A New Strategy for Solid-Phase Depsipeptide Synthesis Using Recoverable Building Blocks

Glycoproteins and glycopeptides are an interesting focus of research, because of their potential use as therapeutic agents, since they are related to carbohydrate-carbohydrate, carbohydrate-protein, and carbohydrate-lipid interactions, which are commonly involved in biological processes. It has been established that natural glycoconjugates could be an important source of templates for the design and development of molecules with therapeutic applications. However, isolating large quantities of glycoconjugates from biological sources with the required purity is extremely complex, because these molecules are found in heterogeneous environments and in very low concentrations. As an alternative to solving this problem, the chemical synthesis of glycoconjugates has been developed. In this context, several methods for the synthesis of glycopeptides in solution and/or solid-phase have been reported. In most of these methods, glycosylated amino acid derivatives are used as building blocks for both solution and solid-phase synthesis. The synthetic viability of glycoconjugates is a critical parameter for allowing their use as drugs to mitigate the impact of microbial resistance and/or cancer. However, the chemical synthesis of glycoconjugates is a challenge, because these molecules possess multiple reaction sites and have a very specific stereochemistry. Therefore, it is necessary to design and implement synthetic routes, which may involve various protection schemes but can be stereoselective, environmentally friendly, and high-yielding. This review focuses on glycopeptide synthesis by recapitulating the progress made over the last 15 years.

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Fully Automated Parallel Oligonucleotide Synthesizer

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc20011299 ◽

2001 ◽

Vol 66 (8) ◽

pp. 1299-1314 ◽

Cited By ~ 14

Author(s):

Michal Lebl ◽

Christine Burger ◽

Brett Ellman ◽

David Heiner ◽

Georges Ibrahim ◽

...

Keyword(s):

Solid Phase ◽

Building Blocks ◽

Solid Support ◽

Continuous Operation ◽

Gear Pump ◽

Oligonucleotide Synthesis ◽

Center Of Rotation ◽

Microtiter Plates ◽

The Individual ◽

Design And Construction

Design and construction of automated synthesizers using the tilted plate centrifugation technology is described. Wash solutions and reagents common to all synthesized species are delivered automatically through a 96-channel distributor connected to a gear pump through two four-port selector valves. Building blocks and other specific reagents are delivered automatically through banks of solenoid valves, positioned over the individual wells of the microtiterplate. These instruments have the following capabilities: Parallel solid-phase oligonucleotide synthesis in the wells of polypropylene microtiter plates, which are slightly tilted down towards the center of rotation, thus generating a pocket in each well, in which the solid support is collected during centrifugation, while the liquid is expelled from the wells. Eight microtiterplates are processed simultaneously, providing thus a synthesizer with a capacity of 768 parallel syntheses. The instruments are capable of unattended continuous operation, providing thus a capacity of over two millions 20-mer oligonucleotides in a year.

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Synthesis and Self-assembly of Amphiphilic Precision Glycomacromolecules

Polymer Chemistry ◽

10.1039/d1py00422k ◽

2021 ◽

Author(s):

Alexander Banger ◽

Julian Sindram ◽

Marius Otten ◽

Jessica Kania ◽

Alexander Strzelczyk ◽

...

Keyword(s):

Self Assembly ◽

Solid Phase ◽

Building Blocks ◽

Polymer Synthesis

We present the synthesis of so called amphiphilic glycomacromolecules (APGs) by using solid-phase polymer synthesis. Based on tailor made building blocks, monosdisperse APGs with varying compositions are synthesized, introducing carbohydrate...

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A new strategy for total solid-phase synthesis of polymyxins

Tetrahedron Letters ◽

10.1016/j.tetlet.2015.06.056 ◽

2015 ◽

Vol 56 (33) ◽

pp. 4796-4799 ◽

Cited By ~ 11

Author(s):

Wei-Liang Xu ◽

A-Long Cui ◽

Xin-Xin Hu ◽

Xue-Fu You ◽

Zhuo-Rong Li ◽

...

Keyword(s):

Solid Phase Synthesis ◽

Solid Phase ◽

Total Solid ◽

Phase Synthesis ◽

New Strategy

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Micro Salting-Out Assisted Matrix Solid-Phase Dispersion: A Simple and Fast Sample Preparation Method for the Analysis of Bisphenol Contaminants in Bee Pollen

Molecules ◽

10.3390/molecules26082350 ◽

2021 ◽

Vol 26 (8) ◽

pp. 2350

Author(s):

Jianing Zhang ◽

Fengjie Yu ◽

Yunmin Tao ◽

Chunping Du ◽

Wenchao Yang ◽

...

Keyword(s):

Sample Preparation ◽

Preparation Method ◽

Solid Phase ◽

Sample Preparation Method ◽

Salting Out ◽

Bee Pollen ◽

Matrix Solid Phase Dispersion ◽

Phase Dispersion ◽

New Strategy ◽

Semi Solid

In the present work, a novel sample preparation method, micro salting-out assisted matrix solid-phase dispersion (μ-SOA-MSPD), was developed for the determination of bisphenol A (BPA) and bisphenol B (BPB) contaminants in bee pollen. The proposed method was designed to combine two classical sample preparation methodologies, matrix solid-phase dispersion (MSPD) and homogenous liquid-liquid extraction (HLLE), to simplify and speed-up the preparation process. Parameters of μ-SOA-MSPD were systematically investigated, and results indicated the significant effect of salt and ACN-H2O extractant on the signal response of analytes. In addition, excellent clean-up ability in removing matrix components was observed when primary secondary amine (PSA) sorbent was introduced into the blending operation. The developed method was fully validated, and the limits of detection for BPA and BPB were 20 μg/kg and 30 μg/kg, respectively. Average recoveries and precisions were ranged from 83.03% to 94.64% and 1.76% to 5.45%, respectively. This is the first report on the analysis of bisphenol contaminants in bee pollen sample, and also on the combination of MSPD and HLLE. The present method might provide a new strategy for simple and fast sample preparation of solid and semi-solid samples.

