Structure-activity relationship study of nitrogen signaling factors.

We have synthesized 10 analogs of oxylipins, which are nitrogen signaling factors (NSFs) that mediate cell-to-cell communication in the fission yeast Schizosaccharomyces pombe, and evaluated their structure-activity relationships with the aim of developing molecular probes for NSFs. We found that the OH or OAc group at C10 could be replaced with a compact amide (17) or carbamate (19). Introducing an alkyne as a detection tag at C10 led to decreased, though still sufficient, activity. Introducing an alkyne at the C18 position showed a similar trend, suggesting tolerance is relatively low even for compact functional groups such as alkynes. Although introduction of a diazirine moiety as a photoreactive group at the C5 position decreased the activity, we found that introducing diazirine at the C13 position was acceptable, and compound 38 exhibited potent NSF activity. These findings will be helpful in the development of molecular probes for NSFs.

Design and synthesis of an environment-sensitive 3-methyleneisoindolin-1-one fluorophore for labeling DNA-interacting proteins.

We designed 6-dimethylamino 3-methyleneisoindolin-1-one as an environment-sensitive fluorophore, examining its applications for protein labeling. Synthesized 3-methyleneisoindolin-1-one exhibits solvatochromic fluorescence (λemmax; 472 nm in 2-PrOH, 512 nm in H2O). A positive linear dependence between λemmax and solvent dielectric constant (DC), as well as between Stokes shift and DC, and a negative correlation between fluorescence quantum yield and DC are observed in protic solvents. These properties are similar to those of the oxygen isosteric fluorophore, 4-dimethylaminophthalimide, a slovatochromic fluorophore utilized for labeling oligodeoxynucleotides (ODNs) and peptides. Notably, fluorescence intensity of 3-methyleneisoindolin-1-one is higher than the phthalimide in protic solvents used in this study. The 3-methyleneisoindolin-1-one demonstrated the higher stability in pH 8 solution than in pH 6 solution in contrast to the stability profile of the phthalimide, which was stable at pH 6 but was hydrolyzed at pH 8. We also synthesized an o-keto benzaldehyde derivative that converts a primary amine to 6-dimethylamino 3-methyleneisoindolin-1-one under biocompatible conditions and introduced it into ODNs for turn-on fluorescent protein labeling. The synthesized ODN with a protein-binding sequence of Escherichia coli DnaA was employed to modify the DNA-binding domain of DnaA, and the fluorescent properties of the modified protein were investigated.

7-Hydroxy-3-methyleneisoindolin-1-one as a New ESIPT-Fluorescent Probe to Monitor Aqueous Environments.

A 7-hydroxy derivative of 3-methyleneisoindolin-1-one 1 was synthesized and its properties as a new fluorophore undergoing excited-state intramolecular proton transfer (ESIPT) were investigated. In alcohols and dimethylsulfoxide, 1 exhibited dual emission at ca. 380 and 525-540 nm when excited at ca. 336 nm, which agreed well with the density functional theory (DFT) and time-dependent (TD)-DFT-calculated emission predictions of 1 and its ESIPT tautomer. In aqueous solutions at near neutral pH, 1 exhibited a broad emission band at ca. 497 nm, presumably caused by the overlap of emissions from 1 and the excited state phenolate species of 1. In binary mixtures of H2O and EtOH, the wavelength and intensity of fluorescence maxima were dependent on the dielectric constant of the solvent, suggesting that 1 could be applied as a fluorescent probe to monitor aqueous environments.

Synthesis and Electron Paramagnetic Resonance Studies of Oligodeoxynucleotides Containing 2-N-tert-Butylaminoxyl-2'-deoxyadenosines.

Oligodeoxynucleotides (ODNs) containing 2-N-tert-butylaminoxyl-2'-deoxyadenosine (A*) residues were synthesized to allow accurate monitoring of adenine motion by EPR spectroscopy through the agency of direct linkage of the acyclic aminoxyl group to the nucleobase, and EPR studies of the ODNs in single- and double-stranded forms were performed. Upon duplex formation, peak broadening and decreases in peak height were observed in EPR spectra, and the synthesized ODNs were shown to be excellent monitors of hybridization. Comparison of peak height and the h1 /h0 signal ratio provided information on the relative mobility of A* in duplexes with different stability. A second set of ODNs each containing two A* residues at different intervals and four dA residues were also synthesized. For these ODNs, correlations were observed between the EPR spectral shapes of the duplexes and the number of dA residues between A* residues, thus demonstrating the potential of A* residues in monitoring of the structures of nucleic acids.

