-18-12-15-25)31-17-11-7-6-10-16-27-24(30)22-14-9-8-13-21(22)23(29)26-5/h8-9,13-14,19-20H,6-7,10-12,16-18H2,1-5H3,(H,26,29)(H,27,30)

Synonyms: 6-(N2-methyl-N'-phthalimidyl)-hexyl-1-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite; 2-cyanoethyl (6-(2-(methylcarbamoyl)benzamido)hexyl) diisopropylphosphoramidite; PDA-Amino-C6 Amidite; 5'-Amino-Modifier C6-PDA

Thiol-Modifier C3 S-S CE Phosphoramidite

Description: Thiol-Modifier C3 S-S CE Phosphoramidite is a specialized reagent used in oligonucleotide synthesis for molecular biology applications. It introduces a thiol (-SH) group into synthetic oligonucleotides at the third carbon position (C3) from the 5' end, connected to a disulfide bridge for stability. This modification enables reversible conjugation reactions, facilitating various applications such as DNA-protein interactions, surface immobilization, and biosensor development.

CAT: BRP-00483

CAS: 1263065-01-5

Molecular Formula: C36H49N2O5PS2

Molecular Weight: 684.89

Purity: ≥95%

Appearance: Colourless oily matter

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InChIKey: CUHXVAZCAZMSBS-UHFFFAOYSA-N

CanonicalSMILES: N#CCCOP(OCCCSSCCCOC(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: 3-((3-(bis(4-methoxyphenyl)(phenyl)methoxy)propyl)disulfaneyl)propyl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C36H49N2O5PS2/c1-29(2)38(30(3)4)44(42-25-10-23-37)43-26-12-28-46-45-27-11-24-41-36(31-13-8-7-9-14-31,32-15-19-34(39-5)20-16-32)33-17-21-35(40-6)22-18-33/h7-9,13-22,29-30H,10-12,24-28H2,1-6H3

Synonyms: 3-[[3-[Bis(4-methoxyphenyl)phenylmethoxy]propyl]dithio]propyl 2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite; Phosphoramidous acid, N,N-bis(1-methylethyl)-, 3-[[3-[bis(4-methoxyphenyl)phenylmethoxy]propyl]dithio]propyl 2-cyanoethyl ester; Thiol-Modifier C3 S-S Phosphoramidite

Spacer C6 CE Phosphoramidite

Description: Spacer phosphamides C3, C9, C12, and C18 are used to insert spacer arms in oligonucleotides, and these compounds can be added multiple times when longer spacer arms are needed.

CAT: BRP-00484

CAS: 158041-82-8

Molecular Formula: C36H49N2O5P

Molecular Weight: 620.77

Purity: ≥98%

Appearance: Colourless oily matter

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InChIKey: AEDFSPMNECTXJM-UHFFFAOYSA-N

CanonicalSMILES: CC(C)N(C(C)C)P(OCCCCCCOC(C1=CC=CC=C1)(C2=CC=C(C=C2)OC)C3=CC=C(C=C3)OC)OCCC#N

IUPAC Name: 3-[6-[bis(4-methoxyphenyl)-phenylmethoxy]hexoxy-[di(propan-2-yl)amino]phosphanyl]oxypropanenitrile

InChI: InChI=1S/C36H49N2O5P/c1-29(2)38(30(3)4)44(43-28-14-25-37)42-27-13-8-7-12-26-41-36(31-15-10-9-11-16-31,32-17-21-34(39-5)22-18-32)33-19-23-35(40-6)24-20-33/h9-11,15-24,29-30H,7-8,12-14,26-28H2,1-6H3

