Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers

In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a “DNA Aptaomics” approach to systematically design functional aptamers as well as to obtain high affinity aptamers.     

Synthesis of acryloyl-type polymer fixing 5-fluorouracil residues through D-glucofuranoses and its antitumor activity

Acryloyl-type polymer fixing 1-β-carbonylethyl-5-fluorouracil residues through D -glucofuranoses via ester bonds was synthesized by means of polymerization of the corresponding monomer and polymer reaction. In order to provide the water-soluble objective polymer, the copolymerization of the acryloyl-type monomer with acrylamide was carried out. The extent of release of 5-FU residues from the copolymer was investigated in the enzyme or nonenzyme system in vitro. Furthermore, the antitumor activities of the water-insoluble homopolymer and water-soluble copolymer obtained were tested in vivo.     

Polymeric organosilicon systems. XVII. Synthesis and photochemical and conducting properties of poly[o-and m-(disilanylene)phenylene]s

Poly[o-(tetramethyldisilanylene)phenylene] ( 2a ), poly[o-(1,2-dimethyldiphenyldisilanylene)-phenylene] ( 2b ), poly[m-(tetramethyldisilanylene)phenylene] ( 2c ), and poly[m-(1,2-dimethyldiphenyldisilanylene)phenylene] ( 2d ) were prepared by the sodium condensation reaction of the corresponding 1,2-and 1,3-bis (chlorosilyl)benzenes in toluene. Irradiation of thin films of 2a-2d in air resulted in a rapid decrease of absorption maxima in the ultraviolet region. The photolysis of 2b and 2d in benzene afforded photodegradation products with low molecular weights. When thin films of 2b and 2d were doped with antimony pentafluoride vapor, films which have conductivities of semi-conductor level were obtained. © 1993 John Wiley & Sons, Inc.     

Intramolecular triplet energy transfer via higher triplet excited state during stepwise two-color two-laser irradiation

We studied the energy transfer processes in the molecular array consisting of pyrene (Py), biphenyl (Ph2), and bisphthalimidethiophene (ImT), (Py-Ph2)2-ImT, during two-color two-laser flash photolysis (2-LFP). The first laser irradiation predominantly generates ImT in the lowest triplet excited state (ImT(T1)) because of the efficient singlet energy transfer from Py in the lowest singlet excited state to ImT and, then, intersystem crossing of ImT. ImT(T1) was excited to the higher triplet excited state (Tn) with the second laser irradiation. Then, the triplet energy was rapidly transferred to Py via a two-step triplet energy transfer (TET) process through Ph2. The efficient generation of Py(T1) was suggested from the nanosecond-picosecond 2-LFP. The back-TET from Py(T1) to ImT was observed for several tens of microseconds after the second laser irradiation. The estimated intramolecular TET rate from Py(T1) to ImT was as slow as 3.1 x 104 s-1. Hence, long-lived Py(T1) was selectively and efficiently produced during the 2-LFP.     

Designed self-assembly of molecular necklaces

This paper reports an efficient strategy to synthesize molecular necklaces, in which a number of small rings are threaded onto a large ring, utilizing the principles of self-assembly and coordination chemistry. Our strategy involves (1) threading a molecular "bead" with a short "string" to make a pseudorotaxane and then (2) linking the pseudorotaxanes with a metal complex with two cis labile ligands acting as an "angle connector" to form a cyclic product (molecular necklace). A 4- or 3-pyridylmethyl group is attached to each end of 1,4-diaminobutane or 1,5-diaminopentane to produce the short "strings" (C4N4(2+), C4N3(2+), C5N4(2+), and C5N3(2+)), which then react with a cucurbituril (CB) "bead" to form stable pseudorotaxanes (PR44(2+), PR43(2+), PR54(2+), and PR53(2+), respectively). The reaction of the pseudorotaxanes with Pt(en)(NO(3))(2) (en = ethylenediamine) produces a molecular necklace [4]MN, in which three molecular "beads" are threaded on a triangular framework, and/or a molecular necklace [5]MN, in which four molecular "beads" are threaded on a square framework. Under refluxing conditions, the reaction with PR44(2+) or PR54(2+) yields exclusively [4]MN (MN44T or MN54T, respectively), whereas that with PR43(2+) or PR53(2+) produces exclusively [5]MN (MN43S or MN53S, respectively). The products have been characterized by various methods including X-ray crystallography. At lower temperatures, on the other hand, the reaction with PR44(2+) or PR54(2+) affords both [4]MN and [5]MN. The supermolecules reported here are the first series of molecular necklaces obtained as thermodynamic products. The overall structures of the molecular necklaces are strongly influenced by the structures of pseudorotaxane building blocks, which is discussed in detail on the basis of the X-ray crystal structures. The temperature dependence of the product distribution observed in this self-assembly process is also discussed.     

