Round Of Synthesis Research Articles

Construction and characterization of a synthesized herpes simplex virus H129-Syn-G2

Herpes simplex virus type 1 (HSV-1) causes lifelong infections worldwide, and currently there is no efficient cure or vaccine. HSV-1-derived tools, such as neuronal circuit tracers and oncolytic viruses, have been used extensively; however, further genetic engineering of HSV-1 is hindered by its complex genome structure. In the present study, we designed and constructed a synthetic platform for HSV-1 based on H129-G4. The complete genome was constructed from 10 fragments through 3 rounds of synthesis using transformation-associated recombination (TAR) in yeast, and was named H129-Syn-G2. The H129-Syn-G2 genome contained two copies of the gfp gene and was transfected into cells to rescue the virus. According to growth curve assay and electron microscopy results, the synthetic viruses exhibited more optimized growth properties and similar morphogenesis compared to the parental virus. This synthetic platform will facilitate further manipulation of the HSV-1 genome for the development of neuronal circuit tracers, oncolytic viruses, and vaccines.

Paintable Carbon Nanotube Coating-Based Textronics for Sustained Holter-Type Electrocardiography.

A growing population suffering from or at high risk of developing cardiovascular diseases can benefit from rapid, precise, and readily available diagnostics. Textronics is an interdisciplinary approach for designing and manufacturing high-performance flexible electronics integrated with textiles for various applications, with electrocardiography (ECG) being the most convenient and most frequently used diagnostic technique for textronic solutions. The key challenges that still exist for textronics include expedient manufacturing, adaptation to human subjects, sustained operational stability for Holter-type data acquisition, reproducibility, and compatibility with existing solutions. The present study demonstrates conveniently paintable ECG electroconductive coatings on T-shirts woven from polyester or 70% polyamide and 30% polyester. The up to 600-μm-thick coatings encompass working electrodes of low resistivity 60 Ω sq-1 sheathed in the insulated pathways-conjugable with a wireless, multichannel ECG recorder. Long (800 μm) multiwalled carbon nanotubes, with scalable reproducibility and purity (18 g per round of synthesis), constituted the electroactive components and were embedded into a commercially available screen-printing acrylic base. The resulting paint had a viscosity of 0.75 Pa·s at 56 s-1 and 25 °C and was conveniently applied using a paintbrush, making this technique accessible to manufacturers. The amplified and nondigitally processed ECG signals were recorded under dry-skin conditions using a certified ECG recorder. The system enabled the collection of ECG signals from two channels, allowing the acquisition of cardiac electrical activity on six ECG leads with quality at par with medical diagnostics. Importantly, the Holter-type ECG allowed ambulatory recording for >24 h under various activities (sitting, sleeping, walking, and running) in three male participants. The ECG signal was stable for >5 cycles of washing, a level of stability not reported yet previously. The developed ECG-textronic application possesses acceptable and reproducible characteristics, making this technology a suitable candidate for further testing in clinical trials.

2-aminobenzimidazoles for leishmaniasis: From initial hit discovery to in vivo profiling.

Leishmaniasis is a major infectious disease with hundreds of thousands of new cases and over 20,000 deaths each year. The current drugs to treat this life-threatening infection have several drawbacks such as toxicity and long treatment regimens. A library of 1.8 million compounds, from which the hits reported here are publicly available, was screened against Leishmania infantum as part of an optimization program; a compound was found with a 2-aminobenzimidazole functionality presenting moderate potency, low metabolic stability and high lipophilicity. Several rounds of synthesis were performed to incorporate chemical groups capable of reducing lipophilicity and clearance, leading to the identification of compounds that are active against different parasite strains and have improved in vitro properties. As a result of this optimization program, a group of compounds was further tested in anticipation of in vivo evaluation. In vivo tests were carried out with compounds 29 (L. infantum IC50: 4.1 μM) and 39 (L. infantum IC50: 0.5 μM) in an acute L. infantum VL mouse model, which showed problems of poor exposure and lack of efficacy, despite the good in vitro potency.

