Recent patents on oligonucleotide synthesis and gene synthesis

Gene synthesis is an emerging field which has widespread implications in synthetic biology and molecular biology. The field is constantly evolving which has led to key advances in oligonucleotide synthesis and gene synthesis technologies, with simplicity, cost effectiveness and high throughput. The miniaturization, multiplexing, microfluidic processing and the integrated microchip engineering will drive down cost and increase productivity without compromising DNA synthesis fidelity, whereas the gigantic amount of genome information provides infinite source of DNA elements and genes as raw material for synthetic biology. This article describes some of the recent patents on oligonucleotide synthesis and gene synthesis.     

Lag-phase and rate of synthesis in light-mediated anthocyanin synthesis

Mustard (Sinapis alba L.) seedlings were irradiated with continuous far-red light either with or without a pretreatment with 3 or 6 h of the same far-red light, separated by a 15 h dark period. The pretreatment increases the initial rate of anthocyanin accumulation — as caused by the 2nd light treatment — at least 6-fold but leads to an earlier cessation of anthocyanin accumulation. Moreover, the pretreatment seems to shorten the apparent lag-phase of anthocyanin accumulation considerably but it does not eliminate the lag. If the pretreatment with far-red light is terminated before the seedling reaches competence (with regard to phytochrome and anthocyanin synthesis) the pretreatment has no effect on the apparent lag-phase even though the future capacity of anthocyanin biogenesis is considerably stimulated by the pretreatment. The time course of induction of anthocyanin and that of phenylalanine ammonia-lyase (PAL) (Acton et al. 1980, Fig. 1) is in line with the concept that induction of PAL by light is a prerequisite for the onset of light-mediated anthocyanin synthesis.Abbreviation PAL phenylalanine ammonia-lyase     

alpha-t-butyl- and alpha-i-propyl-ortho-hydroxybenzylamines: racemic synthesis/resolution and asymmetric synthesis

Efficient routes to alpha-tert-butyl- and alpha-iso-propyl-ortho-hydroxybenzylamines 1a and 1b are described. Highly enantioenriched 1a and 1b were obtained by resolution of the methoxy derivatives 2 by recrystallization of the salts formed with mandelic acid followed by Lewis acid mediated demethylation. The chiral 1,3-amino alcohol 1a has also been obtained in an asymmetric synthesis with the key step a diastereoselective alkylation of the imine obtained by condensation of o-anisaldehyde with phenyl glycinol. The absolute stereochemistry of these 1,3-aminophenols was determined by CD spectroscopy of the salicylideneamines 12 and by an X-ray structure analysis of the salt formed between (R)-mandelic acid and (S)-alpha-tert-butyl-ortho-methoxybenzylamine ((S)-2a).     

Glycoconjugate synthesis during early pregnancy: hyaluronate synthesis and function

The synthesis of various glycoconjugate classes by mouse uteri during the pre- and peri-implantation period has been examined using [3H]glucosamine as a metabolic precursor. A unique and dramatic (five- to sixfold) increase was observed in the synthesis of hyaluronate on the day upon which embryo implantation normally occurs. Mated, but nonpregnant mice did not display increased hyaluronate biosynthesis. In contrast to hyaluronate, the synthesis of most other types of glycoconjugates remained fairly constant during the first 5 days of pregnancy. Low (1500-5000)-molecular-weight N-linked oligosaccharides constituted the major class of oligosaccharides synthesized under all conditions. High (greater than 10,000)-molecular-weight glycoconjugates constituted the second most abundant class of glycoconjugates synthesized (20-30%). Most (85%) of the newly synthesized hyaluronate was associated with the nonepithelial cell types of the uterus. Experiments using ovariectomized mice receiving steroid hormones demonstrated that uterine hyaluronate synthesis was induced preferentially by an artificial decidual stimulus and implicated stromal cells as the site of hyaluronate synthesis. In addition, it was demonstrated that tissue culture plates coated with hyaluronate, but not other polysaccharides, support attachment and spreading of a large fraction (60 to 70%) of embryos cultured in serum-free medium. Collectively, these studies indicate that increased hyaluronate biosynthesis accompanies decidual responses in the endometrium and may promote embryo implantation following initial penetration of the uterine epithelium.     

