Automated Chemical Synthesis Research Articles

Toward Automated Enzymatic Synthesis of Oligosaccharides.

Oligosaccharides together with oligonucleotides and oligopeptides comprise the three major classes of natural biopolymers. Automated systems for oligonucleotide and oligopeptide synthesis have significantly advanced developments in biological science by allowing nonspecialists to rapidly and easily access these biopolymers. Researchers have endeavored for decades to develop a comparable general automated system to synthesize oligosaccharides. Such a system would have a revolutionary impact on the understanding of the roles of glycans in biological systems. The main challenge to achieving automated synthesis is the lack of general synthetic methods for routine synthesis of glycans. Currently, the two main methods to access homogeneous glycans and glycoconjugates are chemical synthesis and enzymatic synthesis. Enzymatic glycosylation can proceed stereo- and regiospecifically without protecting group manipulations. Moreover, the reaction conditions of enzyme-catalyzed glycosylations are extremely mild when compared to chemical glycosylations. Over the past few years methodology toward the automated chemical synthesis of oligosaccharides has been developed. Conversely, while automated enzymatic synthesis is conceptually possible, it is not as well developed. The goal of this survey is to provide a foundation on which continued technological advancements can be made to promote the automated enzymatic synthesis of oligosaccharides.

Automated Synthesis of a 96 Product-Sized Library of Triazole Derivatives Using a Solid Phase Supported Copper Catalyst

This article deal with the parallel synthesis of a 96 product-sized library using a polymer-based copper catalyst that we developed which can be easily separated from the products by simple filtration. This gave us the opportunity to use this catalyst in an automated chemical synthesis station (Chemspeed ASW-2000). Studies and results about the preparation of the catalyst, its use in different solvent systems, its recycling capabilities and its scope and limitations in the synthesis of this library will be addressed. The synthesis of the triazole library and the very good results obtained will finally be discussed.

Identification and Quantification of Protecting Groups Remaining in Commercial Oligonucleotide Products Using Monoclonal Antibodies

Quality control is paramount to reproducibly achieving oligonucleotide therapeutics and diagnostics of superior value. However, incomplete deprotection of nucleoside reactive groups after the automated chemical synthesis of oligonucleotides would result in diminished antisense activity and in erroneous array analysis of gene expression. Mass spectrometry and capillary electrophoresis are used to detect aborted sequences of oligonucleotides, but not to identify and quantify incompletely deprotected oligonucleotides. To address this problem, monoclonal antibodies (MAbs), ELISA, and dot-blot assays were developed for the specific identification and quantification of the commonly used nucleic acid base- and sugar-protecting groups: benzoyl, isobutyryl, isopropylphenoxyacetyl, and dimethoxytrityl. Each MAb was capable of reproducibly detecting 8–32 pmol of the respectively protected nucleoside in an intact DNA or RNA sample composed of 320–640 nmol of the deprotected nucleoside. In a direct comparison, HPLC nucleoside composition analysis of enzyme-hydrolyzed DNA was limited to the detection of 2–5 nmol of protected nucleoside. Using the MAb dot-blot assay, 5 of 16 commercial DNA products obtained from eight different companies were found to have 1.0–5.2% of the benzoyl and isopropylphenoxyacetyl protecting groups remaining. Thus, MAbs selectively identify and quantify picomoles of remaining protecting groups on antisense therapeutics and oligonucleotide diagnostics.

Automated solid-phase synthesis of oligosaccharides.

Traditionally, access to structurally defined complex carbohydrates has been very laborious. Although recent advancements in solid-phase synthesis have made the construction of complex oligosaccharides less tedious, a high level of technical expertise is still necessary to obtain the desired structures. We describe the automated chemical synthesis of several oligosaccharides on a solid-phase synthesizer. A branched dodecasaccharide was synthesized through the use of glycosyl phosphate building blocks and an octenediol functionalized resin. The target oligosaccharide was readily obtained after cleavage from the solid support. Access to certain complex oligosaccharides now has become feasible in a fashion much like the construction of oligopeptides and oligonucleotides.

