Allyl group as a protecting group for internucleotide phosphate and thiophosphate linkages in oligonucleotide synthesis: facile oxidation and deprotection conditions

[reaction: see text] The allyl group, which serves as a protecting group for an internucleotide bond for both phosphates and phosphorothioates, can be easily removed by good nucleophiles under weakly basic or neutral conditions. For a practical synthesis on solid support, camphorsulfonyloxaziridine was used as the oxidizing agent for synthesizing DNA, while the Beaucage reagent was used for preparing phosphorothioate oligomers. Both types of oligonucleotides were easily deprotected by concentrated ammonium hydroxide containing 2% mercaptoethanol.     

The p-nitrophenylethyl (NPE) group: A versatile new blocking group for phosphate and aglycone protection in nucleosides and nucleotides

The syntheses of new monomer building blocks for oligonucleotide synthesis via the phosphotriester approach containing the p-nitrophenylethyl group for phosphate and aglycone protection are described. Blocking of the amide function in guanosines at O⁶ can be achieved by the Mitsunobu reaction forming the corresponding O⁶-p-nitrophenylethyl derivatives (4,5,10). Sugar-protected thymidine (16) and uridine (17) have been alkylated at O⁴ in an S_N1-type reaction by p-nitrophenylethyl iodide-silver carbonate in benzene to form the O⁴-p-nitrophenylethyl derivatives (18,19). Protection of the amino group in 2'-deoxycytidine (25) and cytidine (26) can be performed directly by 1-(p-nitrophenylethoxycarbonyl)-benzotriazole in DMF to obtain the corresponding carbamates (27,28) as a new type of N⁴-acylated cytidine derivative. p Nitrophenylethoxycarbonylation of the amino group in 2'-deoxyadenosine (33) and adenosine (34) requires previous sugar protection by acyl or silyl groups and can then be achieved by p-nitrophenylethyl chloroformate or better by 1-methyl-3-p-nitrophenylethoxycarbonylimidazolium chloride to form N⁶-p-nitrophenylethoxycarbonyladenosines (38,39,40,42). The various /-nitrophenylethyl blocking groups are stable under mild hydrolytic conditions (e.g. ammonia and triethylamine) but can be cleaved selectively by DBU or DBN in aprotic solvents. 5'-O-Monomethoxytritylation (12,29,43) as well as phosphorylations at the 3'-OH group can be effected to give the corresponding 3'-(2,5-dichlorophenyl,/-nitrophenylethyl)-phosphotriesters (13,22,30,44) also in high yields. Oximate cleavage of the latter compounds to the phosphodiesters (14,24,32,46) and detritylation to the 5'-unblocked phosphotriesters (15,23,31,45) do not affect the aglycone protecting groups, thereby demonstrating their general versatility. The newly synthesized compounds have been characterized on the basis of their elementary analyses (C, H, N), and UV- and ¹H-NMR-spectra.     

DBU及DBN与丙炔酸甲酯的迈克尔型加成及其产物的核磁共振谱学研究

1,8-二氮杂二环[5,4,0]十一碳-7-烯(DBU及1,5-二氮杂二环[4,3,0]壬碳-5-烯与丙炔酸甲酯反应可生成成环化合物。通过对成环产物的^1H NMR、^1H-^1H COSY、^13C NMR谱的分析,讨论了其化学位移及J-偶合特征。同时研究了整个反应可能的历程和机理。     

2-Benzamidoethyl group--a novel type of phosphate protecting group for oligonucleotide synthesis.

A number of 5'-O-(4,4'-dimethoxytrityl)thymidine N,N-diisopropylamino phosphoramidites protected at P(III) with derivatives of 2-benzamidoethanol were synthesized and incorporated into synthetic oligonucleotides. Depending on substitution patterns at the alkyl chain, amido group, and phenyl ring, the time required for removal of these protecting groups using concentrated ammonium hydroxide varied from 48 h at 55 degrees C to 25 min at 25 degrees C. Of the 11 groups studied, 2-[N-isopropyl-N- (4-methoxybenzoyl)amino]ethyl- (H) and omega-(thionobenzoylamino)alkyl protections (I and K) were most easily removed. Derivatives of the 2-[N-methyl-N-benzoylamino]ethyl group (E-G) demonstrated moderate stability, but those of the 2-(N-benzoylamino)ethyl group (A-C) were the most stable. For the most reactive group, H, a phosphitylating reagent, bisamidite 60, was synthesized and used in the preparation of four deoxynucleoside phosphoramidites 28 and 65-67, plus the 2'-O-(2-methoxyethyl)-5-methyluridine phosphoramidite 68. All of these novel building blocks were successfully tested in the preparation of natural, 20-mer oligonucleotides and their phosphorothioate analogues. With the model phosphotriester 37, the mechanism of deprotection was studied and revealed, in the case of group H, a pH-independent formation of the 2-oxazolinium cation 47. Under aqueous conditions, 47 gave 54, which in turn was converted in the presence of ammonia to a number of identified products. It is important to note that none of the products formed was reactive toward the oligonucleotide backbone or nucleic bases. Thus, a general strategy for protection of internucleosidic phosphodiester groups is described, which may also find application in synthetic organic chemistry of phosphorus(III) and (V).     

