A convenient route to N-[2-(Fmoc)aminoethyl]glycine esters and PNA oligomerization using a Bis-N-Boc nucleobase protecting group strategy

A simple and practical synthesis of the benzyl, allyl, and 4-nitrobenzyl esters of N-[2-(Fmoc)aminoethyl]glycine is described starting from the known N-(2-aminoethyl)glycine. These esters are stored as stable hydrochloride salts and were used in the synthesis of peptide nucleic acid monomers possessing bis-N-Boc-protected nucleobase moieties on the exocyclic amino groups of ethyl cytosin-1-ylacetate, ethyl adenin-9-ylacetate and ethyl (O(6)-benzylguanin-9-yl)acetate. Upon ester hydrolysis, the corresponding nucleobase acetic acids were coupled to N-[2-(Fmoc)aminoethyl]glycine benzyl ester or to N-[2-(Fmoc)aminoethyl]glycine allyl ester in order to retain the O(6) benzyl ether protecting group of guanine. The Fmoc/bis-N-Boc-protected monomers were successfully used in the Fmoc-mediated solid-phase peptide synthesis of mixed sequence 10-mer PNA oligomers and are shown to be a viable alternative to the currently most widely used Fmoc/Bhoc-protected peptide nucleic acid monomers.     

The 3-(N-tert-butylcarboxamido)-1-propyl group as an attractive phosphate/thiophosphate protecting group for solid-phase oligodeoxyribonucleotide synthesis

Among the various phosphate/thiophosphate protecting groups suitable for solid-phase oligonucleotide synthesis, the 3-(N-tert-butylcarboxamido)-1-propyl group is one of the most convenient, as it can be readily removed, as needed, under thermolytic conditions at neutral pH. The deprotection reaction proceeds rapidly (t(1/2) approximately 100 s) through an intramolecular cyclodeesterification reaction involving the amide function and the release of the phosphate/thiophosphate group as a 2-(tert-butylimino)tetrahydrofuran salt. Incorporation of the 3-(N-tert-butylcarboxamido)-1-propyl group into the deoxyribonucleoside phosphoramidites 1a-d is achieved using inexpensive raw materials. The coupling efficiency of 1a-d in the solid-phase synthesis of d(ATCCGTAGCTAAGGTCATGC) and its phosphorothioate analogue is comparable to that of commercial 2-cyanoethyl deoxyribonucleoside phosphoramidites. These oligonucleotides were phosphate/thiophosphate-deprotected within 30 min upon heating at 90 degrees C in Phosphate-Buffered Saline (PBS buffer, pH 7.2). Since no detectable nucleobase modification or significant phosphorothioate desulfurization occurs, the 3-(N-tert-butylcarboxamido)-1-propyl group represents an attractive alternative to the 2-cyanoethyl group toward the large-scale preparation of therapeutic oligonucleotides.     

Thermolytic properties of 3-(2-pyridyl)-1-propyl and 2-[N-methyl-N-(2-pyridyl)]aminoethyl phosphate/thiophosphate protecting groups in solid-phase synthesis of oligodeoxyribonucleotides

Thermolytic groups may serve as alternatives to the conventional 2-cyanoethyl group for phosphate/thiophosphate protection in solid-phase oligonucleotide synthesis to prevent DNA alkylation by acrylonitrile generated under the basic conditions used for oligonucleotide deprotection. Additionally, thermolytic groups are attractive in the context of engineering a "heat-driven" process for the synthesis of oligonucleotides on diagnostic microarrays. In these regards, the potential application of pyridine derivatives as thermolytic phosphate/thiophosphate protecting groups has been investigated. Specifically, 2-pyridinepropanol and 2-[N-methyl-N-(2-pyridyl)]aminoethanol were incorporated into deoxyribonucleoside phosphoramidites 7a-d and 9, which were found as efficient as 2-cyanoethyl deoxyribonucleoside phosphoramidites in solid-phase oligonucleotide synthesis. Whereas the removal of 3-(2-pyridyl)-1-propyl phosphate/thiophosphate protecting groups from oligonucleotides is effected within 30 min upon heating at 55 degrees C in concentrated NH4OH or in an aqueous buffer at pH 7.0, cleavage of 2-[N-methyl-N-(2-pyridyl)]aminoethyl groups occurs spontaneously when their phosphate or phosphorothioate esters are formed during oligonucleotide synthesis. The deprotection of these groups follows a cyclodeesterification process generating the bicyclic salts 13 and 14 as side products. These salts do not alkylate or otherwise modify any DNA nucleobases and do not desulfurize a phosphorothioate diester model under conditions mimicking large-scale oligonucleotide deprotection.     

