Progress towards a submonomer synthesis of peptide nucleic acid

We report recent developments in the optimization of a submonomer synthesis of peptide nucleic acid based on the Fukuyama-Mitsunobu reaction. The key steps in the submonomer synthesis are the installation of an appropriately protected 2-aminoethyl group on the alpha-nitrogen of an amino acid and its subsequent acylation with a protected nucleobase derivative. The aggressive alkylation conditions require a scheme of maximal protection for the nucleobases and that is proposed herein for the pyrimidines.     

Liquid Phase Synthesis of Peptide Nucleic Acid (or Polyamide Nucleic Acid) Dimers

Abstract

The liquid phase synthesis of “polyamide nucleic acid” (PNA) dimers containing the purine nucleic acid bases adenine and guanine has been achieved in good yields. This strategy was elaborated in order to circumvent difficult direct coupling of protected PNA monomers. This method can be applied to the liquid phase synthesis of short protected polyPNAs fragments, which can then selectively be deprotected.     

A Short,Efficient Synthesis of 2′-Deoxypseudoisocytidine Based on Heck-Chemistry

Abstract

A novel synthesis of 2′-deoxypseudoisocytidine as well as of its phosphoramidite building block for oligonucleotide synthesis is presented. The synthesis is based on Heck-coupling between N-protected pseudoisocytosine and a silyl protected furanoid glycal. With this procedure the corresponding phosphoramidite building block is obtained in 5 steps and an overall yield of 28%.     

Efficient Synthesis of 2′-Deoxynucleoside 3′-C-Phosphonates: Reactivity of Geminal Hydroxyphosphonate Moiety

Abstract

In this report we present a novel, simple way for the synthesis of 3′-C-phosphonate derivatives of all four basic 2′-deoxynucleosides in both fully protected and deprotected forms. The reactivity of the geminal hydroxy phosphonate moiety located at the 3′-carbon atom of the nucleoside was studied with respect to the use of this type of nucleoside phosphonic acid for the preparation of short oligonucleotides, namely, dinucleoside monophosphate analogues.     

The RNA World: Functional Diversity in a Nucleoside by Carboxyamidation of Uridine

Abstract

A facile method for the 5-carboxyamidation of protected uridines is described allowing synthesis of an array of uridines with diverse functionality.     

解淀粉芽胞杆菌HZ-12中ysnE参与吲哚-3-乙酸合成的代谢途径研究

【目的】吲哚-3-乙酸是调控植物生长发育和生理活动的重要激素,吲哚-3-乙酸N-乙酰转移酶YsnE在吲哚-3-乙酸合成中发挥重要作用,本研究拟解析解淀粉芽胞杆菌中YsnE参与吲哚-3-乙酸合成的代谢途径。【方法】通过基因ysnE缺失和强化表达,分析ysnE对吲哚-3-乙酸合成影响,结合吲哚-3-乙酸合成中间物(吲哚丙酮酸、吲哚乙酰胺、色胺和吲哚乙腈)添加和体外酶转化实验,解析ysnE参与吲哚-3-乙酸合成的代谢途径。【结果】明确了YsnE在解淀粉芽胞杆菌HZ-12吲哚-3-乙酸合成中发挥重要作用。发现ysnE缺失菌株中的吲哚丙酮酸、吲哚乙酰胺和吲哚乙腈利用显著降低,揭示了YsnE主要发挥吲哚丙酮酸脱羧酶YclB和吲哚乙酰胺水解酶/腈水解酶/腈水合酶YhcX的功能,并通过参与吲哚丙酮酸、吲哚乙酰胺和吲哚乙腈途径来影响吲哚-3-乙酸合成。【结论】初步揭示了YsnE通过影响吲哚丙酮酸、吲哚乙酰胺和吲哚乙腈途径参与吲哚-3-乙酸合成的代谢机理,为吲哚-3-乙酸合成途径解析和代谢工程育种构建吲哚-3-乙酸高产菌株奠定了基础。     

A Convenient High Yield Synthesis of N4-Isobutyryl-2′-O-Methylcytidine and Its Monomer Units For Incorporation into Oligonucleotides

Abstract

We designed an efficient three step procedure for the synthesis of N⁴-isobutyryl-2′-O-methylcytidine. This protected nucleoside was then used to prepare a methylphosphonamidite monomer for incorporation into oligonucleotides. Transamination at the C⁴ position of cytidine using ethylenediamine, which has been reported for the N⁴-benzoyl cytidine, was not observed with N⁴-isobutyryl protected 2′-O-methylcytidine.     

