Synonym
Propylamino uridine amidite, propylamino U amidite; 2'-O-Trifluoroacetamido propyl Uridine CED phosphoramidite; JON81497; JON-81497; JON 81497;
IUPAC/Chemical Name
(2R,3R,4R,5R)-2-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-(3-(2,2,2-trifluoroacetamido)propoxy)tetrahydrofuran-3-yl (2-cyanoethyl) diisopropylphosphoramidite
InChi Key
JDBCEYQBKYYZNE-OVLVZACUSA-N
InChi Code
InChI=1S/C44H53F3N5O10P/c1-29(2)52(30(3)4)63(60-27-10-23-48)62-38-36(61-40(51-25-22-37(53)50-42(51)55)39(38)58-26-11-24-49-41(54)44(45,46)47)28-59-43(31-12-8-7-9-13-31,32-14-18-34(56-5)19-15-32)33-16-20-35(57-6)21-17-33/h7-9,12-22,25,29-30,36,38-40H,10-11,24,26-28H2,1-6H3,(H,49,54)(H,50,53,55)/t36-,38-,39-,40-,63?/m1/s1
SMILES Code
O=C(NC(C=C1)=O)N1[C@H](O2)[C@H](OCCCNC(C(F)(F)F)=O)[C@H](OP(N(C(C)C)C(C)C)OCCC#N)[C@H]2COC(C3=CC=C(OC)C=C3)(C4=CC=CC=C4)C5=CC=C(OC)C=C5
Purity
>98% (or refer to the Certificate of Analysis)
Shipping Condition
Shipped under ambient temperature as non-hazardous chemical. This product is stable enough for a few weeks during ordinary shipping and time spent in Customs.
Storage Condition
Dry, dark and at 0 - 4 C for short term (days to weeks) or -20 C for long term (months to years).
Solubility
Soluble in DMSO
Shelf Life
>3 years if stored properly
Drug Formulation
This drug may be formulated in DMSO
Stock Solution Storage
0 - 4 C for short term (days to weeks), or -20 C for long term (months).
HS Tariff Code
2934.99.9001
More Info
5'-O-(4,4'-Dimethoxytrityl)-2'-O-trifluoroacetamidopropyl-uridine-3'-(2-cyanoethyl diisopropylphosphoramidite)
Nucleoside phosphoramidites were first introduced in 1981 by Beaucage and Caruthers. To avoid undesired side reactions, reactive hydroxy and exocyclic amino groups present in natural or synthetic nucleosides are appropriately protected. As long as a nucleoside analog contains at least one hydroxy group, the use of the appropriate protecting strategy allows one to convert that to the respective phosphoramidite and to incorporate the latter into synthetic nucleic acids. To be incorporated in the middle of an oligonucleotide chain using phosphoramidite strategy, the nucleoside analog must possess two hydroxy groups or, less often, a hydroxy group and another nucleophilic group (amino or mercapto). Examples include, but are not limited to, alternative nucleotides, LNA, morpholino, nucleosides modified at the 2'-position (OMe, protected NH2, F), nucleosides containing non-canonical bases (hypoxanthine and xanthine contained in natural nucleosides inosine and xanthosine, respectively, tricyclic bases such as G-clamp, etc.) or bases derivatized with a fluorescent group or a linker arm. (https://en.wikipedia.org/wiki/Nucleoside_phosphoramidite). Structurally modified nucleic acid analogs have been introduced to developed probes that act as potent & selected nucleic acid based therapeutics & diagnostics. In addition to this, these probes have also showed potential application molecular biology3 & Nanotechnology research and development. Incorporation of modified purines and pyrimidines has been utilized to optimize DNA-protein interactions and sequence recognition for many proteins and enzymes such as repressor proteins, restriction endonucleases, modification enzymes, and promoters. Applications for a variety of key modifications are described on the following pages. ChemGenes carries a wide variety of modified DNA phosphoramidites and supports and all these modifications are described under these section.
|
Solvent |
mg/mL |
mM |
| Solubility |
| Soluble in DMSO |
0.0 |
0.00 |
Note: There can be variations in solubility for the same chemical from different vendors or different batches from the same vendor. The following factors can affect the solubility of the same chemical: solvent used for crystallization, residual solvent content, polymorphism, salt versus free form, degree of hydration, solvent temperature. Please use the solubility data as a reference only. Warming and sonication will facilitate dissolving. Still have questions? Please contact our Technical Support scientists.
Preparing Stock Solutions
The following data is based on the
product
molecular weight
899.90
Batch specific molecular weights may vary
from batch to batch
due to the degree of hydration, which will
affect the solvent
volumes required to prepare stock solutions.
| Concentration / Solvent Volume / Mass |
1 mg |
5 mg |
10 mg |
| 1 mM |
1.15 mL |
5.76 mL |
11.51 mL |
| 5 mM |
0.23 mL |
1.15 mL |
2.3 mL |
| 10 mM |
0.12 mL |
0.58 mL |
1.15 mL |
| 50 mM |
0.02 mL |
0.12 mL |
0.23 mL |
1: Salinas JC, Seth PP, Hanessian S. Design And Synthesis Of An Azabicyclic Nucleoside Phosphoramidite For Oligonucleotide Antisense Constructs. Nucleosides Nucleotides Nucleic Acids. 2020;39(1-3):384-406. doi: 10.1080/15257770.2019.1646916. Epub 2019 Aug 5. PMID: 31380707.
2: Sato K, Matsuda A. Synthesis of 2-Amino-4-Fluoropyridine-C-Nucleoside Phosphoramidite for Incorporation into Oligonucleotides. Curr Protoc Nucleic Acid Chem. 2019 Jun;77(1):e77. doi: 10.1002/cpnc.77. Epub 2019 Feb 12. PMID: 30747492.
3: Kolganova NA, Florentiev VL, Chudinov AV, Zasedatelev AS, Timofeev EN. Simple and stereoselective preparation of an 4-(aminomethyl)-1,2,3-triazolyl nucleoside phosphoramidite. Chem Biodivers. 2011 Apr;8(4):568-76. doi: 10.1002/cbdv.201000047. PMID: 21480503.
4: Kataoka M, Hayakawa Y. Catalytic use of 1 H-tetrazole in condensation nucleoside and a nucleoside phosphoramidite. Nucleic Acids Symp Ser. 1995;(34):175-6. PMID: 8841609.
5: Gryaznov SM, Letsinger RL. Selective O-phosphitilation with nucleoside phosphoramidite reagents. Nucleic Acids Res. 1992 Apr 25;20(8):1879-82. doi: 10.1093/nar/20.8.1879. PMID: 1579488; PMCID: PMC312301.
6: Roget A, Bazin H, Teoule R. Synthesis and use of labelled nucleoside phosphoramidite building blocks bearing a reporter group: biotinyl, dinitrophenyl, pyrenyl and dansyl. Nucleic Acids Res. 1989 Oct 11;17(19):7643-51. doi: 10.1093/nar/17.19.7643. PMID: 2798121; PMCID: PMC334873.
7: Pon RT, Damha MJ, Ogilvie KK. Modification of guanine bases by nucleoside phosphoramidite reagents during the solid phase synthesis of oligonucleotides. Nucleic Acids Res. 1985 Sep 25;13(18):6447-65. doi: 10.1093/nar/13.18.6447. PMID: 4059050; PMCID: PMC321970.
