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5'-O-DMT-2'-O-Propargyl-Uridine 3'-CE phosphoramidite
5'-O-DMT-2'-O-Propargyl-Uridine 3'-CE phosphoramidite is an indispensable compound in the biomedical sector, serving as a fundamental component for oligonucleotide research and development, extensively employed in gene therapy and diagnostic applications. Its unparalleled chemical attributes allow for highly accurate nucleotide sequence modification, thereby propelling the research of ailments encompassing cancer, genetic disorders and viral ailments.
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Catalog
BRP-00323
Synonyms
2'-O-Propargyl-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)uridine; 5'-O-[Bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(diisopropylamino)phosphino]-2'-O-2-propyn-1-yluridine; 2'-O-Propargyl-Uridine Phosphoramidite; DMTr-2'-O-propargyl-rU-3'-CE-Phosphoramidite; 5'-O-DMTr-2'-O-propargyl-U-3'-phosphoramidite; 5'-O-DMTr-2'-O-propygyluridine 3-CED phosphoramidite; DMT-2'-O-propargyl-U-CE-Phosphoramidite; 2'-O-propargyl Uridine CED phosphoramidite; 5'-O-DMT-2'-O-propynyluridine 3'-CE phosphoramidite
CAS
171486-62-7
IUPAC Name
3-[[(2R,3R,4R,5R)-2-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-5-(2,4-dioxopyrimidin-1-yl)-4-prop-2-ynoxyoxolan-3-yl]oxy-[di(propan-2-yl)amino]phosphanyl]oxypropanenitrile
Molecular Weight
784.83
Molecular Formula
C42H49N4O9P
Canonical SMILES
CC(C)N(C(C)C)P(OCCC#N)OC1C(OC(C1OCC#C)N2C=CC(=O)NC2=O)COC(C3=CC=CC=C3)(C4=CC=C(C=C4)OC)C5=CC=C(C=C5)OC
InChI
InChI=1S/C42H49N4O9P/c1-8-26-51-39-38(55-56(53-27-12-24-43)46(29(2)3)30(4)5)36(54-40(39)45-25-23-37(47)44-41(45)48)28-52-42(31-13-10-9-11-14-31,32-15-19-34(49-6)20-16-32)33-17-21-35(50-7)22-18-33/h1,9-11,13-23,25,29-30,36,38-40H,12,26-28H2,2-7H3,(H,44,47,48)/t36-,38-,39-,40-,56?/m1/s1
InChIKey
SKUHDLBLPLSZJC-CYSIDSPMSA-N
Purity
≥97% by HPLC
Appearance
White, off-white to faint yellow 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.