Synonyms: 6-[Bis(4-methoxyphenyl)phenylmethoxy]hexyl 2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite; Phosphoramidous acid, bis(1-methylethyl)-, 6-[bis(4-methoxyphenyl)phenylmethoxy]hexyl 2-cyanoethyl ester; Phosphoramidous acid, N,N-bis(1-methylethyl)-, 6-[bis(4-methoxyphenyl)phenylmethoxy]hexyl 2-cyanoethyl ester; C6 Spacer Amidite; DMT-1,6-Hexandiol; C6 Spacer Phosphoramidite; Spacer Phosphoramidite C6; DMT-hexane-Diol phosphoramidite; 6-(4,4'-Dimethoxytrityloxy) hexyl-1-[(2-cyanoethyl)-(N,N-diisopropyl)] phosphoramidite

5'-Ferrocene CE Phosphoramidite

Description: 5'-Ferrocene CE Phosphoramidite is an oligonucleotide synthesis reagent that adds the electromagnetic group ferrocene to the oligonucleotide chain for application in oligonucleotide labeling. The absorption wavelength of 5'-Ferrocene CE Phosphoramidite is 438 nm and the extinction coefficient is 230M-1 cm-1.

CAT: BRP-00486

Molecular Formula: C26H40FeN3O3P

Molecular Weight: 529.44

Purity: ≥95%

Appearance: Orange solid

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Synonyms: 5'-Ferrocene Amidite; N-Ferrocenoyl-6-aminohexan-1-(2-cyanoethyl-diisoproylamino phoshoramidite); 5'-Ferrocene Phosphoramidite

rG (iPr-Pac) CE-Phosphoramidite

Description: rG (iPr-Pac) CE-Phosphoramidite is a specialized reagent utilized in oligonucleotide synthesis. It incorporates a guanosine (G) residue modified with a tert-butyldimethylsilyl (TBDMS) group at the 2'-position and an isopropyl-phenoxyacetyl (iPr-Pac) group. The TBDMS group provides stability during chemical synthesis, while the iPr-Pac group enhances functionality. The CE designation indicates its compatibility with controlled-efficiency (CE) phosphoramidite chemistry, ensuring efficient incorporation during solid-phase synthesis. This reagent facilitates the production of modified RNA oligonucleotides with improved stability and functionality, suitable for various molecular biology and biotechnology applications, including RNA interference and gene expression studies.

CAT: BRP-00495

CAS: 689283-85-0

Molecular Formula: C57H74N7O10PSi

Molecular Weight: 1076.32

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InChIKey: NLVBSBWTUJBMAJ-WYRUHZNWSA-N

Solubility: Soluble in Anhydrous Acetonitrile

CanonicalSMILES: N#CCCOP(OC1C(OC(N2C=NC=3C(=O)N=C(NC(=O)COC4=CC=C(C=C4)C(C)C)NC32)C1O[Si](C)(C)C(C)(C)C)COC(C=5C=CC=CC5)(C6=CC=C(OC)C=C6)C7=CC=C(OC)C=C7)N(C(C)C)C(C)C

IUPAC Name: (2R,3R,4R,5R)-2-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-4-((tert-butyldimethylsilyl)oxy)-5-(2-(2-(4-isopropylphenoxy)acetamido)-6-oxo-1,6-dihydro-9H-purin-9-yl)tetrahydrofuran-3-yl (2-cyanoethyl) diisopropylphosphoramidite

InChI: InChI=1S/C57H74N7O10PSi/c1-37(2)40-20-26-46(27-21-40)69-35-48(65)60-55-61-52-49(53(66)62-55)59-36-63(52)54-51(74-76(12,13)56(7,8)9)50(73-75(71-33-17-32-58)64(38(3)4)39(5)6)47(72-54)34-70-57(41-18-15-14-16-19-41,42-22-28-44(67-10)29-23-42)43-24-30-45(68-11)31-25-43/h14-16,18-31,36-39,47,50-51,54H,17,33-35H2,1-13H3,(H2,60,61,62,65,66)/t47-,50-,51-,54-,75?/m1/s1