ATP synthesis and storage

Since 1929, when it was discovered that ATP is a substrate for muscle contraction, the knowledge about this purine nucleotide has been greatly expanded. Many aspects of cell metabolism revolve around ATP production and consumption. It is important to understand the concepts of glucose and oxygen consumption in aerobic and anaerobic life and to link bioenergetics with the vast amount of reactions occurring within cells. ATP is universally seen as the energy exchange factor that connects anabolism and catabolism but also fuels processes such as motile contraction, phosphorylations, and active transport. It is also a signalling molecule in the purinergic signalling mechanisms. In this review, we will discuss all the main mechanisms of ATP production linked to ADP phosphorylation as well the regulation of these mechanisms during stress conditions and in connection with calcium signalling events. Recent advances regarding ATP storage and its special significance for purinergic signalling will also be reviewed.     

Opiomelanins synthesis and properties

Opiomelanins represent a new class of synthetic pigments produced by the tyrosinase-catalyzed oxidation of opioid peptides and other tyrosine aminoterminal peptides. In contrast with dopamelanin, these polymers are fully soluble in hydrophilic media, due to the presence of the peptide moiety. Opiomelanins show paramagnetism as demonstrated by the EPR spectrum identical to that of dopamelanin. The presence of the aminoacidic chain linked to the melaninic moiety, influences the electron transfer properties of opiomelanins i.e. the ability to oxidize NADH. Like dopamelanin Tyr-Gly-melanin exhibits this behaviour whereas leuenkmelanin does not show any oxidizing potential. Opiomelanins UV-Vis spectrum is characterized by an absorption band at 330 nm which disappears upon acid hydrolysis, H2O2 treatment and under simulated solar illumination. Opiomelanins exhibit a fluorescence emission peaked at 440 and 520 nm if excited at 330 nm. These fluorescence bands are due to the oligomeric units and high molecular weight units, respectively. When opioid peptides are allowed to react with tyrosinase in the presence of an excess of cysteine, cysteinyldopaenkephalins are synthesized. These peptides are furtherly oxidized giving rise to pheoopiomelanins. Reactive oxygen species also are able to oxidize non enzymatically both enkephalins and cysteinyldopaenkephalins, producing the corresponding melanin pigments.     

An amalgamation of solid phase peptide synthesis and ribosomal peptide synthesis

Expressed protein ligation (EPL) is a protein semisynthesis technique that allows the site-specific introduction of unnatural amino acids and biophysical probes into proteins. In the present study, we illustrate the utility of the approach through the generation of two semisynthetic proteins bearing spectroscopic probes. Dihydrofolate reductase containing a single (13)C probe in an active site loop was generated through the ligation of a synthetic peptide-alpha-thioester to a recombinantly generated fragment containing an N-terminal Cys. Similarly, c-Crk-II was assembled by the sequential ligation of three recombinant polypeptide building blocks, allowing the incorporation of (15)N isotopes in the central domain of the protein. These examples showcase the scope of the protein ligation strategy for selective introduction of isotopic labels into proteins, and the protocols described will be of value to those interested in using EPL on other systems.     

