Concise synthesis of dl-febrifugine

Racemic compound (1) of the antimalarial agents febrifugine (d-1) was synthesized using an stereoselective Michael reaction of an omega-amidoenone (5) which was prepared by the Wittig reaction of piperidinediol (7).     

Direct construction of bicyclic heterocycles by palladium-catalyzed domino cyclization of propargyl bromides

The palladium-catalyzed domino cyclization of propargyl bromides having two nucleophilic functional groups is described. Treatment of 1,7-diamino-5-bromohept-3-yne derivatives with catalytic Pd(PPh3)4 in the presence of NaH in MeOH gives the 2,7-diazabicyclo[4.3.0]non-5-enes in good yields. Interestingly, the regioselectivity of the reaction is completely controlled by the relative reactivity of the amine functional groups, irrespective of the position of the nucleophiles. The malonate derivative also undergoes domino cyclization to produce a hexahydroindole derivative.     

Palladium(0)-catalyzed synthesis of medium-sized heterocycles by using bromoallenes as an allyl dication equivalent

We have developed a highly regio- and stereoselective synthesis of medium-sized heterocycles containing one or two heteroatoms via cyclization of bromoallenes bearing an oxygen, nitrogen, or carbon nucleophilic functionality in the presence of a palladium(0) catalyst and alcohol. In this reaction, bromoallenes act as an allyl dication equivalent, and the intramolecular nucleophilic attack takes place exclusively at the central carbon atom of the allene moiety. Interestingly, bromoallenes having a carbon nucleophile with a five-atom tether afford eight-membered rings with trans-configuration, while those having an oxygen or a nitrogen nucleophile give the corresponding cis-rings selectively. This is the first example that demonstrates the synthesis of medium-sized rings via cyclization of bromoallenes, and this reaction provides a very useful method for a catalytic synthesis of seven- and eight-membered heterocycles without using high dilution conditions.     

Synthesis of febrifugine derivatives and a solution to the puzzle of the structural determination of febrifugine

The stereo-structure of piperidine lactone (3), a synthetic intermediate of the antimalarial agent febrifugine ((+)-1) with a piperidine ring in the trans relative configuration, was re-revised to the cis-form. We determined that isomerization to the trans-form from the cis-form occurred in the stage (6 from 5) of deprotection in Baker's synthesis.     

Comparative study of urea and betaine solutions by dielectric spectroscopy: liquid structures of a protein denaturant and stabilizer

We performed dielectric spectroscopy measurements on aqueous solutions of glycine betaine (N,N,N-trimethylglycine), which is known to be a strong stabilizer of globular proteins, over a wide concentration range (3-62 wt %) and compared the results with our previously published data for aqueous solutions of urea, a representative protein denaturant. The hydration number of betaine (9), calculated on the basis of the reduction in the dielectric relaxation strength of bulk water with addition of betaine, is significantly larger than that of urea (2). Furthermore, the dielectric relaxation time increased with betaine concentration, while that remained nearly constant for the urea-water system over a wide concentration range. This difference between urea and betaine is probably related to their opposite effects on the protein stabilization.     

Direct Observation Method of Individual Single-Stranded DNA Molecules Using Fluorescent Replication Protein A

Direct observation studies of single molecules have revealed molecular behaviors usually hidden in the ensemble and time-averaging of bulk experiments. Direct single DNA molecule analysis of DNA metabolism reactions such as DNA replication, repair, and recombination is necessary to fully understand these essential processes. Intercalation of fluorescent dyes such as YOYO-1 and SYTOX Orange has been the standard method for observing single molecules of double-stranded DNA (dsDNA), but effective fluorescent dyes for observing single molecules of single-stranded DNA (ssDNA) have not been found. To facilitate direct single-molecule observations of DNA metabolism reactions, it is necessary to establish methods for discriminating ssDNA and dsDNA. To observe ssDNA directly, we prepared a fusion protein consisting of the 70 kDa DNA-binding domain of replication protein A and enhanced yellow fluorescent protein (RPA-YFP). This fusion protein had ssDNA-binding activity. In our experiments, dsDNA was stained by SYTOX Orange and ssDNA by RPA-YFP, and we succeeded in staining ssDNA and dsDNA by using RPA-YFP and SYTOX Orange simultaneously.     

Direct Observation of Fluorescently Labeled Single-stranded λDNA Molecules in a Micro-Flow Channel

We developed two labeling methods for the direct observation of single-stranded DNA (ssDNA), using a ssDNA binding protein and a ssDNA recognition peptide. The first approach involved protein fusion between the 70-kDa ssDNA-binding domain of replication protein A and enhanced yellow fluorescent protein (RPA-YFP). The second method used the ssDNA binding peptide of Escherichia coli RecA labeled with Atto488 (ssBP-488; Atto488-IRMKIGVMFGNPETTTGGNALKFY). The labeled ssλDNA molecules were visualized over time in micro-flow channels. We report substantially different dynamics between these two labeling methods. When ssλDNA molecules were labeled with RPA-YFP, terminally bound fusion proteins were sheared from the free ends of the ssλDNA molecules unless 25-mer oligonucleotides were annealed to the free ends. RPA-YFP-ssλDNA complexes were dissociated by the addition of 0.2 M NaCl, although complex reassembly was possible with injection of additional RPA-YFP. In contrast to the flexible dynamics of RPA-YFP-ssλDNA complexes, the ssBP-488-ssλDNA complexes behaved as rigid rods and were not dissociated even in 2 M NaCl.