Base-Labile Group Protected Biotinphosphoramidite Reagents for Solid Phase Biotinylation of Oligonucleotides

Abstract

A general and rapid method is described for the synthesis of N¹ -base labile group protected biotinphosphoramidite reagents, useful for the synthesis of biotinylated oligonucleotides in automated DNA synthesizer.     

Synthesis of Protected 3′,5′-Di-2′-Deoxythymidine-(α-hydroxy-2-nitrobenzyl)-phosphonate Diesters as Dimer Building Blocks for Oligonucleotides

Abstract

The synthesis of 3′-succinyl-CPG bound 3′,5′-di-2′-deoxythymidyl-(α-hydroxy-2-nitrobenzyl)-phosphonate diester 1 and the 3′-phosphoamidite derivative 2 is descibed. The hydroxyl-groups of the backbone modification were protected with trialkylsilyl groups: TES and TBS. Compounds 1, 2 are suitable blocks for oligonucleotide synthesis.     

Synthesis of Polyamide Nucleic Acids (Pnas), Pna /Dna-Chimeras and Phosphonic Ester Nucleic Acids (Phonas)

Abstract

The synthesis of polyamide nucleic acids (PNAs) and derivatives thereof by different synthetic routes is described. The first strategy makes use of 9-Fluorenylmethoxycarbonyl (Fmoc)/monomethoxytrityl (Mmt) protected building blocks, whereas the second approach involves the use of Mmt/acyl protected monomers, which allows the preparation of PNADNA chimera. Additionally, a block coupling strategy is presented for the synthesis of novel phosphonic ester nucleic acids (PHONAs).     

Synthesis and Properties of O-β-D-Ribofuranosyl-(1″-2′)-Adenosine-5″-O-Phosphate and Its Derivatives

Abstract

The synthesis of O-β-D-ribofuranosyl-(1″-2′)-adenosine-5″-O-phosphate and its suitably protected derivative for oligonucleotide synthesis have been developed.     

Synthesis of Cytidylyl(3′→5′)cytidylyl(3′→5′)-(2′)3′-O-[Lα-alanyl]adenosine

Abstract

A new synthesis of protected C-C-A-[L^α-Ala] 14 is reported using a new set of complementary groups such as 2-phenylsulfonylethoxycarbonyl (PSEC) for the protection of exocyclic amino functions, o-chlorophenyl (o-CIPh) for the internucleotide phosphotriester, 3-methoxy-1,5-dicarbomethoxypentan-3-yl (MDMP) and the 4-monomethoxytrityl (MMTr) for the protection of the ã-amino fuction of the amino acid. 14 could be deprotected in two steps by treatments with 1,1,3,3-tetramethylguanidinium oximate under a dry condition and then by neat trifluoroacetic acid. Treatment with neat trifluoroacetic acid produced a stable salt: [C-C-A-Ala-N^ãH₃+ CF₃CO₂-] and did not promote any internucleotide phosphate migration or degradation of the oligomeric molecule. This salt was considerably more stable than C-C-A-Ala conjugate with a free ã-amino group, and, therefore, it could be easily purified on a silica gel column and was isolated in 82 % yield. This strategy should be useful for the synthesis of longer oligonucleotide-aminoacyl conjugate.     

De novo synthesis of differentially protected l-iduronic acid glycosylating agents

A divergent de novo synthesis of six differentially protected l-iduronic acid thioglycosides from a common advanced precursor is described. The key step of this synthetic sequence is the stereoselective elongation of dithioacetal protected C5-dialdehyde 11 via a highly diastereoselective MgBr₂·OEt₂-mediated cyanation. Orthogonally protected l-iduronic acid building blocks obtained by this synthesis are expected to facilitate access to differentially sulfated heparins for microarray-based structure-activity relationship studies.     

Tetraethylene Glycol-Derived Spacer for Oligonucleotide Synthesis

Abstract

3,6,9-Trioxaundecane-1,11-diisocyanate (6) was synthesised from tetraethylene glycol in 5 steps and 48 % overall yield. Spacer 6 was monofunctionalised with the fully protected adenosyl-3′-O-succinate derivative 7 and linked to aminomethyl polystyrene affording a solid support suitable for oligoribonucleotide synthesis (loading: ～20 μmol/g). The HPLC analysis of a crude oligoribonucleotide synthesis and the yield of the full-length product show that this spacer compares well to hexamethylene diamine.     

