98796-51-1

Usage

Uses

Used in Pharmaceutical Industry:
5'-Dimethoxytrityl-3'-deoxythymidine 2'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite is used as a key reactant in the solid-phase synthesis of phosphorothioate oligonucleotides. These modified oligonucleotides exhibit increased stability and resistance to nuclease degradation, making them suitable for applications such as antisense therapy, where they can modulate gene expression and target specific RNA sequences to treat various diseases.
Used in Diagnostics and Research:
In the field of diagnostics and research, 5'-Dimethoxytrityl-3'-deoxythymidine 2'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite is utilized for the synthesis of lipophilic 5'-phosphoramidate derivatives of DNA and RNA oligonucleotides. These derivatives possess enhanced cellular uptake and membrane permeability, allowing for improved delivery of oligonucleotides into cells for applications such as in situ hybridization, molecular beacons, and other detection techniques.
Used in Drug Development:
5'-Dimethoxytrityl-3'-deoxythymidine 2'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite is also employed in the development of novel therapeutic agents, such as antiviral and anti-cancer drugs. The ability to create stable and lipophilic derivatives of oligonucleotides enables the design of drugs that can effectively target specific genetic sequences and disrupt disease-causing processes.
Overall, 5'-Dimethoxytrityl-3'-deoxythymidine 2'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite is a versatile and essential component in the synthesis of various types of oligonucleotides, with applications spanning across the pharmaceutical, diagnostic, and research industries. Its unique properties and reactivity make it a valuable tool for the development of innovative therapeutic agents and diagnostic techniques.

InChI:InChI=1/C10H14N2O5.C3H6N2O2P/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8;1-3(2-4)7-8(5)6/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16);3H,5H2,1H3/q;-1/t6-,7+,8+;/m0./s1

Upstream product

• 124482-92-4 2-cyanoethyl-N,N-(diisopropylamino)chlorophosphine 
• 40615-39-2 5'-O-(4-4'-dimethoxytrityl)thymidine 
• 102691-36-1 N,N,N',N'-tetraisopropyl 2-cyanoethylphosphorodiamidite 
• 174647-46-2 2-cyanoethoxy(N,N-diisopropylamino)3-nitro-1,2,4-triazolylphosphine 
• 108-18-9 diisopropylamine 
• 148134-86-5 2'-deoxy-3',5'-bis(O-tert-butyldimethylsilyl)-5-iodouridine 
• 40733-26-4 3',5'-O-di(tert-butyldimethylsilyl)thymidine 
• 17425-88-6 N,N-diisopropyl-1,1,1-trimethylsilylamine 
• 40615-36-9 4,4'-dimethoxytrityl chloride 
• 56183-63-2 bis(diisopropylamino)chlorophosphine 
• 109-78-4 3-Hydroxypropionitrile 
• 921-26-6 N,N-diisopropylphosphoramide dichloride 
• 50-89-5 thymidine 

Downstream Products

• 142345-06-0 Phosphorous acid (2R,3S,5R)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl ester 2-cyano-ethyl ester 4-(4'-methyl-[2,2']bipyridinyl-4-yl)-butyl ester 
• 127728-40-9 C₆₅H₆₁N₈O₁₄P 
• 101712-10-1 1-(2'-deoxy-5'-O-dimethoxytrityl-β-D-ribofuranosyl)-5-methyl-4-(1,2,4-triazol-1-yl)-2-pyrimidone 3'-(N,N-diisopropylamido)-β-cyanoethylphosphite 
• 129789-63-5 5'-O-Dimethoxytritylthymidine-3'-O-<β-cyanoethyl-(S-4-chlorobenzyl)>-phosphorodithioate 
• 169049-62-1 Phenylacetyl-phosphoramidous acid (2R,3S,5R)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl ester 2-cyano-ethyl ester 
• 202719-41-3 (3'-O-Acetylthymidin-5'-O-yl)(2-cyanoethoxy)[5'-O-(4,4'-dimethoxytrityl)thymidin-3'-O-yl]phosphane 
• 187539-25-9 C₄₉H₅₄N₅O₁₅PS 
• 813419-53-3 Phosphorous acid (2R,3S,5R)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl ester bis-(2-cyano-ethyl) ester 
• 4719-57-7 TpTpTpTp 

Relevant academic research and scientific papers

Resolved P-metalated nucleoside phosphoramidites

The synthesis of resolved P-metalated nucleoside phosphoramidites is described. These rare compounds were initially prepared with gold as the metal center; however, the gold can be removed using basic phosphines or solid-supported triphenylphosphine. Treatment of the free nucleoside phosphoramidite with a platinum source generated a unique platinated dinucleoside species with a diastereomeric ratio of >99:1.