Synonyms: Guanosine, 5'-O-[bis(4-methoxyphenyl)phenylmethyl]-2'-O-[(1,1-dimethylethyl)dimethylsilyl]-N-[[4-(1-methylethyl)phenoxy]acetyl]-, 3'-[2-cyanoethyl bis(1-methylethyl)phosphoramidite]; 5'-Dimethoxytrityl-N-p-isopropylphenoxyacetyl-Guanosine, 2'-O-TBDMS-3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite; iPr-Pac-G-CE Phosphoramidite; 2'-O-TBDMS-G(iPr-Pac) 3'-CE Phosphoramidite

Quasar 570 Amidite

Description: Quasar 570 Amidite is a specialized reagent utilized in oligonucleotide synthesis. It contains a fluorescent dye molecule that emits light at a wavelength of 570 nanometers, enabling the labeling of nucleic acid sequences during synthesis. This allows for the detection and visualization of the synthesized oligonucleotides in various molecular biology and biotechnology applications, including DNA sequencing, PCR, and fluorescence in situ hybridization (FISH). The Quasar 570 Amidite facilitates the development of labeled probes and primers for sensitive and specific nucleic acid detection assays.

CAT: BRP-00507

CAS: 1207162-64-8

Molecular Formula: C44H65F6N5O4P2

Molecular Weight: 903.95

Appearance: Red solid

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InChIKey: SXRGIEQDPKCFKB-UHFFFAOYSA-O

CanonicalSMILES: N#CCCOP(OCCOCCNC(=O)CCCCCN1C=2C=CC=CC2C(C1=CC=CC3=[N+](C=4C=CC=CC4C3(C)C)CC)(C)C)N(C(C)C)C(C)C.[F-][P+5]([F-])([F-])([F-])([F-])[F-]

IUPAC Name: 2-(3-(1-(6-((2-(2-(((2-cyanoethoxy)(diisopropylamino)phosphaneyl)oxy)ethoxy)ethyl)amino)-6-oxohexyl)-3,3-dimethylindolin-2-ylidene)prop-1-en-1-yl)-1-ethyl-3,3-dimethyl-3H-indol-1-ium;hexafluorophosphate

InChI: InChI=1S/C44H64N5O4P.F6P/c1-10-47-38-22-15-13-20-36(38)43(6,7)40(47)24-18-25-41-44(8,9)37-21-14-16-23-39(37)48(41)29-17-11-12-26-42(50)46-28-31-51-32-33-53-54(52-30-19-27-45)49(34(2)3)35(4)5;1-7(2,3,4,5)6/h13-16,18,20-25,34-35H,10-12,17,19,26,28-33H2,1-9H3;/q;-1/p+1

Synonyms: 3H-Indolium, 2-[3-[1-[14-[bis(1-methylethyl)amino]-17-cyano-6-oxo-10,13,15-trioxa-7-aza-14-phosphaheptadec-1-yl]-1,3-dihydro-3,3-dimethyl-2H-indol-2-ylidene]-1-propen-1-yl]-1-ethyl-3,3-dimethyl-, hexafluorophosphate(1-) (1:1)

Related CAS: 865650-90-4 (free base)

Long trebler phosphoramidite

Description: Long trebler phosphoramidite is a branching reagent for oligonucleotide synthesis allowing to synthesize branched DNA structures using a standard DNA synthesizer.After the condensation of the trebler, three DNA branches begin to grow simultaneously with each step of the synthesis. Deblock of this construct gives rise to DNA containing a branching point. One arm (stem) is attached to the branch point with its 5'-end, and other arms (branches) are attached with their 3'-ends. Reverse amidites can be used to prepare constructs with different branch orientations. Repetitive condensations of trebler results in formation of DNA dendrimers.

CAT: BRP-00509

CAS: 1516489-83-0

Molecular Formula: C89H107N2O15P

Molecular Weight: 1475.78

Purity: NMR 1H, 31P, HPLC-MS (95%)

Appearance: viscous yellowish oil

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Storage: 12 months after receival at -20°C in the dark. Transportation: at room temperature for up to 2 weeks. Avoid prolonged exposure to light. Desiccate.

