Chemical and enzymatic synthesis of glycopolymers

The development of efficient, fast, flexible and general synthetic routes to glycopolymers is an ongoing challenge and much progress has been made in recent years. Chemical coupling methods have become increasingly sophisticated to fine-tune reactivity of reagents by fortuitous choices of anomeric activating group and protecting groups. As a result, oligosaccharide synthesis has become more predictable and reliable even to the extent that first examples of saccharide library syntheses in solution and on the solid phase have been published. In biology, the repertoire of biocatalysts that can be used for glycoside synthesis is ever-increasing, and enzyme-catalysed glycosylation steps have been successfully incorporated into synthetic strategies.     

Time-resolved hydroxyl-radical footprinting of RNA using Fe(II)-EDTA

Chemical footprinting methods have been used extensively to probe the structures of biologically important RNAs at nucleotide resolution. One of these methods, hydroxyl-radical footprinting, has recently been employed to study the kinetics of RNA folding. Hydroxyl radicals can be generated by a number of different methods, including Fe(II)-EDTA complexes, synchrotron radiation, and peroxynitrous acid disproportionation. The latter two methods have been used for kinetic studies of RNA folding. We have taken advantage of rapid hydroxyl-radical generation by Fe(II)-EDTA-hydrogen peroxide solutions to develop a benchtop method to study folding kinetics of RNA complexes. This technique can be performed using commercially available chemicals, and can be used to accurately define RNA folding rate constants slower than 6 min(-1). Here we report the method and an example of time-resolved footprinting on the hairpin ribozyme, a small endoribonuclease and RNA ligase.     

Chemical biology and bacteria: not simply a matter of life or death

Chemical biological approaches to understanding bacteria have largely been confined to screening for antibiotics. More complex phenotypes, such as virulence, have largely been studied using bacterial genetics. However, it has recently become clear that these two methods are complementary and that combining chemical biologic and genetic approaches to studying bacteria brings new power to old problems.     

Incorporation of non-natural amino acids into proteins

Chemical and biological diversity of protein structures and functions can be widely expanded by position-specific incorporation of non-natural amino acids carrying a variety of specialty side groups. After the pioneering works of Schultz's group and Chamberlin's group in 1989, noticeable progress has been made in expanding types of amino acids, in finding novel methods of tRNA aminoacylation and in extending genetic codes for directing the positions. Aminoacylation of tRNA with non-natural amino acids has been achieved by directed evolution of aminoacyl-tRNA synthetases or some ribozymes. Codons have been extended to include four-base codons or non-natural base pairs. Multiple incorporation of different non-natural amino acids has been achieved by the use of a different four-base codon for each tRNA. The combination of these novel techniques has opened the possibility of synthesising non-natural mutant proteins in living cells.     

A rapid method for assaying the metabolism of 7-ethoxyresorufin by microsomal subcellular fractions

Chemical activation of agarose with cyanogen bromide is a routine method when preparing gels for affinity chromatography and for immobilization of macromolecules. Two activation methods are in common use; the titration (1) and the buffer (2) methods.Manipulation of the gels during CNBr activation is complicated due to many steps, some of which have to be carried out as quickly as possible (1,2). In addition, handling the gel is harmful due to the poisonous vapors. In spite of these facts, little effort has been paid to facilitate the practical performance of the activation. We describe here a useful device to eliminate some of the practical troubles in the activation. The main advantages of the device are straight-forward working, speed, and the avoidance of CNBr vapors to a considerable extent. The device is also suitable for handling quantitative gel batches since the loss of gel is minimal.     

Chemical genetics strategies for identification of molecular targets

Chemical genetics is an emerging field that can be used to study the interactions of chemical compounds, including natural products, with proteins. Usually, the identification of molecular targets is the starting point for studying a drug’s mechanism of action and this has been a crucial step in understanding many biological processes. While a great variety of target identification methods have been developed over the last several years, there are still many bioactive compounds whose target proteins have not yet been revealed because no routine protocols can be adopted. This review contains information concerning the most relevant principles of chemical genetics with special emphasis on the different genomic and proteomic approaches used in forward chemical genetics to identify the molecular targets of the bioactive compounds, the advantages and disadvantages of each and a detailed list of successful examples of molecular targets identified with these approaches.     

