N2-Acetyl-2'-O-tert-butyldimethylsilyl-5'-O-DMT-guanosine 3'-CE phosphoramidite - CAS 944138-03-8

Catalog number: BRA-040

Commonly used protected 2-OTBDMS phosphoramidite for incorporation of nucleotide-G into the synthesis of oligonucleotides.

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Synonyms

Ac-G-CE Phosphoramidite

CAS

944138-03-8

IUPAC Name

N-[9-[(2R,3R,4R,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-3-[tert-butyl(dimethyl)silyl]oxy-4-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyoxolan-2-yl]-6-oxo-1H-purin-2-yl]acetamide

Molecular Weight

942.12

Molecular Formula

C48H64N7O9PSi

Canonical SMILES

CC(C)N(C(C)C)P(OCCC#N)OC1C(OC(C1O[Si](C)(C)C(C)(C)C)N2C=NC3=C2N=C(NC3=O)NC(=O)C)COC(C4=CC=CC=C4)(C5=CC=C(C=C5)OC)C6=CC=C(C=C6)OC

InChI

InChI=1S/C48H64N7O9PSi/c1-31(2)55(32(3)4)65(61-28-16-27-49)63-41-39(29-60-48(34-17-14-13-15-18-34,35-19-23-37(58-9)24-20-35)36-21-25-38(59-10)26-22-36)62-45(42(41)64-66(11,12)47(6,7)8)54-30-50-40-43(54)52-46(51-33(5)56)53-44(40)57/h13-15,17-26,30-32,39,41-42,45H,16,28-29H2,1-12H3,(H2,51,52,53,56,57)/t39-,41-,42-,45-,65-/m1/s1

InChIKey

DGDYJRDKFZTURB-WUYIOLTESA-N

Purity

98%

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.