A microenvironment sensitive pillar[5]arene-based fluorescent probe for cell imaging and drug delivery

Dansylamide (DNSA) is a typical ICT probe that has a favorable serum albumin sensitivity. Inspired by this, we designed a microenvironment sensitive fluorescent probe 4C-G through introducing DNSA into pillar[5]arene. Unlike DNSA, 4C-G displayed differentiated sensitivity to multiple proteins, which was benefit from pillar[5]arene assisted the probe to form complexes with proteins. 4C-G could not only be applied in imaging of HepG2, but also act as a favorable drug carrier for regorafenib (REG) encapsulation. The 4C-G-REG complex would aggregate into high drug-loading fluorescent nanoparticles in a physiological environment (pH 7.4). Such nanoparticles exhibited pH-triggered enrichment ability, which rapidly enriched REG in the acidic environment (pH 6.0). Furthermore, the complexation between 4C-G and REG maintained the imaging property of the probe and the excellent anticancer activity of the drug on HepG2.     

Possible cause of G-C-->C-G transversion mutation by guanine oxidation product, imidazolone

BACKGROUND: The genome is constantly assaulted by oxidation reactions which are likely to be associated with oxygen metabolism, and oxidative lesions are generated by many types of oxidants. Such genotoxin-induced alterations in the genomic message have been implicated in aging and in several pathophysiological processes, particularly those associated with cancer. The guanine base (G) in genomic DNA is highly susceptible to oxidative stress due to having the lowest oxidation potential. Therefore, G-C-->T-A and G-C-->C-G transversion mutations frequently occur under oxidative conditions. One typical lesion of G is 8-oxo-7,8-dihydro-guanine (8-oxoG), which can pair with A. This pairing may cause G-C-->T-A transversion mutations. Although the number of G-C-->C-G transversions is rather high under specific oxidation conditions such as riboflavin photosensitization, the molecular basis of G-C-->C-G transversions is not known. RESULTS: To determine which oxidative products are responsible for G-C-->C-G transversion mutations, we photooxidized 5'-d(AAAAAAGGAAAAAA)/5'-d(TTTTTTCCTTTTTT) using either riboflavin or anthraquinone (AQ) carboxylate under UV irradiation. Prolonged low-temperature (4 degrees C) enzymatic digestion of photoirradiated sample indicated that under both conditions the amount of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) initially increased with decreasing amounts of 2'-deoxyguanosine (dG), then decreased with the formation of 2-amino-5-[(2-deoxy-beta-D-erythro-pentofuranosyl)amino]-4H-imidazol-4-one (dIz), suggesting that nascent 8-oxoG was further oxidized to 2,5-diamino-4H-imidazol-4-one (Iz) in duplex DNA. Photoirradiation of an AQ-linked oligomer with a complementary strand containing 8-oxoG indicated that 8-oxoG residues were oxidized to Iz. These results indicate that Iz is formed from 8-oxoG through long-range hole migration. Primer extension experiments using a template containing Iz demonstrated that only dGTP is specifically incorporated opposite Iz suggesting that specific Iz-G base pairs are formed. The 'reverse' approach consisting of DNA polymerization using dIzTP showed that dIzTP is incorporated opposite G, further confirming the formation of a Iz-G base pair. CONCLUSIONS: HPLC product analysis demonstrated that Iz is a key oxidation product of G through 8-oxoG in DNA photosensitized with riboflavin or anthraquinone. Photoreaction of AQ-linked oligomer confirmed that Iz is formed from 8-oxoG through long-range hole migration. Two sets of primer extension experiments demonstrated that Iz can specifically pair with G in vitro. Specific Iz-G base pair formation can explain the G-C-->C-G transversion mutations that appear under oxidative conditions.     

Total synthesis of potent antifungal marine bisoxazole natural products bengazoles A and B

The bengazoles are a family of marine natural products that display potent antifungal activity and a unique structure, containing two oxazole rings flanking a single carbon atom. Total syntheses of bengazole A and B are described, which contain a sensitive stereogenic centre at this position between the two oxazoles. Additionally, the synthesis of 10-epi-bengazole A is reported. Two parallel synthetic routes were investigated, relying on construction of the 2,4-disubstituted oxazole under mild conditions and a diastereoselective 1,3-dipolar cycloaddition. Our successful route is high yielding, provides rapid access to single stereoisomers of the complex natural products and allows the synthesis of analogues for biological evaluation.     

Hamigeromycins C-G, 14-membered macrolides from the fungus Hamigera avellanea BCC 17816

Five new 14-membered macrolides, hamigeromycins C-G, together with the previously described compounds, hamigeromycin A and 89-250904-F1 (radicicol analog A), were isolated from the fungus Hamigera avellanea BCC 17816. Hamigeromycins A, C, D, and E are stereoisomers differing from one another in the absolute configurations of the 4′,5′-diol moiety. Hamigeromycins F and G are unusual 5′-keto-analogs, and they are 6′-epimers to each other. The structures and the stereochemistry of the new compounds were deduced by analyses of the NMR spectroscopic and mass spectrometry data in combination with chemical means.     