RETRACTED ARTICLE: Divergent synthesis of 5-substituted pyrimidine 2′-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases

Recent studies have indicated that 5-methylcytosine (5mC) residues in DNA can be oxidized and potentially deaminated to the corresponding thymine analogs. Some of these oxidative DNA damages have been implicated as new epigenetic markers that could have profound influences on chromatin function as well as disease pathology. In response to oxidative damage, the cells have a complex network of repair systems that recognize, remove and rebuild the lesions. However, how the modified nucleobases are detected and repaired remains elusive, largely due to the limited availability of synthetic oligodeoxynucleotides (ODNs) containing these novel DNA modifications. A concise and divergent synthetic strategy to 5mC derivatives has been developed. These derivatives were further elaborated to the corresponding phosphoramidites to enable the site-specific incorporation of modified nucleobases into ODNs using standard solid-phase DNA synthesis. The synthetic methodology, along with the panel of ODNs, is of great value to investigate the biological functions of epigenetically important nucleobases, and to elucidate the diversity in chemical lesion repair.

Oxidative substitution of boranephosphonate diesters as a route to post-synthetically modified DNA

The introduction of modifications into oligonucleotides is important for a large number of applications in the nucleic acids field. However, the method of solid-phase DNA synthesis presents significant challenges for incorporating many useful modifications that are unstable to the conditions for preparing synthetic DNA. Here we report that boranephosphonate diesters undergo facile nucleophilic substitution in a stereospecific manner upon activation by iodine. We have subsequently used this reactivity to post-synthetically introduce modifications including azides and fluorophores into DNA by first synthesizing boranephosphonate-linked 2′-deoxyoligonucleotides and then treating these oligomers with iodine and various nucleophiles. In addition, we show that this reaction is an attractive method for preparing stereodefined phosphorus-modified oligonucleotides. We have also examined the mechanism of this reaction and show that it proceeds via an iodophosphate intermediate. Beyond nucleic acids synthesis, due to the ubiquity of phosphate derivatives in natural compounds and therapeutics, this stereospecific reaction has many potential applications in organophosphorus chemistry.

Microwave-assisted preparation of nucleoside-phosphoramidites

Microwave-assisted phosphitylation of sterically hindered nucleosides is demonstrated to be an efficient method for the preparation of corresponding phosphoramidites (otherwise onerous under standard conditions) and is shown to be general in its applicability. the Partner Organisations 2014.

Studies on the synthesis of neamine-dinucleosides and neamine-PNA conjugates and their interaction with RNA

Two types of neamine derivatives, neamine-dinucleotide conjugates 8a-g and neamine-PNA conjugates 12a-c and 14a-d, were synthesized. Compound 8a-g were synthesized by the condensation of azido-neamine with dinucleotide-5′-carboxylic acids, followed by reduction and deprotection. Compound 12a-c and 14a-d were synthesized by the similar strategy. The binding affinities of conjugates 8a-g, 12a-c, and 14a-d towards 16S RNA, 18S RNA, and TAR RNA were evaluated by SPR. It indicates that conjugates 12a-c and 14a-d interact with 16S, 18S RNA at the same level as that of neamine, 14a and 14d show about twofold binding affinities to TAR RNA compared to that of neamine. However, the neamine-dinucleotide conjugates 8a-g exhibit very weak binding affinities to 16S, 18S, and TAR RNA, computer modelling results that negative-negative electrostatic repulsion of phosphate group in compound 8a-g and RNA leads to a sharp decrease of the binding affinities compared with that of neamine, neamine-nucleoside and neamine-PNA conjugates.