The Chemical Synthesis of Biochemically Active Oligoribonucleotides Using Dimethylaminomethylene Protected Purine H-Phosphonates

Abstract Dimethylaminomethylene was applied as the protecting group for the exocyclic amino groups of adenosine and guanosine in the automated chemical synthesis of oligoribonucleotides on a polymer bound support. The dimethyl-aminomethylene protecting group can be removed at room temperature under conditions where the concomitant loss of the 2′-protection group can be excluded. The transformation of 2′-O-(t-butyldimethylsilyl)-5′-O-(4,4′-dimethoxytrityl) protected nucleosides to 3′-H-phosphonates yields synthons, well suited for the automated chemical synthesis of oligoribonucleotides. Using these H-phosphonate monomers, a coupling time of two minute: is sufficient to obtain average coupling yields of more than 98 %. Synthesized RNA is recognized as a substrate in an enzymatic reaction, forms the expected secondary structures and is suitable for NMR structural investigations.

ChemInform Abstract: Solution and Solid Phase Chemical Synthesis of Arabinonucleotides.

A fast and convenient procedure for the chemical synthesis of arabinonucleotides, which eliminates the multistep protection of the arabinonucleoside building blocks, is described. The results of these studies were successfully applied to the automated chemical synthesis of the hexanucleotide 5′-aUpaApaUpaApaUpaA-3′. Both solution and solid phase phosphite triester procedures are described. Keywords: arabinonucleotides, arabinophosphoramidites, automated chemical synthesis, protected arabinonucleosides.

Solution and solid phase chemical synthesis of arabinonucleotides

A fast and convenient procedure for the chemical synthesis of arabinonucleotides, which eliminates the multistep protection of the arabinonucleoside building blocks, is described. The results of these studies were successfully applied to the automated chemical synthesis of the hexanucleotide 5′-aUpaApaUpaApaUpaA-3′. Both solution and solid phase phosphite triester procedures are described. Keywords: arabinonucleotides, arabinophosphoramidites, automated chemical synthesis, protected arabinonucleosides.

The automated chemical synthesis of long oligoribuncleotides using 2'-O-silylated ribonucleoside 3'-O-phosphoramidites on a controlled-pore glass support: synthesis of a 43-nucleotide sequence similar to the 3'-half molecule of an Escherichia coli formylmethionine tRNA

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe automated chemical synthesis of long oligoribuncleotides using 2'-O-silylated ribonucleoside 3'-O-phosphoramidites on a controlled-pore glass support: synthesis of a 43-nucleotide sequence similar to the 3'-half molecule of an Escherichia coli formylmethionine tRNAN. Usman, K. K. Ogilvie, M. Y. Jiang, and R. J. CedergrenCite this: J. Am. Chem. Soc. 1987, 109, 25, 7845–7854Publication Date (Print):December 1, 1987Publication History Published online1 May 2002Published inissue 1 December 1987https://doi.org/10.1021/ja00259a037RIGHTS & PERMISSIONSArticle Views1553Altmetric-Citations322LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (4 MB) Get e-Alerts Get e-Alerts

Synthetic Gene Fragments in Genetic Engineering—The Renaissance of Chemistry in Molecular Biology

AbstractChemistry and biology paved the way for a new scientific discipline, molecular genetics. The breathtaking progress in deciphering the genetic machinery of a living being within the last 20 years may be attributed mainly to the experimental skill and ingenuity of molecular biologists. Chemists lost interest in the investigation of biological problems. The advances in genetic engineering exemplify the new demands chemists are confronted with in contemporary science. Following a short introduction on the genetics of bacteria, the articles deals with the molecular basis of gene cloning, which is subdivided into in vitro recombination of nucleic acids and in vivo transformation of cells. Next, the criteria for the selection of passenger DNA, vectors, and host cells are discussed. Recombination and transformation are easy‐to‐learn experimental techniques, whereas the search for the positive clone requires detailed knowledge of microbiology and the ability to handle of a battery of modern biochemical techniques. Finally, the automated chemical synthesis of gene fragments serves to demonstrate that chemistry is starting to make its comeback into molecular biology.

Automated chemical synthesis controlled by computer generated programs--polypeptides.

Instrumentation for the automated chemical synthesis of polypeptides controlled by computer generated paper tape programs is described. The automatic chemical reaction system (ACRS) translated binary coded commands from the paper tape into physical operations resulting in the synthesis of a model polypeptide. The commands for the entire synthesis were generated by computers. Using our computer programs for the synthesis of polypeptides, it is necessary only to specify the amino acid sequence and the computer will set up the appropriate sequence of physical operations (wash cycles, stirring, filtration steps, amino acid additions, etc.) to carry out the synthesis of the desired amino acid sequence. The computer could also automatically make adjustments in the synthetic approach to accommodate the unique problems involved in coupling different amino acids.