Bioconjugation of Oligodeoxynucleotides Carrying 1,4-Dicarbonyl Groups via Reductive Amination with Lysine Residues.

We evaluated the efficacy of bioconjugation of oligodeoxynucleotides (ODNs) containing 1,4-dicarbonyl groups, a C4'-oxidized abasic site (OAS), and a newly designed 2'-methoxy analogue, via reductive amination with lysine residues. Dicarbonyls, aldehyde and ketone at C1- and C4-positions of deoxyribose in the ring-opened form of OAS allowed efficient reaction with amines. Kinetic studies indicated that reductive amination of OAS-containing ODNs with a proximal amine on the complementary strand proceeded 10 times faster than the corresponding reaction of an ODN containing an abasic site with C1-aldehyde. Efficient reductive amination between the DNA-binding domain of Escherichia coli DnaA protein and ODNs carrying OAS in the DnaA-binding sequence proceeded at the lysine residue in proximity to the phosphate group at the 5'-position of the OAS, in contrast to unsuccessful conjugation with abasic site ODNs, even though they have similar aldehydes. Theoretical calculation indicated that the C1-aldehyde of OAS was more accessible to the target lysine than that of the abasic site. These results demonstrate the potential utility of cross-linking strategies that use dicarbonyl-containing ODNs for the study of protein-nucleic acid interactions. Conjugation with a lysine-containing peptide that lacked specific affinity for ODN was also successful, further highlighting the advantages of 1,4-dicarbonyls.

Dialkyl bisphosphonate platinum(II) complex as a potential drug for metastatic bone tumor.

Bisphosphonates have high affinity for hydroxyapatite (HA), which is abundantly present in bone. Also, platinum complexes are known that have a wide spectrum of antitumor activities. The conjugate of bisphosphonate and a platinum complex might have HA affinity and antitumor activity, and become a drug for metastatic bone tumor. In this study, the authors synthesized platinum complexes that had dialkyl bisphosphonic acid as a ligand, and evaluated the possibility of the synthesized complexes as a drug for metastatic bone tumor. The synthesized dialkyl bisphosphonate platinum(II) complex was characterized, and its stability in an aqueous solution was also confirmed. The synthesized platinum complex showed higher HA affinity than other platinum complexes such as cisplatin and carboplatin in an experiment of adsorption to HA. In vitro, the platinum complex showed tumor growth inhibitory effect stronger than or equal to cisplatin, which is the most commonly used antitumor agent. Moreover, the platinum complex showed a bone absorption inhibitory effect on the osteoclast. These results suggest potential of dialkyl bisphosphonate platinum(II) complexes as a drug for metastatic bone tumor.

Water-proton relaxivities of DNA oligomers carrying TEMPO radicals.

5-Uridine derivative carrying a TEMPO radical (UST) was prepared and its single strand (ssUST) and a double strand (dsUST) with its complementary strand were obtained. Similarly, single strands carrying two and five radicals (ssUST2 and ssUST5, respectively) and the corresponding double strands (dsUST2 and dsUST5) were prepared. Their electron paramagnetic resonance (EPR) spectra showed typical anisotropic broadening in the high field line. The rotational correlation times, tau(R), estimated by analyzing the EPR spectra are 1.1 x 10(-10), 5.9 x 10(-10), and 14 x 10(-10) s for UST, ssUSTm, and dsUSTm, respectively. The water-proton relaxivities, r(1) and r(2), at 25 MHz, 0.59 T, and 25 degrees C, also increased in the same order and the r(1) values were 0.26, 0.41, and 0.56 mM(-1) s(-1) for UST, ssUSTm, and dsUSTm, respectively. The r(1) values of 1.00 and 2.06 mM(-1) s(-1) for dsUST2 and dsUST5, respectively, were obtained.