Characterization of direct-current atmospheric-pressure discharges useful for ambient desorption/ionization mass spectrometry

Two relatively new ambient ionization sources, direct analysis in real time (DART) and the flowing atmospheric-pressure afterglow (FAPA), use direct current, atmospheric-pressure discharges to produce reagent ions for the direct ionization of a sample. Although at a first glance these two sources appear similar, a fundamental study reveals otherwise. Specifically, DART was found to operate with a corona-to-glow transition (C-G) discharge whereas the FAPA was found to operate with a glow-to-arc transition (G-A) discharge. The characteristics of both discharges were evaluated on the basis of four factors: reagent-ion production, response to a model analyte (ferrocene), infrared (IR) thermography of the gas used for desorption and ionization, and spatial emission characteristics. The G-A discharge produced a greater abundance and a wider variety of reagent ions than the C-G discharge. In addition, the discharges yielded different adducts and signal strengths for ferrocene. It was also found that the gas exiting the discharge chamber reached a maximum of 235 °C and 55 °C for the G-A and C-G discharges, respectively. Finally, spatially resolved emission maps of both discharges showed clear differences for N₂⁺ and O(I). These findings demonstrate that the discharges used by FAPA and DART are fundamentally different and should have different optimal applications for ambient desorption/ionization mass spectrometry (ADI-MS).     

Triple helical recognition of pyrimidine inversions in polypurine tracts of RNA by nucleobase-modified PNA

Peptide nucleic acids containing 2-pyrimidinone (P) and 3-oxo-2,3-dihydropyridazine (E) heterocycles recognized C-G and U-A inversions in a polypurine tract of double helical RNA with high affinity and sequence selectivity at pH 6.25. E-modified PNA bound strongly to bacterial A-site RNA, while no binding was observed to the human A-site RNA.     

Reductive electron transfer in phenothiazine-modified DNA is dependent on the base sequence

A new DNA assay has been designed, prepared and applied for the chemical investigation of reductive electron transfer through the DNA. It consists of 5-(10-methyl-phenothiazin-3-yl)-2'-deoxyuridine (Ptz-dU, 1) as the photoexcitable electron injector and 5-bromo-2'-deoxyuridine (Br-dU) as the electron trap. The Ptz-dU-modified oligonucleotides were synthesised by means of a Suzuki-Miyaura cross-coupling protocol and subsequent automated phosphoramidite chemistry. Br-dU represents a kinetic electron trap, since it undergoes a chemical modification after its one-electron reduction that can be analysed by piperidine-induced strand cleavage. The quantification of the strand cleavage yields from irradiation experiments reveals important information about the electron-transfer efficiency. The performed DNA studies focused on the base sequence dependence of the electron-transfer efficiency with respect to the proposal that C*- and T*- act as intermediate electron carriers during electron hopping. From our observations it became evident that excess-electron transfer is highly sequence dependent and occurs more efficiently over T-A base pairs than over C-G base pairs.     

Polarizable model potential function for nucleic acid bases

A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculations at the MP2/6-31+G* level. The PMP function consists of Coulomb, van der Waals, and polarization terms. The permanent atomic charges of the Coulomb term are determined by using electrostatic potential (ESP) optimization. The multicenter polarizabilities of the polarization term are determined by using polarized one-electron potential (POP) optimization in which the electron density changes induced by a test charge are target. Isotropic and anisotropic polarizabilities are adopted as the multicenter polarizabilities. In the PMP calculations using the optimized parameters, the interaction energies of Watson-Crick type A-T and C-G base pairs were -15.6 and -29.4 kcal/mol, respectively. The interaction energy of Hoogsteen type A-T base pair was -17.8 kcal/mol. These results reproduce well the quantum chemistry calculations at the MP2/6-311++G(3df,2pd) level within the differences of 0.6 kcal/mol. The stacking energies of A-T and C-G were -9.7 and -10.9 kcal/mol. These reproduce well the calculation results at the MP2/6-311++G (2d,2p) level within the differences of 1.3 kcal/mol. The potential energy surfaces of the system in which a sodium ion or a chloride ion is adjacent to the nucleic acid base are calculated. The interaction energies of the PMP function reproduced well the calculation results at the MP2/6-31+G* or MP2/6-311++G(2d,2p) level. The reason why the PMP function reproduces well the high-level quantum mechanical interaction energies is addressed from the viewpoint of each energy terms.     

