A New Protecting Group Strategy for Amino Groups in Oligonucleotide Chemistry: CEOC Group

Abstract

A new protecting group, 2-cyanoethyloxycarbonyl, or CEOC, has been developed for amino groups and utilized in synthesizing modified oligonucleotides. (CEOC)-oxy-succinimide reagent has been synthesized to introduce this protecting group. The protecting group is removed by standard oligonucleotide deprotection protocols. Using this approach, oligonucleotides have been synthesized with various types of alkylamine substituents.     

Base Labile Protecting Groups for Hydroxyl Functions in Ribonucleosides and Deoxyribonucleosides

Abstract

The use of the base labile 2-(p-nitrophenyl)-ethoxycarbonyl (NPEOC), 2-(2,4-dinitrophenyl)-ethoxycarbonyl (DNPEOC) and 2-cyanoethoxy-carbonyl (CEOC) group for hydroxyl protection of the sugar moiety in ribo-nucleosides and deoxyribonucleosides are described and discussed.     

Lithiation-Stannylation Chemistry of Nucleosides

Abstract

Two examples of anionic stannyl migration practically useful for nucleoside synthesis are presented. One involves the migration from the 8- to 2-position of 6-chloropurine derivatives, which provided a new entry to 2-substituted purine nucleosides. The other is that from the 6- to 2′-position of 1′,2′-unsaturated uridine. The latter enabled the preparation of a hitheroto unknown class of nucleoside analogues, 2′-substituted 1′,2′-unsaturated uridines.     

Chemistry and Dynamics of Interaction of Nucleosides with Pentafluoropyridine

Interaction of pentafluoropyridine with hydroxyl groups of thymidine, uridine, adenosine, and deoxyadenosine at room temperature leads to the formation of aryl ethers of nucleosides with a high yield. Under severe conditions, one more tetrafluoropyridine residue is attached to pyrimidine fragments of T and U, while purine heterocycle in A remains intact. Nucleoside derivatives are formed with a quantitative yield and can be used in situ as intermediates for, as an example, molecular design of arene analogs of nucleic acids. The reaction with thymidine is a successive-parallel process, the limited stage being arylation of the secondary hydroxyl group. The presence of the vicinal hydroxyl group in pentose results in the opposite rate ratio of the formation of primary and secondary tetrafluoropyridyl ethers of adenine and uridine.     

Studies on Nucleotide Chemistry 15. Synthesis of Oligodeoxynucleotides Using Amidine Protected Nucleosides

Abstract

An in situ method is described for synthesizing DNA which incorporates a new series of amidine protected deoxy-nucleosides and bis-dialkylaminophosphines as phosphitylating agents. These procedures were used to synthesize d(GGGAATTCCC) which was digested by EcoRI.     

Mild Detritylation of Nucleic Acid Hydroxyl Groups by Warming Up

It is challenging to effectively deprotect hydroxyl groups of acid-or-base sensitive bio-macromolecules without causing even minor defects and compromising high quality of final products. We report here a mild detritylation strategy in mildly acidic buffers to remove the DMTr protection from the 5′-hydroxyl groups of synthetic nucleic acids. The DMTr-groups can be easily and effectively removed at pH 4.5 or 5.0 with slight warming up (40°C), offering virtually quantitative deprotection. This warming-up strategy is particularly useful for deprotection of the modified nucleic acids that are sensitive to the conventional acid deprotection. As a first step towards our long-term goal of synthesizing defect-free nucleic acids, our novel and simple strategy further increases the quality of synthetic nucleic acids.     

Epimerization of Hydroxyl Group in Lupan Series Triterpenoids

Two methods of obtaining 3-betulinic acid and related compounds from their 3-epimers were studied: the reaction of bimolecular substitution and the stereoselective reduction of 3-ketoderivatives. The substitution of acyloxy by formyloxy group in 3--tosyllupeol or of the belulin hydroxyl by benzoyloxy group resulted only in ^{2, 3}-elimination products, with none of the expected products of bimolecular substitution being found. The catalytic hydrogenation of betulonic acid over Raney nickel resulted only in reduction of the isopropenyl double bond, whereas the use of 5% Ru/C gave a 60 : 40 mixture of epimers of dihydrobetulinic acid. Practically the same mixture of betulinic acid epimers was obtained when reducing betulonic acid with L-Selectride. The cytotoxic activity of 3-betulinic acid increased toward the Bro melanoma cells and decreased toward the MS melanoma cells.     

Photochemistry of the O-Nitrobenzyl Protecting Group in RNA Synthesis

Abstract

UV irradiation of 2′-O (o-nitrobenzyl)adenylyl(3′-5′)uridine in the presence of O₂ yields the corresponding nitrobenzoyl derivative in addition to the expected A-U. A mechanism proposed for this oxidation involves the successive removal of the two benzylic protons with a hydroperoxide as the intermediate between the two steps.     

Effect of Hydroxyl Groups and Rigid Structure in 1,4-Cyclohexanediol on Percutaneous Absorption of Metronidazole

In a previous study, a synergistic retardation effect of 1,4-cyclohexanediol and 1,2-hexanediol on percutaneous absorption and penetration of metronidazole (MTZ) was discovered. A complex formation between 1,4-cyclohexanediol and 1,2-hexanediol was proposed to be responsible for the observed effect. The objective of this study was to investigate the necessity of hydroxyl group and the ring structure in 1,4-cyclohexanediol on percutaneous absorption and penetration of MTZ. Eleven formulations were studied in an in vitro porcine skin model using glass vertical Frans Diffusion Cell. 1,4-Cyclohexanediol was changed into 1,4-cyclohexanedicarboxylic acid, trans (and cis)-1,2-cyclohexanediol and 1,6-hexanediol, respectively, to study if H-bonding or ring structure would influence the retardation effect. MTZ was applied at infinite dose (100 mg), which corresponded to 750 μg of MTZ. Based on modifier ratios (MR) calculated by the flux values, the retardation effect on percutaneous absorption and penetration of MTZ was found in the formulations containing 1,4-cyclohexanedicarboxylic acid or cis-1,2-cyclohexanediol (MR values were 0.47 for which only contains 1,4-cyclohexanedicarboxylic acid, 0.74 for the formulation containing both 1,4-cyclohexanedicarboxylic acid and 1,2-hexanediol, and 0.90 for the formulation containing cis-1,2-cyclohexanediol and 1,2-hexanediol, respectively). The results showed that the hydroxyl group and structure of 1,4-cyclohexanediol played a significant role in retardation effects and provided valuable insight on the mechanisms of retardation effect through structure–activity relationships.     