Trityloxyethylamino group for the protection of phosphoryl group in oligonucleotide synthesis

Trityloxyethylamino group was used for the protection of 5′-phosphoryl group of deoxyribonucleoside. This group is not only protecting group of phosphate also the intermediate for the synthesis of d-ppA and d-pppA.     

Synthesis of onio-, dionio-, and trionio-substituted phosphines; the nucleophilic behavior of DBN and DBU toward main group electrophiles

1,5-Diazabicyclo[4.3.0]non-5-ene (DBN) and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) react with chloro- and dichloro-phosphines leading to onio- and dionio-substituted phosphines. Similarly, onio-substituted silicon and tin derivatives are prepared; they are used as onio-substituent transfer reagents in the synthesis of a trionio-substituted phosphine.     

Unique cascade ring-opening/cyclization reaction of azlactones and DBU or DBN: Synthesis of new pyrrolam A analogues

1-Azabicyclo[3.3.0]oct-3-en-2-one derivatives were synthesized efficiently through the facile cascade reaction of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) or 1,5-diazabicyclo[4.3.0]non-5-ene (DBN) with arylidene azlactones. This research provides a straightforward procedure for the synthesis of a novel class of multicyclic semi-alkaloids which shows good antimicrobial activity. Under catalyst-free, mild, and solventless condition, a wide range of fused tricyclic derivatives was obtained in high yields.     

The use of organophotoacids for deprotection reactions in organic synthesis

o-Hydroxymethylphenol was found to be an effective and environmentally benign organophotoacid. An increased acidity in the excited state, induced by photoirradiation, was sufficient for the deprotection of several protecting groups which are widely used in organic synthesis.     

Phthaloyl group : a new amino protecting group of deoxyadenosine in oligonucleotide synthesis

A phthaloyl group has been introduced into the N⁶-amino group of deoxyadenosine $\text{via}$ silylation followed by acylation. The phthaloyl group resulted in remarkable retarding effects on depurination, while it could be removed under milder conditions than the benzoyl group. Thus, a tetradeoxyadenylate has been successfully synthesized in high yield.     

The use of penicillin acylase for selective N-terminal deprotection in peptide synthesis

Penicillin acylase from E. coli (EC 3.5.1.11) accepts a broad range of N-phenylacetyl-dipeptide esters as substrates. The enzyme hydrolyses the N-terminal protecting group selectively at room temp. and pH=8.1 without affecting the peptide- or the ester-bonds. Alternatively methyl-, benzyl-, tert-butyl and allyl esters can be cleaved chemically leaving the phenylacetamido moiety intact.     

2-diphenylmethylsilylethyl group as a new protecting group of internucleotidic phosphates in oligonucleotide synthesis

Internucleotidic phosphates were protected by 2-diphenylmethylsilylethyl which was selectively removed by treatment with tetrabutylammonium fluoride.     

碳苷研究 V: 用Grignard试剂合成取代苯酚中酚羟基的保护及脱保护

本文报道了一些取代苯酚的合成, 并探讨了用Grignard试剂合成取代苯酚中酚羟基的保护及脱保护的问题. 利用苄基和甲基作为酚羟基的保护基, 对文献报道的切断醚键脱保护方法进行了评价. 找到了两种新体系能在更温和条件下切断醚键的方法, 指出了它们的适用条件. 实验结果符合硬软酸碱理论.     

1-Isopropylallyloxycarbonyl (IPAoc) as a protective group of amines and its deprotection catalysed by palladium-phosphine complex

As a new protective group of amines, 1-isopropylallyloxycarbonyl (IPAoc) group was developed. IPAoc group can be removed by treatment with a palladium-phosphine catalyst forming carbon dioxide and 4-methyl-1,3-pentadiene by the decarboxylation and β-hydrogen elimination of (π-1-isopropylallyl)-palladium intermediate under neutral conditions. The present protection-deprotection was applied to a one-pot peptide synthesis.     