A monomolecularly imprinted dendrimer (MID) capable of selective binding with a tris(2-aminoethyl)amine guest through multiple functional group interactions

A molecularly imprinted dendrimer (MID) with a colorimetric reporter group exhibits three-point binding of tris(aminoethyl)amine in THF with a K(assoc)= 3.3 x 10(6) M(-1).     

SYNTHESIS OF 2-γ-N-(AMINOETHYL)AMINOPROPYL-2-METHYL-6-ALKYL(ARYL,H)-1,3-DIOXA-6-AZA-2-SILACYCLOOCTANES

Some new 2-γ-N-(aminoethyl)aminopropyl-2-methyl-1,3-dioxa-6-aza-2-silacyclooctane and 2-γ-N-(aminoethyl)aminopropyl-2-methyl-6-alkyl(aryl)-1,3-dioxa-6-aza-2-silacyclooctanes have been synthesized from γ-chloropropyldimethoxymethyl silane by ethylenediamine substitution and diethanolamine or N-alkyl(aryl)diethanolamines substitution. The resulting silocanes have been characterized by elemental analyses, IR, and ¹H NMR.     

A Mass Spectrometric Study of γ－Amino－group－containing Propyltriethoxysilanes

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Development of a novel fluorescent tag O-2-[aminoethyl]fluorescein for the electrophoretic separation of oligosaccharides

This study describes the development of a novel fluorescent tag, O-2-[aminoethyl]fluorescein, for the separation of sugars by capillary electrophoresis with fluorescence detection using an argon ion laser. The tag was synthesised using three consecutive steps namely: esterification, alkylation and hydrolysis, specifically designed to offer a flexible way in which to make an assortment of fluorescent tags from cheap and readily available starting reagents (typically less than $1 per g of fluorescent tag). Via this flexible synthetic pathway, O-2-[aminoethyl]fluorescein was designed and synthesised with a spacer group to lower steric effects between the fluorescein backbone and the reducing end of the carbohydrate which were anticipated to improve the reactivity of the tag. The newly synthesised tag, O-2-[aminoethyl]fluorescein was evaluated against structurally similar commercial fluorescent motifs namely fluorescent 5-aminomethylfluorescein and non-fluorescent 5-aminofluorescein. Kinetic studies indicated that O-2-[aminoethyl]fluorescein showed similar labeling efficiencies as 5-aminomethylfluorescein, but were achieved in only 30 min, supporting the notion of improved reactivity of the spacer group. The sensitivity of O-2-[aminoethyl]fluorescein was evaluated using maltoheptaose with a detection limit of 1 nM obtained, which was slightly higher than that of 0.3 nM obtained with 5-aminomethylfluorescein, and was due to its lower quantum yield (0.24) when conjugated to the sugar. The separation performance of the tag was also benchmarked with the two commercial reagents using a range of corn syrup oligosaccharides, from 4 to 10 glucose units, typically found in rice starch. Separations were performed using an electrolyte containing 100 mM boric acid, tris at pH 8.65 as background electrolyte, 30 kV applied voltage, 50 μm I.D. × 40 cm (30 cm effective length) capillary. The novel tag showed better resolution of small oligosaccharides, G3 and G4, than the other two reagents, but slightly worse resolution for the longer oligosaccharides, most likely due to the monovalent charge state of the O-2-[aminoethyl]fluorescein compared to the divalent charge of the other two tags.     

Synthesis, X-ray characterization, NMR and ab initio molecular-orbital studies of some cadmium(II) macrocyclic Schiff-base complexes with two 2-aminoethyl pendant arms

Three new pendant arm Schiff-base macrocyclic complexes, [CdLⁿ]²⁺ (n = 5, 6, 7), have been prepared via cyclocondensation of 2,6-diacetylpyridine with three different branched hexaamines in the presence of Cd(II). The ligands are 15-, 16- and 17-membered pentaaza macrocycles having two 2-aminoethyl pendant arms [L⁵ = 2,13-dimethyl-6,9-bis(aminoethyl)-3,6,9,12,18-pentaazabicyclo[12.3.1]octadeca-1(18),2,12,14,16-pentaene, L⁶ = 2,14-dimethyl-6,10-bis(aminoethyl)-3,6,10,13,19-pentaazabicyclo[13.3.1]nonadeca-1(19),2,13,15,17-pentaene and L⁷ = 2,15-dimethyl-6,11-bis(aminoethyl)-3,6,11,14,20-pentaazabicyclo[14.3.1]eicosa-1(20),2,14,16,18-pentaene]. All complexes were investigated by IR, ¹H and ¹³C NMR, COSY(H,H) and HETCOR(H,C) spectroscopy and X-ray diffraction. In the solid state structure of each complex the Cd(II) ion is situated centrally within an approximately planar pentaaza macrocyclic ring, binding to the five nitrogen atoms, and also to the two pendant amines which are located on opposite sides of the macrocyclic plane. ab initio HF-MO calculations using a standard 3-21G* basis set have been used to verify that these similar basic structures correspond to energy minima in the gas phase.     