Abstract 2757: Discovery and characterization of covalent Pin1 inhibitors targeted to an active site cysteine

Abstract Proline-directed phosphorylation at serine or threonine residues (pSer/Thr-Pro) regulates numerous cellular processes, including the cell cycle, transcription, and differentiation. Deregulation of such signaling networks is a hallmark of transformation and oncogenesis. Pin1, a peptidyl-prolyl isomerase, regulates the function and stability of phosphoproteins by catalyzing the cis/trans isomerization of pSer/Thr-Pro motifs. Pin1 is frequently overexpressed in human cancers, including pancreatic ductal adenocarcinoma (PDAC), and Pin1 is required for activated Ras to induce tumorigenesis. While mutations in KRAS are observed in 90-95% of human PDAC cases, it has historically proven very challenging to develop small molecules that inhibit mutant Ras function. Consequently, drug discovery efforts have turned to targets required for Ras-mediated transformation, such as Pin1. However, existing Pin1 inhibitors lack the potency, selectivity, and/or cell permeability to serve as informative cellular probes. We report a highly potent, cell-permeable Pin1 inhibitor that covalently targets Cys113, a conserved cysteine residue in the Pin1 active site. Through iterative rounds of synthesis and characterization, we developed inhibitor 1b. With a Ki of 15 nM as measured in biochemical binding and isomerase inhibition assays, 1bis currently the most potent Pin1 inhibitor available. Furthermore, in a chemoproteomic study using Covalent Inhibitor Target Site Identification (CITe-Id) to quantify the dose-dependent covalent labeling of 1b to individual cysteines across the proteome, Pin1 Cys113 was the only identified target, highlighting the pronounced selectivity of 1b for Pin1. We show that treatment with 1b diminishes viability of human PDAC cell lines, which can be fully rescued in corresponding Pin1 knockout cells generated using CRISPR/Cas9, showing that this phenotype is on-target. In parallel to inhibitor development, we used CRISPR/Cas9 GFP-dropout screens to further validate the dependence of these cell lines on Pin1. Genetic disruption of Pin1 led to antiproliferative effects, confirming the results of 1b treatment. We also employed the degradation tag (dTAG) approach to assess the effects of rapid and selective targeted Pin1 degradation through generation of FKBP12F36V-Pin1, Pin1-/-human PDAC cell lines. Treatment with a small molecule FKBP12F36V-degrader led to rapid ubiquitination and degradation of FKBP12F36V-Pin1, enabling comparisons of targeted inhibition and Pin1 degradation. Through the development of a selective Pin1 inhibitor coupled with genetic approaches and the chemical-genetic dTAG strategy, we demonstrate that Pin1 inhibition represents a tractable strategy in PDAC. Citation Format: Benika Pinch, Zainab Doctor, Christopher M. Browne, Hyuk-Soo Seo, Behnam Nabet, Shingo Kozono, Xiaolan Lian, Daniel Zaidman, Dina Daitchman, Nir London, Lu Gong, Theresa Manz, Yujin Chun, Li Tan, Jarrod Marto, Stephen Buratowski, Sirano Dhe-Paganon, Xiao Zhou, Kun Ping Lu, Nathanael S. Gray. Discovery and characterization of covalent Pin1 inhibitors targeted to an active site cysteine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2757.

Development of a Glycerol Based Polymer for Additive Manufacturing

This paper presents a proposal to synthetize a thermoplastic polymer from glycerol designed to be used as feedstock for additive manufacturing (AM) based on the material extrusion (ME) principle. A first round of synthesis was carried out considering different variables to search a thermoplastic solid without stickiness. After the evaluation of some AM–ME basic requirements, two other synthesis groups (the second and third rounds) were prepared to verify a proper catalyst amount and reaction time. These trial samples were characterized by infrared spectrometry and thermogravimetric analysis. The material obtained which was considered the most suitable showed an amorphous structure and a glass transition slightly below room temperature. In the end, this polymer was used as feedstock to print basic geometric specimens and evaluate both filament and layer adhesion. The result suggests the feasibility to synthetize a thermoplastic polymer from glycerol for AM–ME technology. The polymer obtained from the renewable resource has the potential to become an option for this technology. However, further studies considering additives are required to improve the polymer properties, starting by increasing its glass transition temperature. In summary, the polymer obtained from the renewable resource has the potential to become an option for AM–ME technology.

