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5'-O-DMT-2'-O-TBDMS-5-Methy-Uridine 3'-CE phosphoramidite
5'-O-DMT-2'-O-TBDMS-5-Methyl-Uridine 3'-CE phosphoramidite is a modified phosphoramidite reagent used in oligonucleotide synthesis. This compound features protective groups: a dimethoxytrityl (DMT) group at the 5'-hydroxyl position, a tert-butyldimethylsilyl (TBDMS) group at the 2'-hydroxyl position, and a cyanoethyl (CE) protecting group on the phosphoramidite moiety. These modifications allow for the efficient incorporation of 5-methyluridine into synthetic oligonucleotides, enhancing their stability and binding affinity, which is crucial for applications in genetic research and therapeutic development.
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Catalog
BRP-02176
Synonyms
Uridine, 5'-O-[bis(4-methoxyphenyl)phenylmethyl]-2'-O-[(1,1-dimethylethyl)dimethylsilyl]-5-methyl-, 3'-[2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite]; 5-Methyl-5'-O-(4,4'-Dimethoxytrityl)-2'-O-(t-butyldimethylsilyl)-uridine-3'-cyanoethyl phosphoramidite; 5-O-(4,4'-dimethoxytrityl)-3-O-(diisopropylamino-2-cyanoethoxyphosphanyl)-2-O-(tert-butyl-dimethyl-silyl)-1-deoxy-1-thymin-1-yl-beta-D-ribo-pentofuranose; 5'-O-[Bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(diisopropylamino)phosphino]-2'-O-[dimethyl(2-methyl-2-propanyl)silyl]-5-methyluridine; DMT-2'-O-TBDMS-5-Me-rU Phosphoramidite; 5'-O-DMT-2'-O-TBDMS-rT Phosphoramidite; 5'-O-DMTr-2'-O-TBDMS-5-Me-U-3'-CE-Phosphoramidite; 2'-OTBS T amidite; 2'-O-tert-Butyldimethylsilyl-5'-O-DMT-5-methyluridine 3'-CE phosphoramidite; 5-Me-U-CE Phosphoramidite
CAS
159639-78-8
IUPAC Name
3-[[(2R,3R,4R,5R)-2-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[tert-butyl(dimethyl)silyl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxy-[di(propan-2-yl)amino]phosphanyl]oxypropanenitrile
Molecular Weight
875.09
Molecular Formula
C46H63N4O9PSi
Canonical SMILES
CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COC(C3=CC=CC=C3)(C4=CC=C(C=C4)OC)C5=CC=C(C=C5)OC)OP(N(C(C)C)C(C)C)OCCC#N)O[Si](C)(C)C(C)(C)C
InChI
InChI=1S/C46H63N4O9PSi/c1-31(2)50(32(3)4)60(56-28-16-27-47)58-40-39(57-43(41(40)59-61(11,12)45(6,7)8)49-29-33(5)42(51)48-44(49)52)30-55-46(34-17-14-13-15-18-34,35-19-23-37(53-9)24-20-35)36-21-25-38(54-10)26-22-36/h13-15,17-26,29,31-32,39-41,43H,16,28,30H2,1-12H3,(H,48,51,52)/t39-,40-,41-,43-,60?/m1/s1
InChIKey
KYRSLFQMFXXGLW-IEXCOMMKSA-N
Purity
≥98% by HPLC
Appearance
White powder
Storage
Store at -20 °C
Chemical Structure:
Reference Reading
1. A universal, photocleavable DNA base: nitropiperonyl 2'-deoxyriboside
M C Pirrung, X Zhao, S V Harris. J Org Chem. 2001 Mar 23;66(6):2067-71. doi: 10.1021/jo001594r.
A universal, photochemically cleavable DNA base analogue would add desirable versatility to a number of methods in molecular biology. A novel C-nucleoside, nitropiperonyl deoxyriboside (NPdR, P), has been investigated for this purpose. NPdR can be converted to its 5'-DMTr-3'-CE-phosphoramidite and was incorporated into pentacosanucleotides by conventional synthesis techniques. The destabilizing effect on hybrid formation with a complementary strand when this P base opposes A, T, and G was found to be 3-5 kcal/mol, but 9 kcal/mol when it opposes C. Brief irradiation (lambda > 360 nm, 20 min) of DNA containing the P base and piperidine treatment causes strand cleavage giving the 3'- and 5'-phosphates. Two significant recent interests, universal/non-hydrogen-bonding base analogues and photochemical backbone cleavage, have thus been combined in a single molecule that serves as a light-based DNA scissors.