Fluorescence Tumor-Imaging Using a Thermo-Responsive Molecule with an Emissive Aminoquinoline Derivative.

We synthesized (2,4-trifluoromethyl-7-N-bis(2,5,8,11-tetraoxatridecane-13-yl)-aminoquinoline) TFMAQ-diEg4, an emissive aminoquinoline derivative that incorporated two tetraethyleneglycol chains into an amino group. TFMAQ-diEg4 showed fluorescence and thermo-responsive properties accompanied by a lower critical solution temperature (LCST), due to the introduction of the oligoethylene glycol chain. This thermo-responsive LCST behavior occurred at the border of a cloud point. Below and above the cloud point, self-assemblies of 6-7-nm nanoparticles and ~2000-nm microparticles were observed, in vitro. In addition, TFMAQ-diEg4 showed a high solubility, over 20 mM for aqueous solution, in vivo, which not only prevented thrombosis but also allowed various examinations, such as single intravenous administration and intravenous drips. Intravenous administration of TFMAQ-diEg4, to tumor-bearing, mice led to the accumulation of the molecule in the tumor tissue, as observed by fluorescence imaging. A subset of mice was treated with local heat around their tumor tissue and an intravenous drip of TFMAQ-diEg4, which led to a high intensity of TFMAQ-diEg4 emission within the tumor tissue. Therefore, we revealed that TFMAQ-diEg4 was useful as a fluorescence probe with thermo-responsive properties.

Photochemical generation of C4'-oxidized abasic site containing oligodeoxynucleotide and its efficient amine modification.

[Structure: see text] We synthesized oligodeoxynucleotide (ODN, 3), which contains 4'-o-nitrobenzyloxythymidine (4) as a caged precursor of C4'-oxidized abasic site (1). Photoirradiation of 3 at 365 nm followed by amine treatment under neutral conditions afforded the lactam (2) efficiently. Duplexed ODN 3 was converted to 1 faster and more efficiently than single stranded 3, whereas amine treatment of 1 formed from single stranded 3 resulted in slightly faster lactam formation than with the duplex.

Site-Specific Turn-On Fluorescent Labeling of DNA-Interacting Protein Using Oligodeoxynucleotides That Modify Lysines To Produce 5,6-Dimethoxy 3-Methyleneisoindolin-1-one.

We have developed oligodeoxynucleotides (ODNs) that modify primary amines to produce 5,6-dimethoxy 3-methyleneisoindolin-1-one. Compared to the oxygen isosteric fluorophore, 4,5-dimethoxyphthalimide, this methyleneisoindolinone was more stable and exhibited an 85 nm blue-shifted fluorescent emission (λmax at 425 nm) with an intensity comparable to that of the phthalimide. Reaction of the DNA-binding domain of Escherichia coli DnaA protein with an ODN containing its binding sequence efficiently afforded a modified fluorescent protein at a specific lysine residue in the proximity of the ODN. A full-length DnaA protein was also successfully fluorescently labeled. These results demonstrate the potential utility of the ODNs developed in this study for the fluorescent labeling of DNA-interacting protein at the lysine residue of interest.

Synthesis and EPR studies of 2-N-tert-butylaminoxylpurine derivatives.

[Structure: see text] 2'-Deoxyribofuranosylpurine derivatives bearing an N-tert-butylaminoxyl group (1a and 2a) were synthesized via oxidation of the corresponding N-tert-butylhydroxylamines (1b and 2b), which were synthesized by lithiation of 8-TIPS-6-chloropurine (3) at the 2-position and the following reaction with 2-methyl-2-nitrosopropane. Treatment of 1b and 2b with 1 equiv of NaIO4 resulted in efficient formation of 1a and 2a, which were isolated as purple and red solids, respectively. The EPR spectra of 1a showed pH dependency due to structural change of purine moiety.

Cerebroside Langmuir monolayers originated from the echinoderms I. Binary systems of cerebrosides and phospholipids.