A facile method towards rough morphology polymer brush for increased mobility of embedded nanoparticles

The control of polymer brush morphology is important in determining its performance for various applications such as for anti-fouling coatings or as a host for polymer brush-nanoparticle nanocomposites. Herein we introduce a novel method to vary the surface roughness of polymer brushes by sequential growth in different solvent qualities. Poly(oligo ethylene glycol) methacrylate (POEGMA) was first grown homogeneously using a solvent of 20% water in methanol. A second round of synthesis was then performed with varying ratio of methanol-to-water and ethanol-to-water. We found that roughness generally increased with higher water content during the second round synthesis. Finally we observed, through incorporating as-prepared gold nanoparticles into POEGMA, that nanoparticle distribution and mobility could be improved by having a rougher surface morphology. These findings could be beneficial in designing localized surface plasmon resonance (LSPR)-based solid phase sensing platforms that rely on gold nanoparticle re-organization in polymer brushes.

Synthesis of Potent Dishevelled PDZ Domain Inhibitors Guided by Virtual Screening and NMR Studies

Dishevelled (Dvl) PDZ domains transduce Wnt signals from the membrane-bound receptor Frizzled to the downstream. As abnormal Wnt signaling has been implicated in tumorigenesis, the Dvl PDZ domain is a potential target for small-molecule inhibitors that block Wnt signaling at the Dvl level. We expanded our in silico search to examine the chemical space near previously developed PDZ binders and identified nine additional compounds bind to the Dvl PDZ. We then performed a quantitative structure-activity relationship (QSAR) analysis of these compounds and combined these results with structural studies of the PDZ domain in complex with the compounds to design and synthesize a group of new, further optimized compounds. Two rounds of synthesis and testing yielded a total of six compounds that have greatly improved binding affinity to the Dvl PDZ domain and most potent ones competitively displace Dapper peptide from the PDZ domain. In addition to providing more potent Dvl PDZ domain inhibitors, this study demonstrates that virtual screening and structural studies can be powerful tools in guiding the chemical synthesis hit-to-lead optimization stage during the drug discovery process.

Design of Intelligent Rehabilitation Crutch Based on Accelerometer

In order to meet the daily needs of the elderly patients and walking ability of injury rehabilitation, design an intelligent rehabilitation crutch. This design combine with empowered walking aid’s mechanical features and robot technology, its signal is collected by MMA7260 accelerometer, this greatly improved the sensitivity direction without swerve on the plane through the analysis of the acceleration signal processing and controlling the velocity composition of three omnidirectional wheel rounds of synthesis of all to realize the intelligent walking stick of the whole direction and intellectuality of the walking aids. The motion mechanism of crutch using omnidirectional wheel structure and using ATmega 16 microcontroller to establish low-level control system. The crutch can move in any n of free movement. The kinematics analysis shows the design feasibility. In the manual and automatic control experiments, it can meet designer quarrymen’s and achieve design function.

Parallel on-chip gene synthesis and application to optimization of protein expression

Low-cost, high-throughput gene synthesis and precise control of protein expression are of critical importance to synthetic biology and biotechnology. Here we describe the development of an on-chip gene synthesis technology, which integrates on a single microchip the synthesis of DNA oligonucleotides using inkjet printing, isothermal oligonucleotide amplification and parallel gene assembly. Use of a mismatch-specific endonuclease for error correction results in an error rate of ~0.19 errors per kb. We applied this approach to synthesize pools of thousands of codon-usage variants of lacZα and 74 challenging Drosophila protein antigens, which were then screened for expression in Escherichia coli. In one round of synthesis and screening, we obtained DNA sequences that were expressed at a wide range of levels, from zero to almost 60% of the total cell protein mass. This technology may facilitate systematic investigation of the molecular mechanisms of protein translation and the design, construction and evolution of macromolecular machines, metabolic networks and synthetic cells.