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Validating Soot Models in LES of Turbulent Flames: The Contribution of Soot Subgrid Intermittency Model to The Prediction of Soot Production in an Aero-Engine Model Combustor

10.1115/gt2021-60296 ◽

2021 ◽

Author(s):

Lívia Pereira Tardelli ◽

Nasser Darabiha ◽

Denis Veynante ◽

Benedetta Franzelli

Keyword(s):

Gas Phase ◽

Reference Model ◽

Solid Phase ◽

Phase Evolution ◽

Turbulent Flames ◽

Engine Model ◽

Aero Engine ◽

New Strategy ◽

Parametric Studies ◽

Soot Model

Abstract Predicting soot production in industrial systems using an LES approach represents a great challenge. Besides the complexity in modeling the multi-scale physicochemical soot processes and their interaction with turbulence, the validation of newly developed models is critical under turbulent conditions. This work illustrates the difficulties in evaluating model performances specific to soot prediction in turbulent flames by considering soot production in an aero-engine combustor. It is proven that soot production occurs only for scarce local gaseous conditions. Therefore, to obtain a statistical representation of such rare soot events, massive CPU resources would be required. For this reason, evaluating soot model performances based on parametric studies, i.e., multiple simulations, as classically done for purely gaseous flames, is CPU high-demanding for sooting flames. Then, a new strategy to investigate modeling impact on the solid phase is proposed. It is based on a unique simulation, where the set of equations describing the solid phase are duplicated. One set accounts for the reference model, while the other set is treated with the model under the scope. Assuming neglected solid phase retro-coupling on the gas phase, the soot scalars from both sets experience the same unique temporal and spatial gas phase evolution isolating the soot model effects from the uncertainties on gaseous models and numerical sensitivities. Finally, the strategy capability is proven by investigating the contribution of the soot subgrid intermittency model to the prediction of soot production in the DLR burner.

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Synthesis of Trinucleotide Building Blocks in Solution and on Solid Phase

Current Protocols in Nucleic Acid Chemistry ◽

10.1002/cpnc.60 ◽

2018 ◽

Vol 75 (1) ◽

pp. e60 ◽

Cited By ~ 2

Author(s):

Ruth Suchsland ◽

Bettina Appel ◽

Sabine Müller

Keyword(s):

Solid Phase ◽

Building Blocks

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Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.10.245 ◽

2014 ◽

Vol 10 ◽

pp. 2348-2360 ◽

Cited By ~ 13

Author(s):

Kristen K Merritt ◽

Kevin M Bradley ◽

Daniel Hutter ◽

Mariko F Matsuura ◽

Diane J Rowold ◽

...

Keyword(s):

Solid Phase ◽

Pcr Amplification ◽

Kanamycin Resistance ◽

Dna Fragments ◽

Gene Encoding ◽

Synthetic Dna ◽

Information Density ◽

Letter Alphabet ◽

New Strategy ◽

Autonomous Assembly

Background: Many synthetic biologists seek to increase the degree of autonomy in the assembly of long DNA (L-DNA) constructs from short synthetic DNA fragments, which are today quite inexpensive because of automated solid-phase synthesis. However, the low information density of DNA built from just four nucleotide “letters”, the presence of strong (G:C) and weak (A:T) nucleobase pairs, the non-canonical folded structures that compete with Watson–Crick pairing, and other features intrinsic to natural DNA, generally prevent the autonomous assembly of short single-stranded oligonucleotides greater than a dozen or so. Results: We describe a new strategy to autonomously assemble L-DNA constructs from fragments of synthetic single-stranded DNA. This strategy uses an artificially expanded genetic information system (AEGIS) that adds nucleotides to the four (G, A, C, and T) found in standard DNA by shuffling hydrogen-bonding units on the nucleobases, all while retaining the overall Watson–Crick base-pairing geometry. The added information density allows larger numbers of synthetic fragments to self-assemble without off-target hybridization, hairpin formation, and non-canonical folding interactions. The AEGIS pairs are then converted into standard pairs to produce a fully natural L-DNA product. Here, we report the autonomous assembly of a gene encoding kanamycin resistance using this strategy. Synthetic fragments were built from a six-letter alphabet having two AEGIS components, 5-methyl-2’-deoxyisocytidine and 2’-deoxyisoguanosine (respectively S and B), at their overlapping ends. Gaps in the overlapped assembly were then filled in using DNA polymerases, and the nicks were sealed by ligase. The S:B pairs in the ligated construct were then converted to T:A pairs during PCR amplification. When cloned into a plasmid, the product was shown to make Escherichia coli resistant to kanamycin. A parallel study that attempted to assemble similarly sized genes with optimally designed standard nucleotides lacking AEGIS components gave successful assemblies of up to 16 fragments, but generally failed when larger autonomous assemblies were attempted. Conclusion: AEGIS nucleotides, by increasing the information density of DNA, allow larger numbers of DNA fragments to autonomously self-assemble into large DNA constructs. This technology can therefore increase the size of DNA constructs that might be used in synthetic biology.

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