Enantioselective α-Silyl Amino Acid Synthesis by Reverse-Aza-Brook Rearrangement

Asymmetric reverse-aza-Brook rearrangement of N-Boc-N-trialkylsilyl allylamine yields an enantiomerically enriched α-amino allylsilane. Oxidative cleavage of the alkene leads to a Boc-protected amino acid with the configuration of naturally occurring amino acids (l). Standard coupling protocols, including the use of trifluoroacetic acid for removal of the Boc group, yield a tripeptide with a central silane amino acid

α-Trialkylsilyl Amino Acid Stability

α-Trialkylsilyl amino acids have been evaluated for their stability toward methanolysis as a model for physiological conditions. The juxtaposition of amine and carbonyl groups significantly destabilizes the silicon−carbon bond, but changing a single methyl on silicon to an ethyl led to a dramatic stability enhancement. Converting the ester to an amide gave an additional jump in stability, suggesting broad potential for these novel amino acids in bioactive peptides and pharmaceuticals

Image2_Collection and Curation of Transcriptional Regulatory Interactions in Aspergillus nidulans and Neurospora crassa Reveal Structural and Evolutionary Features of the Regulatory Networks.PDF

Transcriptional regulation has important roles in various biological processes (e.g., development and metabolism) in filamentous fungi. However, regulatory interactions between transcription factors (TFs) and their target genes in these species have only been described in different forms by primary scientific literature, which limits the integrated analysis of these data. Here, we extensively curated the reported transcriptional regulatory interactions in Aspergillus nidulans and Neurospora crassa. For each interaction, the identifiers of involved proteins or genes were unified, and the types of supporting experiments were recorded. Then, transcriptional regulatory networks were reconstructed from the interactions supported by classical low-throughput experiments. Analysis of the networks revealed the presence of hub targets regulated by multiple TFs and network motifs of other structures (e.g., regulatory loops). Comparison of the regulatory interactions between the two species identified 33 conserved interactions supported by classical experiments in both species, most of which are involved in the regulation of metabolic genes. We anticipate the curated data would serve as a catalog for the studies of transcriptional regulation in filamentous fungi.</p

Image1_Collection and Curation of Transcriptional Regulatory Interactions in Aspergillus nidulans and Neurospora crassa Reveal Structural and Evolutionary Features of the Regulatory Networks.TIF

Transcriptional regulation has important roles in various biological processes (e.g., development and metabolism) in filamentous fungi. However, regulatory interactions between transcription factors (TFs) and their target genes in these species have only been described in different forms by primary scientific literature, which limits the integrated analysis of these data. Here, we extensively curated the reported transcriptional regulatory interactions in Aspergillus nidulans and Neurospora crassa. For each interaction, the identifiers of involved proteins or genes were unified, and the types of supporting experiments were recorded. Then, transcriptional regulatory networks were reconstructed from the interactions supported by classical low-throughput experiments. Analysis of the networks revealed the presence of hub targets regulated by multiple TFs and network motifs of other structures (e.g., regulatory loops). Comparison of the regulatory interactions between the two species identified 33 conserved interactions supported by classical experiments in both species, most of which are involved in the regulation of metabolic genes. We anticipate the curated data would serve as a catalog for the studies of transcriptional regulation in filamentous fungi.</p

Indium Microrod Tags for Electrochemical Detection of DNA Hybridization

The preparation and advantages of indium microrod tracers for solid-state electrochemical detection of DNA hybridization are described. The cylindrical metal particles were prepared by a template-directed electrochemical synthetic route involving plating of indium into the pores of a host membrane. The linear relationship between the charge passed during the preparation and the resulting particle size allows tailoring of the sensitivity of the electrical DNA assay. The resulting micrometer-long rods thus offer a greatly lower detection limit (250 zmol), as compared to common bioassays' spherical nanoparticle tags. Indium offers a very attractive electrochemical stripping behavior and is not normally present in biological samples or reagents. Solid-state derivative-chronopotentiometric measurements of the indium tracer have been realized through a “magnetic” collection of the DNA-linked particle assembly onto a thick-film electrode transducer. Factors affecting the performance, including the preparation of the microrods and pretreatment of the transducer surface, were evaluated and optimized. The resulting protocol offers great promise for other affinity bioassays, as well as for electrical coding and identification (through the plating of different metal markers and of multimetal redox-encoded tags)

Image3_Collection and Curation of Transcriptional Regulatory Interactions in Aspergillus nidulans and Neurospora crassa Reveal Structural and Evolutionary Features of the Regulatory Networks.TIF

Transcriptional regulation has important roles in various biological processes (e.g., development and metabolism) in filamentous fungi. However, regulatory interactions between transcription factors (TFs) and their target genes in these species have only been described in different forms by primary scientific literature, which limits the integrated analysis of these data. Here, we extensively curated the reported transcriptional regulatory interactions in Aspergillus nidulans and Neurospora crassa. For each interaction, the identifiers of involved proteins or genes were unified, and the types of supporting experiments were recorded. Then, transcriptional regulatory networks were reconstructed from the interactions supported by classical low-throughput experiments. Analysis of the networks revealed the presence of hub targets regulated by multiple TFs and network motifs of other structures (e.g., regulatory loops). Comparison of the regulatory interactions between the two species identified 33 conserved interactions supported by classical experiments in both species, most of which are involved in the regulation of metabolic genes. We anticipate the curated data would serve as a catalog for the studies of transcriptional regulation in filamentous fungi.</p