Protecting Groups Transfer: Unusual Method of Removal of Tr and Tbdms Groups by Transetherification

The triphenylmethyl (Tr) group undergoes a transfer (transetherification or disproportionation) between the molecules of 5′-O-Tr-2′-deoxynucleosides in a process mediated by anhydrous sulfates of Cu⁺², Fe⁺², or Ni⁺² to yield mixtures of 3′,5′-bis-O-Tr and 3′-O-Tr products. If phenylmethanol is present in a reaction medium, detritylation results with concomitant formation of phenylmethyl triphenylmethyl ether. The behavior of t-butyldimethylsilyl (TBDMS) group in 5′-O-TBDMS-2′-deoxynucleosides is exactly the same. Such type of transetherifications was not observed before for the O-Tr and O-TBDMS groups.     

Electrochemical Removal of Allylic Protecting Groups in Nucleotide Synthesis a

Abstract

Electrochemical, palladium(0)-mediated removal of allylic protecting groups of nucleosides and nucleotides is described. This method required no chromatographic treatment for isolation of the products.

     

Protecting Groups as a Factor of Stereocontrol in Glycosylation Reactions

Russian Journal of Bioorganic Chemistry - Synthetic oligosaccharides are objects of interest as model compounds in studies on the biological activity of natural compounds, but also as components...     

Preparation of O-Aminoacyl Sugars as Enzymatically Removable Protections for Hydroxyl Groups in Carbohydrates

To confirm the potential usefulness of amino acid residues as the protecting group of sugar hydroxyls, N-(benzyloxycarbonyl) and N-(t-butoxycarbonyl) amino acids were condensed with methyl 4,6-O-benzylidene-α-d-glucopyranoside (1) and methyl 2,3-di-O-methyl-α-d-glucopyranoside (2), and the conditions were studied for the removal of aminoacyl groups from sugar moieties. The aminoacyl groups were easily removed by enzymatic hydrolysis using pronase E, trypsin and chymotrypsin, as well as alkaline treatment as with conventional acyls. We determined the utility of aminoacyl sugars as new protecting groups having some useful characteristics which never exist in normal circumstances.     

Use of Bioreversible Phosphate Protecting Groups for the Intracellular Delivery of Antisense Oligodeoxyribonucleotides

Abstract

The aim of this work was to design phosphorothioate oligonucleotides, the negative charges of which are temporarily masked by a group which facilitates the cellular uptake of these analogues. Then, selective removal of this group by enzymes normally present in the cells will deliver intracellularly the intact charged phosphorothioate oligomers able to hybridize to their complementary RNA targets and to elicit RNase H activity.     

Substrate Specificity of Thymidine Phosphorylase of E. Coli: Role of Hydroxyl Groups

Substrate specificity of E. coli thymidine phosphorylase to pyrimidine nucleoside modified at 5 ′-, 3 ′-, and 2 ′-positions of sugar moiety has been studied. Equilibrium (K_eq) and kinetics constants of phosphorolysis reaction of nucleosides were measured. The most important hydrogen bonds in enzyme-substrate complex have been determined.     

RNA-Synthesis Using the H-Phosphonate Approach and an Improved Protecting Group Strategy

Abstract

An improved version of the H-phosphonate approach to RNA-synthesis is presented and the studies that led to alterations in the protecting group strategy are discussed.     

Role of Hydroxyl Group at C-2 on Pyranoid Moiety in Interaction with Pea Phytohemagglutinin

A simplified procedure for the purification of pea phytohemagglutinin, which involves fractionation with ammonium sulfate and column chromatography to give two active components, has been developed. The main component of the purified hemagglutinin gave one single band with disc electrophoresis. Molecular weight of the hemagglutinin was calculated as 61,000 (Vρ = 0.75). Using this hemagglutinin, the experiment was carried out to aim from the viewpoint of conformational feature of sugars at an explanation of the role of a hydroxyl group on gluco- or mannopyranoid moiety of the sugars capable of interaction with the hemagglutinin. A possible concern of orientation of hydroxyl group at the C–2 position on pyranoid moiety of sugars is proposed to interpret the hemagglutination with the phytohemagglutinin from the results of inhibition tests and from the consideration on conformational feature of sugars reported previously.     

Arenesulfonylethoxycarbonyl- a Set of Amino Protecting Groups for DNA and RNA Synthesis

Abstract

Phenyl-, 4-chlorophenyl- and 4-nitrophenylsufonylethoxycarbonyl groups have been reported for the first time as the exocyclic amino protecting groups in nucleoside chemistry. They are all stable under the standard conditions of manipulations in phosphotriester and phosphiteamidite chemistry, they are removable both under the alkaline hydrolytic conditions and also under the influence of non-nucleophilic tertiary bases. N³-Phenyl- and 4-toluenesulfonylethoxycarbonyl derivatives of uridine have been also prepared and characterized by ¹⁵N-NMR spectroscopy, their stabilities under different conditions have been tested.