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Spacer Phosphoramidite 18
Spacer phosphoramidites 18 is used to insert a spacer arm in an oligonucleotide and may be added in multiple additions when a longer spacer is required.
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Catalog
BRP-00231
Synonyms
1,1-Bis(4-methoxyphenyl)-1-phenyl-2,5,8,11,14,17-hexaoxanonadecan-19-yl (2-cyanoethyl) diisopropylphosphoramidite; Spacer C18 CE Phosphoramidite; Spacer 18 Amidite; Hexaethylene glycol phosphoramidite; 18-O-(4,4'-Dimethoxytrityl)-hexaethylene glycol-1-[[(2-cyanoethyl)-(N,N-diisopropyl)]-Phosphoramidite; Spacer 18 Phosphoramidite; Phosphoramidous acid, N,N-bis(1-methylethyl)-, 19,19-bis(4-methoxyphenyl)-19-phenyl-3,6,9,12,15,18-hexaoxanonadec-1-yl 2-cyanoethyl ester; 19,19-Bis(4-methoxyphenyl)-19-phenyl-3,6,9,12,15,18-hexaoxanonadec-1-yl 2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite; DMT Hexaethylene Glycol phosphoramidite
CAS
125607-09-2
IUPAC Name
3-[2-[2-[2-[2-[2-[2-[bis(4-methoxyphenyl)-phenylmethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy-[di(propan-2-yl)amino]phosphanyl]oxypropanenitrile
Molecular Weight
784.93
Molecular Formula
C42H61N2O10P
Canonical SMILES
CC(C)N(C(C)C)P(OCCC#N)OCCOCCOCCOCCOCCOCCOC(C1=CC=CC=C1)(C2=CC=C(C=C2)OC)C3=CC=C(C=C3)OC
InChI
InChI=1S/C42H61N2O10P/c1-35(2)44(36(3)4)55(53-22-10-21-43)54-34-32-51-30-28-49-26-24-47-23-25-48-27-29-50-31-33-52-42(37-11-8-7-9-12-37,38-13-17-40(45-5)18-14-38)39-15-19-41(46-6)20-16-39/h7-9,11-20,35-36H,10,22-34H2,1-6H3
InChIKey
ZTCKUVQHKIMCLI-UHFFFAOYSA-N
Boiling Point
763.6±60.0 °C at 760 mmHg
Purity
>95% by HPLC
Appearance
Colorless to light yellow oily matter
Storage
Store at -20 °C
Chemical Structure:
Reference Reading
1. Synthesis of zwitterionic 1,1'-glycosylphosphodiester: a partial structure of galactosamine-modified Francisella lipid A
David Baum, Paul Kosma, Alla Zamyatina. Org Lett. 2014 Jul 18;16(14):3772-5. doi: 10.1021/ol501639c.
Synthesis of a "double glycosidic" phosphodiester comprising anomeric centers of two 2-amino-2-deoxy-sugars is reported. The carbohydrate epitope of Francisella lipid A modified with α-d-galactosamine at the anomerically linked phosphate has been stereoselectively prepared and coupled to maleimide-activated bovine serum albumin via an amide-linked thiol-terminated spacer group. H-Phosphonate and phosphoramidite approaches have been explored for the coupling of 4,6-DTBS-2-azido-protected GalN lactol and peracetylated spacer-equipped reducing βGlcN(1→6)GlcN disaccharide via phosphodiester linkage. Deprotection conditions preserving the integrity of the labile glycosidic zwitterionic phosphodiester were elaborated.
2. Synthesis, cell-surface binding, and cellular uptake of fluorescently labeled glucose-DNA conjugates with different carbohydrate presentation
Begoña Ugarte-Uribe, Sonia Pérez-Rentero, Ricardo Lucas, Anna Aviñó, José J Reina, Itziar Alkorta, Ramón Eritja, Juan C Morales. Bioconjug Chem. 2010 Jul 21;21(7):1280-7. doi: 10.1021/bc100079n.
Oligonucleotide conjugates carrying carbohydrates at the 5'-end have been prepared. Glucose, fucose, and saccharides containing glucose at the nonreducing end were attached to DNA strands using the classical phosphoramidite chemistry. Two types of spacers and a dendron scaffold helped to obtain a diversity of sugar presentations in the DNA conjugates. Cellular surface adsorption and cellular uptake of carbohydrate oligonucleotide antisense sequences were measured using flow cytometric analysis. Conjugates with the glucose moiety linked through long spacers (15 to 18 atom distances) were internalized better than those with short linkers (4 atom distance) and than DNA control strands without sugar modification. Conjugates with tetravalent presentation of glucose did not improve cell uptake.
3. A protected biotin containing deoxycytidine building block for solid phase synthesis of biotinylated oligonucleotides
U Pieles, B S Sproat, G M Lamm. Nucleic Acids Res. 1990 Aug 11;18(15):4355-60. doi: 10.1093/nar/18.15.4355.
The synthesis of a modified 2'-deoxycytidine-3'-O-phosphoramidite carrying an N-t-butylbenzoyl protected biotin on a long polar spacer arm attached to the 4-N position is described. The presence of the bulky lipophilic t-butylbenzoyl protecting group enables the direct solid phase synthesis of biotinylated oligoribonucleotides and a variety of analogues in high yield without modification of the biotin moiety. Biotinylated antisense oligonucleotides incorporating this new derivative allow convenient isolation and purification of ribonucleic acid-protein complexes. The kinetics of biotin binding to streptavidin agarose is facilitated by the long polar spacer arm.