New mu-opioid receptor agonists with phenoxyacetic acid moiety

New muq-opioid receptor (MOR) agonists containing 4-hydroxypiperidine, piperidine and piperazine moieties were synthesized and evaluated to find a peripheral opioid analgesic. Among the synthesized compounds, 12-[1-[3-(N,N-dimethylcarbamoyl)-3,3-diphenylpropyl]-4-hydroxypiperidin-4-yl]phenoxy]acetic acid (8: SS620) having phenoxyacetic acid and 4-hydroxypiperidine moieties showed the highest agonist potency on the MOR in an isolated guinea-pig ileum preparation, and it also had selectivity to the human MOR expressed in Chinese hamster ovary (CHO)-K1 cells compared with the same types of delta- and kappa-opioid receptors (DOR and KOR). In addition, compound 8 showed a 10 times more potent MOR agonist activity than loperamide. Furthermore, compound 8 showed a peripheral analgesic activity in vivo screening on rat.     

A novel [60]fullerene receptor with a Pd(II)-switched bisporphyrin cleft

Porphyrin dimer 1, which does not have an inside cavity and cannot interact with [60]fullerene (C60), becomes an excellent C60-acceptor with a large cavity in the presence of a Pd(II) complex.     

Nucleophilic addition reaction of 2-trimethylsilyloxyfuran to N-gulosyl-C-alkoxymethylnitrones: synthetic approach to polyoxin C

[reaction: see text] The stereoselectivity of nucleophilic addition of 2-trimethylsilyloxyfuran to N-gulosyl-C-alkoxymethylnitrones was investigated. It was found that the selectivity was highly dependent on the bulkiness of the C-substituent of the nitrone. The major adducts were elaborated into the key intermediate of polyoxin C.     

Orientation of iron bleomycin and porphyrin complexes on DNA fibers

Bleomycin (Blm) is an antitumor agent that requires iron and oxygen for strand cleavage of DNA. In this study, ferric bleomycin, Fe(III)Blm, or the nitric oxide adduct of ferrous bleomycin, ON-Fe(II)Blm, were bound to one-dimensionally oriented DNA fibers. Reductive nitrosylation of Fe(III) complexes took place in situ on B-form DNA fibers. Electron paramagnetic resonance (EPR) spectra were obtained as a function of the angle phi between the magnetic field B and the fiber axis Zf. For comparison, EPR spectra were acquired for ON-Fe(II)TMpyP and ON-Fe(II)TMpyP-Im on oriented DNA fibers, where TMpyP is 5,10,15,20-tetrakis(1-methyl-4-pyridino)porphyrin and Im is imidazole. EPR spectra showed both low-spin Fe(III)Blm and ON-Fe(II)Blm bound to B-form DNA in two slightly different binding orientations in the ratio of 1:0.2. With A-form DNA, a fraction of bound Fe(III)Blm was high spin. Specifically, the angle beta between the fiber axis Zf and the g axis, gz, perpendicular to or nearly perpendicular to the equatorial plane of the iron complex was estimated as 20 degrees and 25 degrees for ON-Fe(II)Blm and 30 degrees and 25 degrees for Fe(III)Blm, respectively. The angle gamma that determines the orientation of gx and gy axes was estimated as 90 degrees for the two ON-Fe(II)Blm species and 10 degrees for the two Fe(III)Blm species, respectively. The NO was held rigidly in place as the temperature increased from 123 K to room temperature for ON-Fe(II)Blm but not for ON-Fe(II)TMpyP or ON-Fe(II)TMpyP-Im. It is hypothesized that the NO is structurally oriented by hydrogen bonding like the peroxide is held in HO2(-)-Co(III)Blm (Wu et al. J. Am. Chem. Soc. 1996, 118, 1281-1294). The EPR parameters are consistent with a six-coordinate complex for ON-Fe(II)Blm, although the superhyperfine structure from the trans nitrogen was not detected. The increase in g value anisotropy upon binding ON-Fe(II)Blm to DNA fiber may be caused by an increase in the overlap of d pi and 2p pi* orbitals induced by an interaction of NO with DNA and/or by a perturbation of d orbitals due to the pyrimidine-guanine interaction. It is concluded that the EPR parameters of ON-Fe(II)Blm and Fe(III)Blm bound to oriented DNA support the hypothesis that FeBlm species bind to DNA with adduct structures similar to those formed by related CoBlm species and DNA.     

Polymer support assisted selective functionalization of azoles using a palladium-catalyzed coupling reaction

Regioselective palladium-catalyzed monoarylation of azoles was achieved using iodobenzoate immobilized on an insoluble polymer support. The positional selectivity for the coupling reaction was dramatically influenced by the presence of CuI. No diarylation was observed in either case. Unsymmetrical diarylation was also obtained with the polymer support using sequential coupling reactions.