Synthesis and DNA Binding Properties of a New Benzo[f]Imidazo[1,5b]-Isoquinoline-Butan-1,2-Diol Derivative

A benzo[f]imidazo[1,5b]-isoquinoline derivative 4 with a 1,2-butandiol linker was prepared by reaction of a trimethylsilylated 5-naphthylidenehydantoin 3 with a 2,3-dideoxy-D-glycero-pentafuranoside 2 in 22% yield. After deprotection, the resulting compound 5 was converted to a DMT protected phosphoramidite building block 7 for standard DNA synthesis. DNA/DNA, DNA/RNA duplexes with 5 inserted as bulges were destabilized, except when the new amidite was used for the synthesis of a zipping duplex.     

Ribo-, Xylo-, and Arabino-Configured Adenine-Based Nucleoside Phosphonates: Synthesis of Monomers for Solid-Phase Oligonucleotide Assembly

Abstract

Adenine-based, regioisomeric nucleoside phosphonates with ribo, xylo and arabino configuration were synthesized in the protected form suitable for the phosphotriester-like, solid-phase synthesis of oligonucleotides. Phosphonate moiety was protected by 4-methoxy-1-oxido-2-picolyl group and the furanose hydroxyl by the dimethoxytrityl group.     

Solution‐phase submonomer diversification of aza‐dipeptide building blocks and their application in aza‐peptide and aza‐DKP synthesis

Aza‐peptides have been used as tools for studying SARs in programs aimed at drug discovery and chemical biology. Protected aza‐dipeptides were synthesized by a solution‐phase submonomer approach featuring alkylation of N‐terminal benzophenone semicarbazone aza‐Gly‐Xaa dipeptides using different alkyl halides in the presence of potassium tert‐butoxide as base. Benzophenone protected aza‐dipeptide tert‐butyl ester 31c was selectively deprotected at the C‐terminal ester or N‐terminal hydrazone to afford, respectively, aza‐dipeptide acid and amine building blocks 36c and 40c, which were introduced into longer aza‐peptides. Alternatively, removal of the benzophenone semicarbazone protection from aza‐dipeptide methyl esters 29a–c led to intramolecular cyclization to produce aza‐DKPs 39a–c. In light of the importance of aza‐peptides and DKPs as therapeutic agents and probes of biological processes, this diversity‐oriented solution‐phase approach may provide useful tools for studying peptide science. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Enantioselective Synthesis of the Carbocyclic Tetrazole C-Ribonucleosides

Abstract

Enantioselective synthesis of the protected derivative of the carbocyclic 5-(β-D-ribofuranosyl)tetrazole 10, a suitable intermediate for further transformation to the carbocyclic formycin analogs, was accomplished via the lactone (+)-4.     

Antioxidant property of an active component purified from the leaves of paraquat-tolerant Rehmannia glutinosa

Abstract

Acteoside extracted from the leaves of Rehmannia glutinosa was examined to determine the mechanism(s) of its antioxidant properties. The deoxyribose assay system showed that acteoside has a high redox potential as electron donor, which generates hydroxyl radicals in an Fe³⁺-dependent manner similar to ascorbic acid. However, the antioxidant properties of acteoside differ from those of ascorbic acid in that the superoxide anion-mediated reduction of nitroblue tetrazolium was actively inhibited by acteoside but not by ascorbic acid. Acteoside protected cells against glucose oxidase-mediated cytotoxicity and apoptosis in a dose-dependent manner. In addition, acteoside had immune stimulating effects, as shown by the acteoside-mediated increase in the level of DNA synthesis, viability, and cytokine secretion in mouse splenocytes. Moreover, acteoside inhibited the gelatinolytic activity of MMP proteins in a dose-dependent manner. Considering these results and the fact that acteoside is a water-soluble natural product, acteoside might have potential as a preventative treatment for oxidative stress-mediated diseases and have possibilities in the cosmetic industry.     

Incorporation of chemoselective functionalities into peptoids via solid-phase submonomer synthesis

A simple route to the introduction of a number of chemoselective functional groups into peptoids (oligo(N-substituted glycines)) by an extension of the standard solid-phase submonomer method is reported. The following groups were introduced: aminooxyacetamide, N-(carbamoylmethyl)acetohydrazide, mercaptoacetamide, 2-pyridinesulfenylmercaptoacetamide, and aldehyde-terminated peptoids. The method uses commercially available reagents, is fully compatible with standard peptoid submonomer synthesis conditions, is easily automated, and generates the desired functionalized peptoid in high yield and purity. Peptoids with suitable pairs of chemoselective ligation groups were joined in high yield.