Transformation of type polysaccharide antigen synthesis and hemolysin synthesis in streptococci

Transformation of the ability to synthesize type polysaccharide antigen and beta-hemolysin has been obtained in group F streptococci. Colonies possessing cells transformed to antigen synthesis were detected on the agar surface with fluorescein-labeled anti-type serum. This selection method, in contrast to those with antibiotics, allowed both transformed and nontransformed cells to grow, resulting in sectored colonies. These colonies could be subcultured to further establish the synthesis of antigen. Group F, group A, and group-like z deoxyribonucleic acid (DNA) labeled with type II antigen and hemolysin, and streptomycin resistance transferred each marker to a group F strain lacking a type antigen. DNA from group F and z3 strains labeled with type III antigen, and streptomycin resistance transferred both markers to group F and z3 strains lacking type antigen. A second F strain without type antigen was not transformed with any of these markers. A group H strain was transformed to streptomycin resistance only by the same types of DNA. Transformation to type II antigen synthesis always resulted in the formation of beta-hemolysin. All strains isolated from natural sources contained both markers. A mutant, obtained by nitrosoguanidine treatment of an FII(sr) strain, did not synthesize either the hemolysin or the antigen. This mutant still possessed the group antigen and streptomycin resistance. A close linkage of type II antigen and beta-hemolysin is indicated. The fluorescent-antibody staining of cells containing both group and type antigens showed a more intense ultraviolet adsorption for type than group antigen. A surface location (microcapsular) for the type antigen appeared likely. These results are of interest for studies on antigen biosynthesis, genetics, and classification of the streptococci.     

Starch synthesis in Arabidopsis. Granule synthesis,composition, and structure

The aim of this work was to characterize starch synthesis, composition, and granule structure in Arabidopsis leaves. First, the potential role of starch-degrading enzymes during starch accumulation was investigated. To discover whether simultaneous synthesis and degradation of starch occurred during net accumulation, starch was labeled by supplying (14)CO(2) to intact, photosynthesizing plants. Release of this label from starch was monitored during a chase period in air, using different light intensities to vary the net rate of starch synthesis. No release of label was detected unless there was net degradation of starch during the chase. Similar experiments were performed on a mutant line (dbe1) that accumulates the soluble polysaccharide, phytoglycogen. Label was not released from phytoglycogen during the chase indicating that, even when in a soluble form, glucan is not appreciably degraded during accumulation. Second, the effect on starch composition of growth conditions and mutations causing starch accumulation was studied. An increase in starch content correlated with an increased amylose content of the starch and with an increase in the ratio of granule-bound starch synthase to soluble starch synthase activity. Third, the structural organization and morphology of Arabidopsis starch granules was studied. The starch granules were birefringent, indicating a radial organization of the polymers, and x-ray scatter analyses revealed that granules contained alternating crystalline and amorphous lamellae with a periodicity of 9 nm. Granules from the wild type and the high-starch mutant sex1 were flattened and discoid, whereas those of the high-starch mutant sex4 were larger and more rounded. These larger granules contained "growth rings" with a periodicity of 200 to 300 nm. We conclude that leaf starch is synthesized without appreciable turnover and comprises similar polymers and contains similar levels of molecular organization to storage starches, making Arabidopsis an excellent model system for studying granule biosynthesis.     

A convenient one-step synthesis of L-aminotryptophans and improved synthesis of 5-fluorotryptophan

A one-pot biotransformation for the generation of a series of L-aminotryptophans using a readily prepared protein extract containing tryptophan synthase is reported. The extract exhibits remarkable stability upon freeze-drying, and may be stored and used for long periods after its preparation without significant loss of activity.     

Trisindoline synthesis and anticancer activity

Expression of a Rhodococcus-derived oxygenase gene in Escherichia coli yielded indigo metabolites with cytotoxic activity against cancer cells. Bioactivity-guided fractionation of these indigo metabolites led to the isolation of trisindoline as the agent responsible for the observed in vitro cytotoxic activity against cancer cells. While the cytotoxicity of etoposide, a common anticancer drug, was dramatically decreased in multidrug-resistant (MDR) cancer cells compared with treatment of parental cells, trisindoline was found to have similar cytotoxicity effects on both parental and MDR cell lines. In addition, the cytotoxic effects of trisindoline were resistant to P-glycoprotein overexpression, one of the most common mechanisms of drug resistance in cancer cells, supporting its use to kill MDR cancer cells.