A chemical method for investigating disulfide-coupled peptide and protein folding

Investigations of protein folding have largely involved studies using disulfide-containing proteins, as disulfide-coupled folding of proteins permits the folding intermediates to be trapped and their conformations determined. Over the last decade, a combination of new biotechnical and chemical methodology has resulted in a remarkable acceleration in our understanding of the mechanism of disulfide-coupled protein folding. In particular, expressed protein ligation, a combination of native chemical ligation and an intein-based approach, permits specifically labeled proteins to be easily produced for studies of protein folding using biophysical methods, such as NMR spectroscopy and X-ray crystallography. A method for regio-selective formation of disulfide bonds using chemical procedures has also been established. This strategy is particularly relevant for the study of disulfide-coupled protein folding, and provides us not only with the native conformation, but also the kinetically trapped topological isomer with native disulfide bonds. Here we review recent developments and applications of biotechnical and chemical methods to investigations of disulfide-coupled peptide and protein folding. Chemical additives designed to accelerate correct protein folding and to avoid non-specific aggregation are also discussed.     

Separation of viable and nonviable animal cell using dielectrophoretic filter

Selective separation of cells using dielectrophoresis (DEP) has recently been studied and methods have been proposed. However, these methods are not applicable to large‐scale separation because they cannot be performed efficiently. In DEP separation, the DEP force is effective only when it is applied close to the electrodes. Utilizing a DEP filter is a solution for large‐scale separation. In this article, the separation efficiency for viable and nonviable cells in a DEP filter was examined. The effects of an applied AC electric field frequency and the gradient of the squared electric field intensity on a DEP velocity for the viable and nonviable animal cells (3‐2H3 cell) were discussed. The frequency response of the DEP velocity differed between the viable and the nonviable cells. We deducted an empirical equation that can be used as guiding principle for the DEP separation. The results indicate that the viable and the nonviable cells were separated using the DEP filter, and the best operating conditions such as the applied voltage and the flow rate were discussed. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Synthesis and enzymatic properties of deoxyribooligonucleotides containing methyl and phenylphosphonate linkages.

Chemical methods for the synthesis of short deoxyribooligonucleotides containing methyl and phenylphosphonodiester linkages have been developed. The interaction of two such nonionic dinucleotide analogs, T(pCH3)T and T(pC6H5)T, with several enzymes has been investigated. Because of the phosphonate linkage each dinucleotide exists as a diastereomeric pair as shown by thin layer chromatography and enzymatic studies. Both isomers of each dinucleotide can be phosphorylated by T4-polynucleotide kinase in the presence of [gamma-32P]ATP. Only one of the diastereoisomers of each dinucleotide is slowly hydrolyzed by snake venom phosphodiesterase and acts as an inhibitor of the enzyme-catalyzed hydrolysis of 5'-labeled oligothymidylic acid. Both isomers of each dinucleotide analog are completely resistant to hydrolysis by spleen phosphodiesterase.     

To tag or not to tag: a comparative evaluation of immunoaffinity-labeling and tandem mass spectrometry for the identification and localization of posttranslational protein carbonylation by 4-hydroxy-2-nonenal, an end-product of lipid peroxidation

Posttranslational carbonylation of proteins by the covalent attachment of the lipid peroxidation product 4-hydroxy-2-nonenal (HNE) is a biomarker of oxidative stress. Tandem mass spectrometry (MS/MS) has become an essential tool for characterization of this modification. Chemical tagging methods have been used to facilitate the immunoaffinity-based enrichment or even quantification of HNE-modified peptides and proteins. With MS/MS spectra of the untagged modified peptides considered as references, a comparative evaluation is presented focusing on the impact of affinity-tagging with four carbonyl-specific reagents (2,4-dinitrophenyl hydrazine, biotin hydrazide, biotinamidohexanoic acid hydrazide and N'-aminooxymethylcarbonyl-hydrazino D-biotin) on collision-induced dissociation of the tagged HNE-carbonylated peptides. Our study has shown that chemical labeling may not be carried out successfully for all the peptides and with all the reagents. The attachment of a tag usually cannot circumvent the occurrence of strong neutral losses observed with untagged species and, in addition, fragmentation of the introduced tag may also happen. Chemical tagging of certain peptides may, nevertheless, afford more sequence ions upon MS/MS than the untagged carbonylated peptide, especially when Michael addition of the lipid peroxidation product occurs on cysteine residues. Therefore, tagging may increase the confidence of identifications of HNE-modified peptides by database searches.     