The surface pressure (pi)-area (A), the surface potential (DeltaV)-A and the dipole moment (mu( perpendicular))-A isotherms were obtained for two-component monolayers of two different cerebrosides (LMC-1 and LMC-2) with phospholipids of dipalmitoylphosphatidylcholine (DPPC) and with dipalmitoylphosphatidylethanolamine (DPPE) on a subphase of 0.5 M sodium chloride solution as a function of phospholipid compositions by employing the Langmuir method, the ionizing electrode method, and the fluorescence microscopy. Surface potentials (DeltaV) of pure components were analyzed using the three-layer model proposed by Demchak and Fort. The contributions of the hydrophilic saccharide group and the head group to the vertical component of the dipole moment (mu( perpendicular)) were estimated. The miscibility of cerebroside and phospholipid in the two-component monolayers was examined by plotting the variation of the molecular area and the surface potential as a function of the phospholipid molar fraction (X(phospholipid)), using the additivity rule. From the A-X(phospholipid) and DeltaV(m)-X(phospholipid) plots, partial molecular surface area (PMA) and apparent partial molecular surface potential (APSP) were determined at the discrete surface pressure. The PMA and APSP with the mole fraction were extensively discussed for the miscible system. Judging from the two-dimensional phase diagrams, these can be classified into two types. The first is a positive azeotropic type; the combinations of cerebrosides with DPPC are miscible with each other. The second is a completely immiscible type: the combination of cerebrosides with DPPE. Furthermore, a regular surface mixture, for which the Joos equation was used for the analysis of the collapse pressure of two-component monolayers, allowed calculation of the interaction parameter (xi) and the interaction energy (-Delta epsilon) between the cerebrosides and DPPC component. The miscibility of cerebroside and phospholipid components in the monolayer state was also supported by fluorescence microscopy.

Cerebroside Langmuir monolayers originated from the echinoderms: II. Binary systems of cerebrosides and steroids.

Two-component Langmuir monolayers formed on a subphase of 0.5M sodium chloride solution were investigated for two different cerebrosides (LMC-1 and LMC-2) with steroids of cholesterol (Ch) and cholesteryl sodium sulfate (Ch-S); i.e. LMC-1/Ch, LMC-1/Ch-S, LMC-2/Ch, and LMC-2/Ch-S were examined in terms of surface pressure (pi), the surface potential (DeltaV) and the dipole moment (mu( perpendicular)) as a function of surface area (A) by employing the Langmuir method, the ionizing electrode method, and the fluorescence microscopy. Surface potentials (DeltaV) of steroids were analyzed using the three-layer model proposed by Demchak and Fort. The miscibility of cerebrosides and steroids in the insoluble monolayers was examined by plotting the variation of the molecular area and the surface potential as a function of the steroid molar fraction (X(steroid)) based upon the additivity rule. From the A-X(steroid) and DeltaV(m)-X(steroid) plots, partial molecular surface area (PMA) and apparent partial molecular surface potential (APSP) were determined at the different surface pressures. The PMA and APSP with the mole fraction were discussed for the miscible system. Judging from the two-dimensional phase diagrams, they can be classified into two types. The first is a completely immiscible type; the combination of cerebrosides with cholesterol. The second is a negative azeotropic type, where cerebrosides and cholesteryl sodium sulfate are completely miscible both in the expanded state and in the condensed state. In addition, a regular surface mixture (the Joos equation for the analysis of the collapse pressure of two-component monolayers) allowed calculation of the interaction parameter (xi) and the interaction energy (-Delta epsilon) between the cerebrosides and Ch-S. The miscibility of cerebroside and steroid components in the monolayer state was also supported by fluorescence microscopy.

A simple and efficient method for synthesis of 5-substituted 2'-deoxyuridine nucleosides using metal-halogen exchange reaction of 5-iodo-2'-deoxyuridine sodium salt.

Treatment of the sodium salt of 2'-deoxy-3', 5'-bis-O-(tert-butyldimethylsilyl)-5-iodouridine (3) with n-BuLi effected regioselective lithiation at the 5-position and the following reaction with various electrophiles afforded 5-substituted 2'-deoxyuridines including 1b, the precursor of stable spin-labeled 1a, in good yields.

Production and characterization of highly specific monoclonal antibodies to D-glutamic acid.

