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5'-Amino Modifier
MMT-Hexylaminolinker Phosphoramidite is designed for use in automatic synthesizers to functionalize the sequence of the 5'end of the target oligonucleotide. The use of trityl-protected amino-modifiers is recommended when purification is required prior to use.
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Catalog
BRP-02210
Synonyms
6-(4-Monomethoxytrityl)-hexyl-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite; N-MMT-C6 Amino Modifier; 5'-Amino C6 Modifier Amidite
CAS
114616-27-2
IUPAC Name
3-[[di(propan-2-yl)amino]-[6-[[(4-methoxyphenyl)-diphenylmethyl]amino]hexoxy]phosphanyl]oxypropanenitrile
Molecular Weight
589.75
Molecular Formula
C35H48N3O3P
Canonical SMILES
CC(C)N(C(C)C)P(OCCCCCCNC(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=C(C=C3)OC)OCCC#N
InChI
InChI=1S/C35H48N3O3P/c1-29(2)38(30(3)4)42(41-28-16-25-36)40-27-15-7-6-14-26-37-35(31-17-10-8-11-18-31,32-19-12-9-13-20-32)33-21-23-34(39-5)24-22-33/h8-13,17-24,29-30,37H,6-7,14-16,26-28H2,1-5H3
InChIKey
YBANXOPIYSVPMH-UHFFFAOYSA-N
Boiling Point
634.0±55.0 °C at 760 mmHg
Purity
≥97.0%
Appearance
Colorless to light yellow oil
Storage
Store at -20 °C
Symbol
MMT-hexylamine-linker amidite; N-MMT-C6 Amino Modifier
Formulation
Dilute with anhydrous acetonitrile
Shipping
Dry ice
Chemical Structure:
Reference Reading
1. Chemical synthesis and properties of modified oligonucleotides containing 5'-amino-5'-deoxy-5'-hydroxymethylthymidine residues
Akihiro Ohkubo, Kousuke Muto, Rintaro Watanabe, Shuhei Nishizawa, Shugo Hisamatsu, Takashi Kanamori. Bioorg Med Chem. 2020 Apr 15;28(8):115407. doi: 10.1016/j.bmc.2020.115407.
In this study, we designed 5'-amino-5'-deoxy-5'-hydroxymethylthymidine as a new oligonucleotide modification with an amino group directly attached to the 5'-carbon atom. We successfully synthesized two isomers of 5'-amino-5'-deoxy-5'-hydroxymethylthymidine via dihydroxylation of the 5'-vinyl group incorporated into 5'-deoxy-5'-C-methenylthymidine derivative. Moreover, it was found that the nuclease resistance, binding selectivity to single-stranded RNA, and triplex-forming ability of an oligonucleotide containing RT residues of the new compound were higher than those of the unmodified oligonucleotide.
2. Chemical Synthesis of Modified Oligonucleotides Containing 5'-Amino-5'-Deoxy-5'-Hydroxymethylthymidine Residues
Akihiro Ohkubo, Kousuke Muto, Rintaro Watanabe, Daisuke Ogata. Curr Protoc. 2021 Mar;1(3):e70. doi: 10.1002/cpz1.70.
Introduction of cationic modifications into an oligonucleotide can increase its nuclease resistance and duplex- or triplex-forming abilities. In a recent study, we found that the nuclease resistance and RNA binding selectivity of an oligonucleotide containing a 5'-(R)-amino-5'-deoxy-5'-(R)-hydroxymethylthymidine residue were greater than those of the unmodified oligonucleotide. In this article, we describe the synthesis of 5'-amino-5'-deoxy-5'-hydroxymethylthymidine via dihydroxylation of the 5'-alkene derivative using either of two commercial AD (asymmetric dehydroxylation) mixes or via epoxidation and ring opening. We also provide detailed protocols for the syntheses of oligonucleotides containing 5'-amino-5'-deoxy-5'-hydroxymethylthymidine residues. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 5'-amino-5'-deoxy-5'-hydroxymethylthymidine phosphoramidites 9a and 9b Basic Protocol 2: Synthesis of oligonucleotides 1 and 2 containing 5'-amino-5'-deoxy-5'-hydoxymethylthymidine residues (R T and S T).
3. Synthesis and polymerase incorporation of 5'-amino-2',5'-dideoxy-5'-N-triphosphate nucleotides
Jia Liu Wolfe, Tomohiko Kawate. Curr Protoc Nucleic Acid Chem. 2004 Oct;Chapter 13:Unit 13.3. doi: 10.1002/0471142700.nc1303s18.
This unit presents synthetic procedures for the preparation of 5'-amino-2',5'-dideoxy analogs of adenosine, cytidine, guanosine, and thymidine, as well as corresponding 5'-N-triphosphate nucleotides, using commercially available reagents. The modified nucleosides are prepared in high yields from naturally occurring 2'-deoxynucleosides using robust chemical reactions including tosylation, azide exchange, and the Staudinger reaction. Efficient conversion of these 5'-amino nucleosides to corresponding 5'-N-triphosphate nucleotides is achieved through a one-step reaction with trimetaphosphate in Tris-buffered aqueous solution. The 5'-amino modification renders these nucleoside and nucleotide analogs markedly increased reactivity, which is useful for a variety of biochemical, pharmaceutical, and genomic applications. Also included in this unit are protocols for polymerase incorporation of the 5'-amino nucleotides, either partially or completely replacing their naturally occurring counterparts, and subsequent sequence-specific cleavage at the modified nucleotides under mildly acidic conditions.