Thermolytic 4-methylthio-1-butyl group for phosphate/thiophosphate protection in solid-phase synthesis of DNA oligonucleotides

The thermolabile 4-methylthio-1-butyl phosphate/thiophosphate protecting group for DNA oligonucleotides has been investigated for its potential application to a "heat-driven" process for either oligonucleotide synthesis on diagnostic microarrays or, oppositely, to the large-scale preparation of therapeutic oligonucleotides. The preparation of phosphoramidites 10a-d is straightforward, and the incorporation of these amidites into oligonucleotides via solid-phase techniques proceeds as efficiently as that achieved with 2-cyanoethyl deoxyribonucleoside phosphoramidites. The versatility of the 4-methylthio-1-butyl phosphate/thiophosphate protecting group is exemplified by its facile removal from oligonucleotides upon heating for 30 min at 55 degrees C in an aqueous buffer under neutral conditions or within 2 h at 55 degrees C in concentrated NH(4)OH. The deprotection reaction occurs through an intramolecular cyclodeesterification mechanism leading to the formation of sulfonium salt 18. When mixed with deoxyribonucleosides and N-protected 2'-deoxyribonucleosides or with a model phosphorothioate diester under conditions approximating those of large-scale (>50 mmol) oligonucleotide deprotection reactions, the salt 18 did not significantly alter DNA nucleobases or desulfurize the phosphorothioate diester model to an appreciable extent.     

Formation of unexpected products in the attempted aziridination of styrene with trifluoromethanesulfonyl nitrene

The reaction of styrene with trifluoromethanesulfonyl nitrene generated from trifluoromethanesulfonamide in the system (t-BuOCl+NaI) results in the formation of trifluoro-N-[2-phenyl-2-(trifluoromethylsulfonyl)aminoethyl]methanesulfonamide, 1-phenyl-2-iodo-ethanol, and 2,5-diphenyl-1,4-bis(trifluoromethylsulfonyl)piperazine rather than the expected product of aziridination, 2-phenyl-1-(trifluoromethylsulfonyl)aziridine. The mechanism of the reaction is discussed.     

Crystal structure of 1-[N-2-aminoethyl)-aminopropyl]silatrane

The crystal structure of 1-[N-(2-aminoethyl)aminopropyl]silatrane has been determined by x-ray diffraction at room temperature. The Si←N bond distance (2.165(2) Å) is in the range observed for other 1-X-propylsilatranes (X = CN, OH, SH, Cl and SCN). The structure is partially disordered: the silatrane moiety displays a disorder that is typical for silatranes and the aminoethyl group terminating the planar chain linked to silicon is rotationally disordered.     

The synthesis of a conformationally restricted analog of the anti-migraine drug sumatriptan

The synthesis of 5-N-Methylaminosulfonylmethyl-3-(N-methylpyrrolidin-2-ylmethyl)indole (1), a conformationally restricted analog of the anti-migraine drug, sumatriptan, is described. To incorporate our novel stereogenic replacement for the aminoethyl sidechain in sumatriptan, a convergent synthesis of the 3,5-disubstituted indole (1) was employed which utilized an intramolecular Heck reaction as the cornerstone reaction.     

Magnesium aminoethyl phosphonate (Mg(AEP)(H2O)): an inorganic-organic hybrid nanomaterial with high CO2:N2 sorption selectivity

The inorganic-organic hybrid magnesium aminoethyl phosphonate (Mg(AEP)(H(2)O), particle diameter: 20 nm; specific surface area: 322(10) m(2) g(-1); pore volume: 0.9(1) cm(3) g(-1)) shows reversible CO(2) sorption (152(5) mg g(-1)) at high pressure (≤110 bar). In contrast, N(2) uptake remains below 1.0(1) mg g(-1). Based on this selectivity (～100%) Mg(AEP)(H(2)O) expands the range of materials available for CO(2) capture.     

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).     