Most of the functions of D-amino acids (D-AA) remain unclear because of little analytic methods for specific detection/determination. In this study, a highly specific monoclonal antibody to D-glutamic acid (D-Glu-MAb) was produced using a hybridoma method. Characterization of D-Glu-MAb by indirect enzyme-linked immunosorbent assay (ELISA) revealed that it has high selectivity against D-Glu-glutaraldehyde (GA) conjugates, while no cross-reaction was observed when 38 other kinds of AA-GA conjugates were used. Moreover, subsequent indirect competitive ELISA disclosed that an epitope of D-Glu-MAb is a D-Glu-GA molecule in the conjugates, suggesting that D-Glu-MAb could be a useful tool to investigate the functional analysis of D-Glu in immunostaining.

Difluoro-C4'-oxidized abasic site for efficient amine modification in biological systems.

An oligodeoxynucleotide (ODN) containing a 2',2'-difluorinated analogue of a C4'-oxidized abasic site (C4'-OAS) was designed for the amine modification of biomolecules that interact with nucleic acids. In contrast to the parent C4'-OAS, which yielded amine-modified products accompanied by DNA strand scission, the ODN containing the difluoro C4'-OAS efficiently yielded products carrying ODNs. The amine modification proceeded without additional reagents being required and might be applicable to reactions in biological systems.

Evaluation of mobility of 2-N-tert-butylaminoxyladenosine incorporated into oligodeoxynucleotides.

We synthesized oligodeoxynucleotide (ODN, 3) containing 2-N-tert-butylaminoxyladenosine (1) and studied EPR spectra of 3 and its duplexes. The h(+)/h(0) values in the EPR spectra of duplexes between 3 and 5-8 well correlated with Tm values. We also synthesized ODN 4 containing 2, which has a cyclic aminoxyl via a linker, to compare with ODN 3. The h(+)/h(0) values in the EPR spectra of duplexes between 4 and 5-8 did not correlate with Tm values. These results indicate that 1 has a potential to monitor of motion of the nucleobase.

Photochemical generation and reaction of 2'-substituted analogues of C4'-oxidized abasic lesion.

The C4'-oxidized abasic site (1) is one of the oxidatively damaged DNA lesions induced by antitumor bleomycins. The reactivity of 1 with amine under neutral conditions giving lactam 2 and its structural similarity to unmodified DNA suggested the possibility that ODN containing 1 could react with proteins which interact with DNA at lysine residue. In order to provide nucleic acid analogues with useful lysine modifying reactivity, we planned to study reaction of 2'-substituted analogues of 1, such as 3-5, with amine and their corresponding caged precursors 6-8 were synthesized. Uncaging reaction of 16 containing 6 proceeded efficiently. The reaction of obtained 17 containing 3 with Z-Lys-OH did not afford products corresponding to lactam. However, HPLC analysis of the reaction mixture suggested interaction of 3 with Z-Lys-OH.

Photochemical generation of oligodeoxynucleotide containing a C4'-oxidized abasic site and its efficient amine modification: dependence on structure and microenvironment.

Bleomycin-induced oxidative DNA damage under limited oxygen conditions results in the formation of the C4'-oxidized abasic site (1). We synthesized the oligodeoxynucleotides (ODN) 5, which contains 4'-o-nitrobenzyloxythymidine (3), and 6, which contains 2-nitrobenzyloxy-4'-methoxy-2'-deoxy-d-ribofuranoside (4), as the caged precursors of 7, an ODN containing 1, to study its reactivity with amines. Photoirradiation of the single- and double-stranded 5 led to the formation of 7. Uncaging of the duplex was faster and the yield of 7 was higher with the double-stranded than with the single-stranded ODN. It was suggested that a low dielectric environment of the o-nitrobenzyloxy group in the minor groove of the duplex might accelerate the uncaging rate. Similarly, 6 and its duplex yielded 7 by photoirradiation. However, the yields of 7 were lower than those of 5, and duplex formation slowed the uncaging rate. Reaction of the obtained 7 with an amine resulted in the formation of the lactam 2b in good yield in both single- and double-stranded forms, showing that amine modification of biomolecules by an ODN containing 1 is possible under physiologic conditions.