Table2_Collection and Curation of Transcriptional Regulatory Interactions in Aspergillus nidulans and Neurospora crassa Reveal Structural and Evolutionary Features of the Regulatory Networks.XLSX

Transcriptional regulation has important roles in various biological processes (e.g., development and metabolism) in filamentous fungi. However, regulatory interactions between transcription factors (TFs) and their target genes in these species have only been described in different forms by primary scientific literature, which limits the integrated analysis of these data. Here, we extensively curated the reported transcriptional regulatory interactions in Aspergillus nidulans and Neurospora crassa. For each interaction, the identifiers of involved proteins or genes were unified, and the types of supporting experiments were recorded. Then, transcriptional regulatory networks were reconstructed from the interactions supported by classical low-throughput experiments. Analysis of the networks revealed the presence of hub targets regulated by multiple TFs and network motifs of other structures (e.g., regulatory loops). Comparison of the regulatory interactions between the two species identified 33 conserved interactions supported by classical experiments in both species, most of which are involved in the regulation of metabolic genes. We anticipate the curated data would serve as a catalog for the studies of transcriptional regulation in filamentous fungi.</p

Ultrasensitive Electrical Biosensing of Proteins and DNA: Carbon-Nanotube Derived Amplification of the Recognition and Transduction Events

A new strategy for dramatically amplifying enzyme-linked electrical detection of proteins and DNA using carbon nanotubes (CNTs) for carrying numerous enzyme tracers and accumulating the enzymatically liberated product on CNT-modified transducer is described. Such a CNT-derived double-step amplification pathway (of both the recognition and transduction events) allows the detection of DNA and proteins down to 1.3 and 160 zmol, respectively, in 25−50 μL samples and indicates great promise for PCR-free DNA analysis. The new protocol is illustrated for monitoring sandwich hybridization and antibody−antigen interactions in connection with alkaline-phosphatase tracers. The DNA-linking of CNTs and particles holds promise also for assembling hybrid nanostructures relevant to molecular electronic devices

Electrochemical Coding Technology for Simultaneous Detection of Multiple DNA Targets

Nucleic-acid hybridization assays based on the use of different inorganic-colloid (quantum dots) nanocrystal tracers for the simultaneous electrochemical measurements of multiple DNA targets are described. Three encoding nanoparticles (zinc sulfide, cadmium sulfide, and lead sulfide) are used to differentiate the signals of three DNA targets in connection to stripping-voltammetric measurements of the heavy metal dissolution products. These products yield well-defined and resolved stripping peaks at −1.12 V (Zn), −0.68 V (Cd), and −0.53 V (Pb) at the mercury-coated glassy-carbon electrode (vs Ag/AgCl reference). The position and size of these peaks reflect the identity and level of the corresponding DNA target. The multi-target detection capability is coupled to the amplification feature of stripping voltammetry (to yield femtomole detection limits) and with an efficient magnetic removal of nonhybridized nucleic acids to offer high sensitivity and selectivity. The protocol is illustrated for the simultaneous detection of three DNA sequences related to the BCRA1 breast-cancer gene in a single sample in connection to magnetic beads bearing the corresponding oligonucleotide probes. The new electrochemical coding is expected to bring new capabilities for DNA diagnostics, and for bioanalysis, in general

Hydrogen-Bonding Catalysis and Inhibition by Simple Solvents in the Stereoselective Kinetic Epoxide-Opening Spirocyclization of Glycal Epoxides to Form Spiroketals

Mechanistic investigations of a MeOH-induced kinetic epoxide-opening spirocyclization of glycal epoxides have revealed dramatic, specific roles for simple solvents in hydrogen-bonding catalysis of this reaction to form spiroketal products stereoselectively with inversion of configuration at the anomeric carbon. A series of electronically tuned C1-aryl glycal epoxides was used to study the mechanism of this reaction based on differential reaction rates and inherent preferences for SN2 versus SN1 reaction manifolds. Hammett analysis of reaction kinetics with these substrates is consistent with an SN2 or SN2-like mechanism (ρ = −1.3 vs ρ = –5.1 for corresponding SN1 reactions of these substrates). Notably, the spirocyclization reaction is second-order dependent on MeOH, and the glycal ring oxygen is required for second-order MeOH catalysis. However, acetone cosolvent is a first-order inhibitor of the reaction. A transition state consistent with the experimental data is proposed in which one equivalent of MeOH activates the epoxide electrophile via a hydrogen bond while a second equivalent of MeOH chelates the side-chain nucleophile and glycal ring oxygen. A paradoxical previous observation that decreased MeOH concentration leads to increased competing intermolecular methyl glycoside formation is resolved by the finding that this side reaction is only first-order dependent on MeOH. This study highlights the unusual abilities of simple solvents to act as hydrogen-bonding catalysts and inhibitors in epoxide-opening reactions, providing both stereoselectivity and discrimination between competing reaction manifolds. This spirocyclization reaction provides efficient, stereocontrolled access to spiroketals that are key structural motifs in natural products