New chiral benzothiazine ligand and its use in the synthesis of a chiral receptor

The development of chiral ligands to direct the course and stereoselectivity of many catalytic asymmetric reactions is an important area of interest for many research groups. As part of a program examining the chemistry of 2,1-benzothiazines, we have prepared a new chiral benzothiazine ligand. This ligand can be made in as few as three steps from commercially available starting materials. Presented herein is the synthesis of the ligand along with the synthesis of a chiral molecular receptor that potentially presages a new class of chiral molecular tweezers.     

A new, lipophilic p-alkoxybenzyl ether protecting group and its use in the synthesis of a disaccharide

[formula: see text] In contrast to major advances in the chemical synthesis of oligosaccharides, the methods of purification of the intermediates are essentially the same as they were decades ago. Here, the synthesis of p-(dodecyloxy)benzyl chloride is described and it is demonstrated that the new p-(dodecyloxy)benzyl ether protecting group can render a protected disaccharide sufficiently lipophilic for selective adsorption on C18 silica, thus sidestepping the expensive silica gel chromatography traditionally used for the isolation of protected oligosaccharides.     

A mild deprotection strategy for allyl-protecting groups and its implications in sequence specific dendrimer synthesis

A mild deprotection strategy for allyl ethers under basic conditions in the presence of a palladium catalyst is described. Under these conditions, aryl allyl ethers can be cleaved selectively in the presence of alkyl allyl ethers. These conditions are also effective in the deprotection of allyloxycarbonyl groups. The utility of the current methodology in sequence specific dendrimer synthesis is demonstrated.     

The effect of phosphate group replacement by sulfate groups on the phase formation in the synthesis of hydroxyapatite

Sulfate-substituted hydroxyapatite materials with a degree of substitution of up to 20 mol % (Ca₁₀(PO₄)_{(6 – 0.06x)}(SO₄)_0.09x (OH)₂, x = 0, 0.1, 0.5, 1, 5, 10, and 20) were synthesized. For substitutions of 0, 0.1, 0.5, and 1 mol %, a single-phase material with the apatite structure is formed. On further increase in the concentration of SO₄ ^2? groups up to 20 mol %, a second phase, CaSO₄, is formed; the amount of this phase increases for higher degrees of substitution. The unit cell parameters of hydroxyapatite-based materials change slightly upon the replacement of phosphate groups by sulfate groups: the parameter a tends to increase, while c tends to decrease. The introduction of sulfate groups results in decreasing particle size.     

Novel synthesis of polyimide with pendant 1-phenylethyl ester using DBU and its thermal acid-catalyzed deesterification

A model reaction of o-(N-phenylcarbamoyl)benzoic acid (amic acid) with threefold amounts of 1-phenylethyl bromide (PEB) and 1,8-diazabicyclo-[5,4,0]-7-undecene (DBU) was carried out in NMP. The reaction gave N-[m-(1-phenylethoxycarbonyl)phenyl]phthalimide in almost quantitative yield at room temperature for 2 h. Polyimide containing pendant 1-phenylethyl ester (P-1a) was also prepared from polyamic acid with PEB using DBU according to the model reaction. The obtained polymer was exactly consistent with P-1a synthesized stepwise from the esterification of the corresponding polyimide containing pendant carboxylic acid with PEB. Therefore, the reaction of polyamic acid bearing pendant carboxylic acid with alkyl bromide proceeded quantitatively to give polyimide containing pendant ester in the presence of DBU. Also, this method was applied to the synthesis of polyimide containing 1-phenylethyl ether. However, the polyimide with quantitative etherification was not synthesized. The acid-catalyzed deesterification of P-1a film was carried out by heating the irradiated polymer film containing 10 wt % of p-nitrobenzyl 9,10-diethoxyanthracene-2-sulfonate, which produced sulfonic acid by irradiation, at various temperatures. Although thermal deesterification of P-1a started at 220°C without any acid catalyst, the deesterification occurred when the irradiated film was heated at the lower temperature. The degree of esterification can be determined from the disappearance of absorption at 700 cm⁻¹. The deesterification obeyed first-order kinetics. © 1996 John Wiley & Sons, Inc.     

5-Chloro-8-quinolyl group as high efficient phosphate protecting group for the synthesis of oligoribonucleotides

5-Chloro-8-quinolyl group is found to be very suitable for the protecting group on phosphates in the internucleotidic bonds. The oligoribonucleotides were obtained in good yields by a simple procedure using this phosphate protecting group.