Compounds having thiourea moiety as derivatization reagents in liquid chromatography/electrospray ionization–tandem mass spectrometry (LC/ESI‐MS/MS): synthesis of derivatization reagents for carboxylic acids

The derivatization reagents for carboxylic acids, N‐(Pyridin‐3‐yl)hydrazinecarbothioamide, N‐[4‐(dimethylamino)phenyl]hydrazinecarbothioamide, 1‐(2‐aminoethyl)‐3‐(pyridin‐3‐yl)thiourea, 1‐(2‐aminoethyl)‐3‐[4‐(dimethylamino)phenyl]thiourea and 4‐(2‐aminoethyl)‐N‐phenylpiperazine‐1‐carbothioamide were synthesized. These reagents reacted with carboxylic acids at 60°C for 45 min in the presence of the condensation reagents. The generated derivatives were favorably separated on the reversed‐phase column and sensitively detected by electrospray ionization tandem mass spectrometry. These reagents enhanced the electrospray ionization response of the analyte and generated a particular product ion efficiently by collision‐induced dissociation, and thus they were suitable for MS/MS detection. Copyright © 2010 John Wiley & Sons, Ltd.     

pH-Independent triplex formation: hairpin DNA containing isoguanine or 9-deaza-9-propynylguanine in place of protonated cytosine

Triplex-forming oligonucleotides (TFOs) containing 2'-deoxyisoguanosine (2), 7-bromo-7-deaza-2'-deoxyisoguanosine (2) as well as the propynylated 9-deazaguanine N7-(2'-deoxyribonucleoside) were prepared. For this the phosphoramidites 9a, b of the nucleoside 1 and, the phosphoramidites 19, 20 of compound 3b were synthesized. They were employed in solid-phase oligonucleotide synthesis to yield the protected 31-mer oligonucleotides. The deblocking of the allyl-protected oligonucleotides containing 1 was carried out by Pd(0)[PPh3]4-PPh3 followed by 25% aq. NH3. Formation of the 31-mer single-stranded intramolecular triplexes was studied by UV-melting curve analysis. In the single-stranded 31-mer oligonucleotides the protonated dC in the dCH(+)-dG-dC base triad was replaced by 2'-deoxyisoguanosine (1), 7-bromo-7-deaza-2'-deoxyisoguanosine (2) and, 9-deaza-9-propynylguanine N7-(2'-deoxyribonucleoside) (3b). The replacement of protonated dC by compounds 1 and 3b resulted in intramolecular triplexes which are formed pH-independently and are stable under neutral conditions. These triplexes contain "purine" nucleosides in the third pyrimidine rich strand of the oligonucleotide hairpin.     

Synthesis of Purine and 2-Aminopurine Conjugates with N-(4-Aminobenzoyl)-(S)-glutamic Acid

Russian Journal of Organic Chemistry - Purine and 2-aminopurine conjugates with N-(4-aminobenzoyl)-(S)-glutamic acid connected to C6 of the purine system either directly or through an aminoethyl...     

Synthesis and application of new organometallic compounds of silicon and germanium in chemical radioprotection

Several organosilicon and organogermanium compounds possessing radioprotective activity have been synthesized. In this paper, we describe the preparation and study of the pharmacological properties of new organometallic compounds such as metallathiazolidines and metalladithioacetals derived from 1‐[N‐(2‐mercaptoethyl)‐­2‐aminoethyl] ‐ 2 ‐ (1‐naphthylmethyl) ‐2‐ imidazoline and 1‐[N‐(2‐mercaptopropyl)‐2‐aminoethyl]‐2‐(1‐naphthylmethyl)‐2‐imidazoline. We have noted a decrease in the toxicity and a rather important increase in the radioprotective activity of these new organometallic derivatives in comparison with the starting organic compounds. Copyright © 1999 John Wiley & Sons, Ltd.     

硫堇与寡核苷酸结合序列选择性的光谱研究

用UV-Vis吸收光谱、荧光光谱、圆二色谱以及核磁共振光谱等手段研究了硫堇(TH)与两个不同序列寡核苷酸的作用。TH与寡核苷酸作用后的吸收光谱和荧光光谱产生了明显的减色红移和荧光猝灭效应。分别计算了TH与[oligo d(GC)]2和[oligo d(AT)]2作用的荧光猝灭常数和结合常数,结果表明TH与GC序列的结合能力比与AT序列更强。通过TH与[oligo d(GC)]2作用后双螺旋链构象变化以及TH质子的1HNMR谱峰明显变宽,进一步说明TH与寡核苷酸结合的序列选择性。     

Synthesis of oligodeoxyribonucleotides containing a 3'-terminal phosphate group

Two methods for synthesizing oligodeoxyribonucleotides containing 3'-terminal phosphosphate groups have been developed. The first consists in the synthesis and the introduction into the oligonucleotides of a block containing a 3'-terminal bis(2-cyanoethyl) phosphate group and the second in the use of the transesterification reaction of oligonucleotides with 2-cyanoethanol in the presence of cesium fluoride. Both methods permit the fairly effective synthesis of oligodeoxyribonucleotide 3'-phosphates.M. V. Lomonosov Moscow State University. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 637–641, September–October, 1984.