PROCESS FOR PRODUCING PHOSPHOROAMIDITE

The present invention provides high purity phosphoroamidite products by reducing the amount of impurities of triphosphite which has been additionally produced according to the conventional technique.Phosphoroamidites can be obtained with high purity such that the excess reaction is suppressed by using a reaction activator hardly generating triphosphite.According to the present invention, phosphoroamides can be obtained with high purity, which has heretofore been difficult to suppress the generation of impurities of triphosphite.

Chemical synthesis of an artificially branched hairpin ribozyme variant with RNA cleavage activity

Due to the development in the field of RNA synthesis over the past decade of years, preparation of RNA oligonucleotides longer than 50 nucleotides is possible today. In this report, we describe the chemical preparation of a branched RNA molecule with RNA cleavage activity consisting of 81 nucleotides. It is derived from the hairpin ribozyme, a small catalytic RNA occurring in nature. The hairpin ribozyme consists of two separately folded domains (loop A and loop B domain), which can be joined in a number of different ways without loss of activity. In the construct presented here, 2′-deoxy-N4-(6- hydroxyhexyl)-5-methylcytidine was introduced to connect the loop B domain with the loop A domain via an artificial branch. The synthesized branched RNA is able to catalyze the cleavage of a number of suitable substrates. Compared with the corresponding non-branched reverse-joined ribozyme it cleaves its substrates only 5-fold slower. Surprisingly, no ligation activity could be detected.

Methods of producing phosphitylated compounds

Provided are methods of producing phosphitylated compounds, including 3′-O-phosphoramidites, comprising the step of reacting a hydroxyl-containing compound with a phosphitylating agent in the presence of a phosphitylation activator selected from the group consisting of: (1) acid-base complexes derived from an amine base of Formula I 1wherein R, R1, and R2 are independently C1-C10 alkyl, C1-C10 cycloalkyl, C1-C10 aryl, C1-C10 aralkyl, C1-C10 heteroalkyl, or C1-C10 heteroaryl; (2) acid-base complexes derived from an amine base of Formula II 2wherein R3, R4, R5, R6, and R7 are independently hydrogen, C1-C10 alkyl, C1-C10 cycloalkyl, C1-C10 aryl, C1-C10 aralkyl, C1-C10 heteroalkyl, or C1-C10 heteroaryl, and at least one of R3, R4, R5 R6, and R7 is not hydrogen.; (3) acid-base complexes derived from a diazabicyclo amine base; (4) zwitterionic amine complexes; and (5) combinations of two or more thereof, to produce a phosphitylated compound.

Antisense molecules and method of controlling expression of gene function by using the same

An antisense molecule which acts on both directions of the inhibition and expression of a gene function and is capable of on-off switching of a gene function appropriately depending on the external factors (orientation controlling factors); and a method for reversibly controlling the expression of a gene function by using the antisense molecule. Such an antisense molecule, which has at least one sugar-base moiety consisting of sugar and a purine or pyrimidine base bonded thereto via a glucoside bond, can bind to a mRNA/gene and/or dissociate therefrom under the orientation control of the base moiety in the molecule by the orientation controlling factors.

Nucleoside derivatives

Novel nucleoside derivatives represented by the following general formula (1): 1wherein X is(are) the same or different and each represents a pyrimidine or purine base or a derivative thereof, Y-and Y′ are the same or different and each represents at least one amino acid or amino acid derivative selected from the group consisting of serine, threonine, ornithine, aspartic acid, glutamic acid, lysine, arginine, cysteine, methionine, δ-hydroxylysine, N-aminoethylglycine, N-aminoethylserine, N-aminoethyllysine, N-aminoethylornithine, N-aminoethylaspartic acid, N-aminoethylglutamic acid, homoglutamic acid, β-thiocarbonylaspartic acid, γ-thiocarbonylglutamic acid, and δ-thiocarbonylhomoglutamic acid, R1 represents a hydrogen atom or a hydroxyl group, A represents a single bond or a carbonyl or thiocarbonyl group, 1 is an integer of 0 to 5, and n is an integer of 1 to 100.