Mechanism of Inhibition of Vaccinia Virus DNA Polymerase by Cidofovir Diphosphate

Cidofovir (CDV) is a broad-spectrum antiviral agent that has been approved for clinical use in the treatment of cytomegalovirus retinitis. It has also been used off label to treat a variety of other viral infections, including those caused by orf and molluscum contagiosum poxviruses. Because it is a dCMP analog, CDV is thought to act by inhibiting viral DNA polymerases. However, the details of the inhibitory mechanism are not well established and nothing is known about the mechanism by which the drug inhibits poxvirus DNA polymerases. To address this concern, we have studied the effect of the active intracellular metabolite of CDV, CDV diphosphate (CDVpp), on reactions catalyzed by vaccinia virus DNA polymerase. Using different primer-template pairs and purified vaccinia virus polymerase, we observed that CDV is incorporated into the growing DNA strand opposite template G's but the enzyme exhibits a lower catalytic efficiency compared with dCTP. CDV-terminated primers are also good substrates for the next deoxynucleoside monophosphate addition step, but these CDV + 1 reaction products are poor substrates for further rounds of synthesis. We also noted that although CDV can be excised from the primer 3' terminus by the 3'-to-5' proofreading exonuclease activity of vaccinia virus polymerase, DNAs bearing CDV as the penultimate 3' residue are completely resistant to exonuclease attack. These results show that vaccinia virus DNA polymerase can use CDVpp as a dCTP analog, albeit one that slows the rate of primer extension. By inhibiting the activity of the proofreading exonuclease, the misincorporation of CDV could also promote error-prone DNA synthesis during poxvirus replication.

Waiting for 4.1

What better way to clarify a topic and allow it to come alive than to provide students with a way to actually see it? Images, diagrams, and flowcharts can draw students in. Animated, interactive materials can provide an even bigger pull. Since my own skills in both drawing and interpretive dance are quite limited, I always look for multimedia containing strong background material and thought-provoking, timely topics. Materials that make the final cut must also meet other criteria: the presentation must be clear, I must be able to run the materials on my lecture hall computers and make them available for the students for viewing outside of class, and presentation and navigation ease are important. When considering use in undergraduate classes, the Roche Genetics: Education Program CD-ROM version 4.0 meets some, but not all, of these criteria. Its main shortcomings lie in its lack of proofreading.

Dendrimer-Coated Nanoparticles

CHEMISTRY Most polymers are synthesized by adding units to one end of a growing chain, but other architectures can be created by adding several monomer units at sites around a growing core. Dendrimers are the most ordered type of these polymers, in which each round of synthesis (or “generation”) geometrically increases the number of units added. A relatively open structure after one or two generations is converted to an almost spherical structure after about five generations. Gopidas et al. adapted a synthesis route for gold nanoparticles that assembles dendrimer “wedges” (which grow out in a limited number of directions) into a spherical structure. Polyaryl ether wedges that are linked initially via disulfide bonds react with a stabilized solution of HAuCl4 and sodium borohydride. A gold core about 2 to 3 nm in diameter forms. For low-generation number wedges (less than three), this spherical core gives the final structure more dendrimer-like properties. The fifth-generation wedges, however, still retain some openness that allows access to the gold core from solution.— PDS J. Am. Chem. Soc. 10.1021/ja029544m (2003).

Signal and noise in bridging PCR

BackgroundIn a variant of the standard PCR reaction termed bridging, or jumping, PCR the primer-bound sequences are originally on separate template molecules. Bridging can occur if, and only if, the templates contain a region of sequence similarity. A 3' end of synthesis in one round of synthesis that terminates in this region of similarity can prime on the other. In principle, Bridging PCR (BPCR) can detect a subpopulation of one template that terminates synthesis in the region of sequence shared by the other template. This study considers the sensitivity and noise of BPCR as a quantitative assay for backbone interruptions. Bridging synthesis is also important to some methods for computing with DNA.ResultsIn this study, BPCR was tested over a 328 base pair segment of the E. coli lac operon and a signal to noise ratio (S/N) of approximately 10 was obtained under normal PCR conditions with Taq polymerase. With special precautions in the case of Taq or by using the Stoffel fragment the S/N was improved to 100, i.e. 1 part of cut input DNA yielded the same output as 100 parts of intact input DNA.ConclusionsIn the E. coli lac operator region studied here, depending on details of protocol, between 3 and 30% per kilobase of final PCR product resulted from bridging. Other systems are expected to differ in the proportion of product that is bridged consequent to PCR protocol and the sequence analyzed. In many cases physical bridging during PCR will have no informational consequence because the bridged templates are of identical sequence, but in a number of special cases bridging creates, or, destroys, information.