Biological alternatives for termite control: A review

Termites are a serious menace to both plants and structures. They are the most problematic pest threatening agriculture and the urban environment. They cause significant losses to annual and perennial crops and damage to wooden components in buildings, especially in the semi-arid and sub-humid tropics. Chemical control has been a successful method of preventing termite attack, but the effects of these chemicals are of concern as they create problems for our health and the environment. Biological methods could be suitable alternatives in this regard. The present paper reviews the various methods (physical, chemical, and biological) for termite control. Recent advances and past research done on termite control emphasizing biological methods are reviewed. Biological methods described include botanicals (essential oil, seed, bark, leaf, fruit, root, wood, resin), as well as fungal, bacterial, and nematode approaches. The relationship between chemical structure of active components responsible for termite control and termiticidal activity is discussed. The plants reviewed show good insecticidal properties against termites. These botanicals can be used for termite control singly and in combination. The active component from biomass can be extracted to prepare efficacious and potent biocidal formulations.     

Role of garlic (Allium sativum L.) in human and plant diseases

A resurgence of interest in garlic due to recent revelations of its beneficial effects in the treatment of various human and plant diseases and also due to validation of claims made in traditional systems of medicine has resulted a plethora of publications on different aspects of garlic in recent years. Chemical constituents of garlic and their variations on the methods of isolation have been discussed in the present review. Effect of garlic and its constituents against various human and plant pathogenic and saprophytic microorganisms has also been reviewed.     

Advances in the synthesis and recent therapeutic applications of 1,2,4-thiadiazole heterocycles

Chemical properties of 1,2,4-thiadiazole have been reviewed in the last few years. However, the usefulness of 1,2,4-thiadiazole as a privileged system in medicinal chemistry has prompted the advances on the therapeutic potential of this system. This review provides a brief summary of the medicinal chemistry of 1,2,4-thiadiazole system and highlights some examples of 1,2,4-thiadiazole-containing drug substances in the current literature. A survey of representative literature procedures for the preparation of 1,2,4-thiadiazole is presented in sections by generalized synthetic methods.     

植物性杀虫剂防治白蚁研究进展

白蚁是建筑物和树木的重要害虫,利用化学方法对其种群进行控制仍是当前减少白蚁危害的主要措施。但使用化学杀虫剂对生态环境和人类健康带来的问题促使人类去寻找一些环境友好型生物农药来代替化学制品,而植物性杀虫剂由于其优点而越来越受到重视。本文综述了目前在白蚁防治中有杀虫潜能的植物种类、主要分布科目及作用效果,探讨了植物性杀虫剂防治白蚁存在的问题,同时对植物性杀虫剂应用于白蚁防治进行了展望。     

Chemical modification of enzymes for enhanced functionality.

The explosion in commercial and synthetic applications of enzymes has stimulated much of the interest in enhancing enzyme functionality and stability. Covalent chemical modification, the original method available for altering protein properties, has now re-emerged as a powerful complementary approach to site-directed mutagenesis and directed evolution for tailoring proteins and enzymes. Glutaraldehyde crosslinking of enzyme crystals and polyethylene glycol (PEG) modification of enzyme surface amino groups are practical methods to enhance biocatalyst stability. Whereas crosslinking of enzyme crystals generates easily recoverable insoluble biocatalysts, PEGylation increases solubility in organic solvents. Chemical modification has been exploited for the incorporation of cofactors onto protein templates and for atom replacement in order to generate new functionality, such as the conversion of a hydrolase into a peroxidase. Despite the breadth of applicability of chemically modified enzymes, a difficulty that has previously impeded their implementation is the lack of chemo- or regio-specificity of chemical modifications, which can yield heterogeneous and irreproducible product mixtures. This challenge has recently been addressed by the introduction of a unique position for modification by a site-directed mutation that can subsequently be chemically modified to introduce an unnatural amino acid sidechain in a highly chemo- and regio-specific manner.     