InChIKey: GLIQPXBAWPTSHZ-UHFFFAOYSA-N

Solubility: soluble in acetonitrile, dichloromethane

CanonicalSMILES: CC(C)N(C(C)C)P(OCCCOCC(COCCCOC(C1=CC=CC=C1)(C2=CC=C(C=C2)OC)C3=CC=C(C=C3)OC)(COCCCOC(C4=CC=CC=C4)(C5=CC=C(C=C5)OC)C6=CC=C(C=C6)OC)COCCCOC(C7=CC=CC=C7)(C8=CC=C(C=C8)OC)C9=CC=C(C=C9)OC)OCCC#N

IUPAC Name: 3-[3-[3-[3-[bis(4-methoxyphenyl)-phenylmethoxy]propoxy]-2,2-bis[3-[bis(4-methoxyphenyl)-phenylmethoxy]propoxymethyl]propoxy]propoxy-[di(propan-2-yl)amino]phosphanyl]oxypropanenitrile

InChI: InChI=1S/C89H107N2O15P/c1-69(2)91(70(3)4)107(105-63-20-55-90)106-64-24-59-101-68-86(65-98-56-21-60-102-87(71-25-14-11-15-26-71,74-31-43-80(92-5)44-32-74)75-33-45-81(93-6)46-34-75,66-99-57-22-61-103-88(72-27-16-12-17-28-72,76-35-47-82(94-7)48-36-76)77-37-49-83(95-8)50-38-77)67-100-58-23-62-104-89(73-29-18-13-19-30-73,78-39-51-84(96-9)52-40-78)79-41-53-85(97-10)54-42-79/h11-19,25-54,69-70H,20-24,56-68H2,1-10H3

Synonyms: Phosphoramidous acid, N,N-bis(1-methylethyl)-, 3-[3-[3-[bis(4-methoxyphenyl)phenylmethoxy]propoxy]-2,2-bis[[3-[bis(4-methoxyphenyl)phenylmethoxy]propoxy]methyl]propoxy]propyl 2-cyanoethyl ester; 3-[3-[3-[Bis(4-methoxyphenyl)phenylmethoxy]propoxy]-2,2-bis[[3-[bis(4-methoxyphenyl)phenylmethoxy]propoxy]methyl]propoxy]propyl 2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite; Tris-2,2,2-[3-(4,4'-dimethoxytrityloxy)propyloxymethyl]methyleneoxypropyl-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite

6-Bromohexyl phosphoramidite

Description: 6-Bromohexyl Phosphoramidite is a specialized reagent utilized in oligonucleotide synthesis. It contains a 6-bromohexyl group attached to the phosphoramidite backbone. This modification allows for the introduction of a bromohexyl moiety into the oligonucleotide sequence, facilitating further functionalization or conjugation reactions. This reagent enables the synthesis of modified oligonucleotides with specific chemical properties, suitable for various molecular biology and biotechnology applications, including DNA/RNA labeling, cross-linking, and affinity purification.

CAT: BRP-00513

CAS: 956093-29-1

Molecular Formula: C15H30BrN2O2P

Molecular Weight: 381.29

Purity: ≥95%

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InChIKey: SJNZBRJYEIWFFW-UHFFFAOYSA-N

CanonicalSMILES: CC(C)N(C(C)C)P(OCCCCCCBr)OCCC#N

IUPAC Name: 3-[6-bromohexoxy-[di(propan-2-yl)amino]phosphanyl]oxypropanenitrile

InChI: InChI=1S/C15H30BrN2O2P/c1-14(2)18(15(3)4)21(20-13-9-11-17)19-12-8-6-5-7-10-16/h14-15H,5-10,12-13H2,1-4H3

Synonyms: 5'-Bromohexyl Phosphoramidite; Phosphoramidous acid, N,N-bis(1-methylethyl)-, 6-bromohexyl 2-cyanoethyl ester; 6-Bromohexyl 2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite; 6-Bromo-hex-1-yl-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite