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ssH-Linker
ssH-Linker refers to a specific type of linker used in the synthesis of oligonucleotides, particularly in the context of RNA or DNA synthesis. This linker is designed to introduce a specific functional group or a spacer within an oligonucleotide sequence.
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Catalog
BRP-02208
Synonyms
9,11-Dioxa-2-aza-10-phosphatridecanoic acid, 10-[bis(1-methylethyl)amino]-13-cyano-, 2-[[(4-methoxyphenyl)diphenylmethyl]amino]ethyl ester; 2-[[(4-Methoxyphenyl)diphenylmethyl]amino]ethyl 10-[bis(1-methylethyl)amino]-13-cyano-9,11-dioxa-2-aza-10-phosphatridecanoate; ssH-H Amino Modifier
CAS
922522-12-1
IUPAC Name
2-[[(4-methoxyphenyl)-diphenylmethyl]amino]ethyl N-[6-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyhexyl]carbamate
Molecular Weight
676.83
Molecular Formula
C38H53N4O5P
Canonical SMILES
CC(C)N(C(C)C)P(OCCCCCCNC(=O)OCCNC(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=C(C=C3)OC)OCCC#N
InChI
InChI=1S/C38H53N4O5P/c1-31(2)42(32(3)4)48(47-29-16-25-39)46-28-15-7-6-14-26-40-37(43)45-30-27-41-38(33-17-10-8-11-18-33,34-19-12-9-13-20-34)35-21-23-36(44-5)24-22-35/h8-13,17-24,31-32,41H,6-7,14-16,26-30H2,1-5H3,(H,40,43)
InChIKey
VTFLXOVDKJUHER-UHFFFAOYSA-N
Purity
≥97% by HPLC
Appearance
Solid
Storage
Store at -20 °C
Shipping
Dry ice
Chemical Structure:
Reference Reading
1. Efficient synthesis of oligonucleotide conjugates on solid-support using an (aminoethoxycarbonyl)aminohexyl group for 5'-terminal modification
Naoshi Kojima, Toshie Takebayashi, Akiko Mikami, Eiko Ohtsuka, Yasuo Komatsu. Bioorg Med Chem Lett. 2009 Apr 15;19(8):2144-7. doi: 10.1016/j.bmcl.2009.02.121.
Solid-support conjugation at the 5'-terminal primary amine of oligonucleotides is a convenient and powerful method for introducing various functional groups. However, conventional aliphatic amines do not necessarily provide conjugates with sufficient yields. To improve the modification efficacy, we used the amino-linker (aminoethoxycarbonyl)aminohexyl group (ssH-linker), for solid-support conjugation. In the ssH-linker terminal modification, reactive free amino group could be easily presented onto a solid-support due to rapid removal of the amino-protecting group, and activated amino acids or cholesterol molecules could be covalently connected more efficiently than to typical 6-aminohexyl-linkers. Based on these results, the ssH-linker can be a useful terminal modification for the solid-support conjugation of functional molecules.
2. Comparison of the chemical properties of a novel amino-linker with various amino modifications
Naoshi Kojima, Toshie Takebayashi, Akiko Mikami, Maiko Sugino, Eiko Ohtsuka, Yasuo Komatsu. Nucleic Acids Symp Ser (Oxf). 2008;(52):463-4. doi: 10.1093/nass/nrn235.
We previously reported a series of new amino-linkers, consisting of an aminoethyl carbamate structure (Komatsu, 2008). We have now examined the chemical properties of oligonucleotides modified with an ssH-linker, which is the simplest and most cost-effective derivative of the series. Although it was previously shown that monomethoxytrityl protection on a primary amine of the ssH-linker was cleaved under weakly acidic conditions (1% acetic acid), we found that the deprotection also proceeded in aqueous buffer solutions (pH 6.0, 7.0). The MMT group was removed much faster than other commercially available amino-linkers, and this property enabled the ssH-modified oligonucleotides to be conveniently purified with a cartridge column. Furthermore, the ssH-modified oligonucleotides were utilized in on-support labeling reactions. As compared with other amino-linkers, the ssH-linker was superior in terms of its purification and reaction efficiencies.