A solution-phase combinatorial synthesis of selective dopamine D4 ligands.

Utilizing combinatorial synthesis and a preparative LC-MS automated chromatography system we have prepared and purified a library of 4-[2-(1,2,4-oxadiazolyl)]piperidines that were designed to be novel and selective dopamine D4 ligands. In one round of synthesis we identified N-4-chlorobenzyl-4-[2-(3-(2-thienyl)-1,2, 4-oxadiazolyl)]piperidine with a Kd of 5 nM for the human D4 receptor.

DNA Yields and Optimization of RAPD Patterns Using Spruce Embryogenic Lines, Seedlings, and Needles

Genetic analysis of plants relies on high yields of pure DNA samples. In conifers, such DNA samples are usually derived from tissue cultures. However, it is labourious to use embryogenic cultures for projects that require large sample numbers because the starting material has to be initiated from the seed in vitro. As an alternative, we have used seedlings as source material for DNA extraction and have obtained yields and purities comparable to embryogenic cultures. RAPD profiles obtained with DNA from embryogenic cultures and seedlings were similar and highly reproducible. Efficient and consistent amplification was achieved using primer concentrations ranging from 1.6 and 6.4 μM with 0.1 to 1.0 μg of template DNA. The intensity and resolution of faint bands resulting from non-optimized conditions were easily improved through further rounds of synthesis in a fresh PCR with amplified DNA diluted 500-fold.

Inhibition of the 26 S Proteasome by Polyubiquitin Chains Synthesized to Have Defined Lengths

Ubiquitin is a covalent signal that targets cellular proteins to the 26 S proteasome. Multiple ubiquitins can be ligated together through the formation of isopeptide bonds between Lys48 and Gly76 of successive ubiquitins. Such a polyubiquitin chain constitutes a highly effective proteolytic targeting signal, but its mode of interaction with the proteasome is not well understood. Experiments to address this issue have been limited by difficulties in preparing useful quantities of polyubiquitin chains of uniform length. We report a simple method for large scale synthesis of Lys48-linked polyubiquitin chains of defined length. In the first round of synthesis, two ubiquitin derivatives (K48C-ubiquitin and Asp77-ubiquitin) were used as substrates for the well characterized ubiquitin-conjugating enzyme E2-25K. Diubiquitin blocked at the nascent proximal and distal chain termini was obtained in quantitative yield. Appropriately deblocked chains were then combined to synthesize higher order chains (tetramer and octamer in the present study). Deblocking was achieved either enzymatically (proximal terminus) or by chemical alkylation (distal terminus). Chains synthesized by this method were used to obtain the first quantitative information concerning the influence of polyubiquitin chain length on binding to the 26 S proteasome; this was done through comparison of different length (unanchored) polyubiquitin chains as inhibitors of ubiquitin-conjugate degradation. K0.5 was found to decrease approximately 90-fold, from 430 to 4.8 microM, as the chain was lengthened from two to eight ubiquitins. The implications of these results for the molecular basis of chain recognition are discussed.

In vitro expansion of GGC:GCC repeats: identification of the preferred strand of expansion.