Modeling of purification operations in biotechnology: enabling process development, optimization, and scale-up

Process modeling involves the use of a set of mathematical equations to represent key physical phenomena involved in the process. An appropriately validated model can be used to predict process behavior with limited experimental data, identify critical ranges for process variables, and guide further process development. Although process modeling is extensively used in the chemical process industries, it has not been widely used in purification unit operations in biotechnology. Recent FDA guidelines encourage the use of process modeling during process development, along with multivariate statistical methods, detailed risk assessment, and other quantifiers of uncertainty. This paper will review recent advances in the modeling of key downstream unit operations: chromatography, filtration, and centrifugation. The focus will be on the application of modeling for industrial applications. Relevant papers presented at a session on this topic at the recent American Chemical Society National Meeting in San Francisco will also be reviewed.     

Polyhydroxyalkanoates: Properties and chemical modification approaches for their functionalization

Polyhydroxyalkanoates (PHAs) have become an attractive biomaterial in research in the past few years due to their extensive potential industrial applications. Being long chain hydroxyl fatty acid molecules, the PHAs are hydrophobic in nature, and have less functional groups. These features limit their applications in various areas. To enhance their usage, these polymers may need to be modified including surface and chemical modifications. Such modifications may alter their mechanical properties, surface structure, amphiphilic character and rate of degradation to fulfil the requirements for their future applications. Chemical modifications allow incorporation of functional groups to PHAs that could not be introduced through biotechnological methods. These chemically reformed PHAs, with enhanced properties, could be used for broad range of applications. This review aims to introduce different chemical modification approaches including some recent methods that had not been explored or discussed so far for PHAs as possible technologies for widening the range of product and application potentials. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:29–41, 2018     

Current aspects on the radiation induced base damage in DNA

In this short review, some current aspects of our knowledge about base damage in DNA induced by ionizing radiation will be summarized. It is not intended, to describe all the literature in this field; a very extensive review has been given in the book of Hüttermann et al. (1978) and also in later by Cadet and Berger (1985), Hutchinson (1985) and v. Sonntag and Schuchmann (1986). However, in this review, current ideas and unsolved problems concerning DNA base damage will be discussed, which may outline possible future research in this field. The understanding of DNA base damage requires the analysis of radicals formed in irradiated single DNA moieties as well as in whole DNA. Chemical studies about can be used for the molecular alterations of bases and biochemical methods for DNA-sequencing. In addition enzymes recognizing DNA damage and immunological methods with specific antibodies can be employed. However special emphasis should be given to the analysis of DNA base damage in irradiated cells and it will be shown, that a distinct gap in knowledge exists in this field in contrast to the radiation chemistry in aqueous solutions of DNA.     

Phenanthroline-Cu(II) cleavage as a probe of rRNA structure

Chemical cleavage is developing into a powerful tool for analysis and characterization of nucleic acids. Phenanthroline-Cu(II) cleavage has been used extensively for studies of DNA for the last two decades, but recently has been applied to structural studies of RNA as well. This approach has been used to study the structure and structural changes occurring in ribosomal RNA within the ribosomes. In this article we discuss the mechanism by which phenanthroline cleaves, the applications possible using this approach, and the results that can be obtained. Protocols for use of phenanthroline are outlined as well.     

Mechanistic studies on acyl-transferase ribozymes and beyond

In vitro selection has allowed the isolation of many new ribozymes that are able to catalyze an ever-widening array of chemical transformations. Mechanistic studies on these selected ribozymes have provided valuable insight into the methods that RNA can invoke to overcome different catalytic tasks. We focus on the methods employed in these mechanistic studies using the acyl-transferase family of selected ribozymes as well-studied reference systems. Chemical and biochemical techniques have been used in tandem in order to draw conclusions on the various modes of catalysis employed by the different family members. In turn, this type of mechanistic information may provide a means for the redesign and optimization of existing ribozymes or the basis for new selection systems for more powerful RNA catalysts.