The human fragile-X syndrome, a major cause of inherited mental retardation, is associated with expansion of the trinucleotide repeat GGC:GCC. Repetitive sequences in DNA are subject to slippage during catalysis by DNA polymerases. We characterized the extent of slippage of synthetic GGC:GCC repeats by various DNA polymerases: Taq DNA polymerase, Klenow fragment of DNA polymerase I, DNA Sequence, DNA polymerase-alpha and polymerase-beta, as well as HIV reverse transcriptase. All of these enzymes were found to expand GGC:GCC repeats, with the most extensive expansion exhibited by Taq DNA polymerase. Starting with a template and primer, each 15 nucleotides (nt) in length, the product of one round of synthesis by Taq polymerase is as long as 250 nt. Sequence analysis of cloned DNA fragments expanded by Taq polymerase indicates that expansion involves multiple triplet additions and that it is asymmetric. The asymmetric distribution of terminal nucleotides in the expanded product is consistent with active expansion of the GCC strand and passive additions onto the GGC strand. The preferential elongation and expansion of the GCC strand was confirmed in studies utilizing longer repeats within a single-stranded M-13 template.

Coordinating DNA Replication To Produce One Copy of the Genome Requires Genes That Act in Ubiquitin Metabolism

We have developed a genetic screen of the yeast Saccharomyces cerevisiae to identify genes that act to coordinate DNA replication so that each part of the genome is copied exactly once per cell cycle. A mutant was recovered in this screen that accumulates aberrantly high DNA contents but does not complete a second round of synthesis. The mutation principally responsible for this phenotype is in the DOA4 gene, which encodes a ubiquitin hydrolase, one of several yeast genes that encode enzymes that can remove the signalling polypeptide ubiquitin hydrolase, one of several yeast genes that encode enzymes that can remove the signaling polypeptide ubiquitin from its covalently linked conjugated forms. DOA4 is nonessential, and deleting this gene causes uncoordinated replication. Overreplication does not occur in cells with limiting amounts of Cdc7 protein kinase, suggesting that entry into S phase is required for this phenotype. The DNA formed in doa4 mutants is not highly unusual in the sense that mitotic recombination rates are normal, implying that a high level of repair is not induced. The temperature sensitivity of doa4 mutations is partially suppressed by extra copies of the polyubiquitin gene UB14, but overreplication still occurs in the presence of this suppressor. Mutations in DOA4 cause loss of the free ubiquitin pool in cells under heat stress conditions, and extra copies of UB14 restore this pool without restoring coordination of replication. We conclude that a ubiquitin-mediated signaling event directly involving the ubiquitin hydrolase encoded by DOA4 is needed in S. cerevisiae to prevent uncoordinated DNA replication.

Polymerase chain reaction.

The melding of a technique for repeated rounds of DNA synthesis with the discovery of a thermostable DNA polymerase has given scientists the very powerful technique known as polymerase chain reaction (PCR). PCR is based on three simple steps required for any DNA synthesis reaction: (1) denaturation of the template into single strands; (2) annealing of primers to each original strand for new strand synthesis; and (3) extension of the new DNA strands from the primers. These reactions may be carried out with any DNA polymerase and result in the synthesis of defined portions of the original DNA sequence. However, in order to achieve more than one round of synthesis, the templates must again be denatured, which requires temperatures well above those that inactivate most enzymes. Therefore, initial attempts at cyclic DNA synthesis were carried out by adding fresh polymerase after each denaturation step (,). The cost of such a protocol becomes rapidly prohibitive.

Simple Methods for Preparing Oligonucleotides Containing 1) Thiol Groups at their 5′-Termini, 2) 5′-Phosphates

Abstract A simple method has been developed for synthesising oligonucleotides containing a thiol group at their 5′-termini. The sequence required is prepared using standard solid phase phosphoramidite methods and an extra round of synthesis is then performed with S-triphenylmethyl O-methoxymorpholino-phosphinyl 3-mercaptopropan (1) ol. After normal deblocking this gives an oligonucleotide containing a tritylthiol group attached to the 5′-phosphate of an oligonucleotide via a 3-carbon spacer arm. The trityl group can be removed with AgNO3 at pH 5 to give the free thiol. This compound is stable at pH 8 and reacts cleanly and rapidly with sulphydryl specific probes (eg fluorescent iodoacetates) at this pH value. This method can be used to prepare a wide variety of usefully labelled oligonucleotides and it is envisaged that fluorescent oligonucleotides will be useful in the study of protein nucleic acid interactions and to replace 32P labelled hybridisation probes.