Structural analysis of metal interactions with the dinucleotide duplex, dCG x dCG, using ion mobility mass spectrometry

The metal binding properties of the dinucleotide duplex, dCG x dCG, were analyzed in the gas phase with ion mobility mass spectrometry. Both MALDI and ESI were used to generate [M(dCG x dCG)]+ complexes. The collision cross section of each complex was measured in helium using ion mobility based methods and compared to calculated cross sections of theoretical structures. When metal cations classified as hard acids were combined with dCG x dCG, the [M(dCG x dCG)]+ complex organized into a globular structure. However, when soft acid metal cations were examined, a structure was observed where the two C-G base pairs were Watson-Crick bound.     

Direct and facile syntheses of heterocyclic vinyl-C-nucleosides for recognition of inverted base pairs by DNA triple helix formation: first report by direct Wittig route

The ability to recognize specific gene sequences canonically would allow precise means for genetic intervention. However, specific recognition of two of the four possible base pairs by triplex-forming oligonucleotides (TFO) as X.T-A and Y.C-G within a triplex currently remains elusive. A series of C1-vinyl nucleosides have been proposed, and their stability and specificity have been evaluated extensively by molecular dynamics simulation. Because most C-nucleoside syntheses extend through direct substitution at the C1-position, a more convenient strategy for their syntheses via a direct Wittig coupling is presented here.     

A Janus-Wedge DNA triplex with A-W1-T and G-W2-C base triplets

A new type of double-stranded DNA targeting format by formation of a Janus-Wedge (J-W) triple helix is described. The "wedge" residue W1 is used for A-T and T-A base pairs while W2 is used for G-C and C-G base pairs. Both wedge residues are attached to a PNA backbone that is designed to insert the probe strand into double-stranded DNA and base pair with both Watson-Crick faces. To study the stability of such an assembly, we have examined the formation of the J-W triplex with various sequences.     

Interstrand and intrastrand DNA-DNA cross-linking by 1,2,3,4-diepoxybutane: role of stereochemistry

1,2,3,4-Diepoxybutane (DEB) is a bifunctional electrophile capable of forming DNA-DNA and DNA-protein cross-links. DNA alkylation by DEB produces N7-(2'-hydroxy-3',4'-epoxybut-1'-yl)-guanine monoadducts, which can then form 1,4-bis-(guan-7-yl)-2,3-butanediol (bis-N7G-BD) lesions. All three optical isomers of DEB are produced metabolically from 1,3-butadiene, but S,S-DEB is the most cytotoxic and genotoxic. In the present work, interstrand and intrastrand DNA-DNA cross-linking by individual DEB stereoisomers was investigated by PAGE, mass spectrometry, and stable isotope labeling. S,S-, R,R-, and meso-diepoxides were synthesized from l-dimethyl-2,3-O-isopropylidene-tartrate, d-dimethyl-2,3-O-isopropylidene-tartrate, and meso-erythritol, respectively. Total numbers of bis-N7G-BD lesions (intrastrand and interstrand) in calf thymus DNA treated separately with S,S-, R,R-, or meso-DEB (0.01-0.5 mM) were similar as determined by capillary HPLC-ESI(+)-MS/MS of DNA hydrolysates. However, denaturing PAGE has revealed that S,S-DEB produced the highest number of interchain cross-links in 5'-GGC-3'/3'-CCG-5' sequences. Intrastrand adduct formation by DEB was investigated by a novel methodology based on stable isotope labeling HPLC-ESI(+)-MS/MS. Meso DEB treatment of DNA duplexes containing 5'-[1,7, NH(2)-(15)N(3),2-(13)C-G]GC-3'/3'-CCG-5' and 5'-GGC-3'/3'-CC[(15)N(3),2-(13)C-G]-5' trinucleotides gave rise to comparable numbers of 1,2-intrastrand and 1,3-interstrand bis-N7G-BD cross-links, while S,S DEB produced few intrastrand lesions. R,R-DEB treated DNA contained mostly 1,3-interstrand bis-N7G-BD, along with smaller amounts of 1,2-interstrand and 1,2-intrastrand adducts. The effects of DEB stereochemistry on its ability to form DNA-DNA cross-links may be rationalized by the spatial relationships between the epoxy alcohol side chains in stereoisomeric N7-(2'-hydroxy-3',4'-epoxybut-1'-yl)-guanine adducts and their DNA environment. Different cross-linking specificities of DEB stereoisomers provide a likely structural basis for their distinct biological activities.     

Conformational studies of double-helical polynucleotides by the method of pair-wise potential functions

Double-helical polynucleotide conformations, poly(dA)·poly(dT), poly(d(A-T))·poly(d(T-A))·poly(dG)·poly(dC), and poly(d(G-C))·poly(d(C-G)) are analyzed by the atom–atom potential method. The energy optimization is carried out in the space of eight independent geometric parameters using analytical procedures for the constraints, taking into account the flexibility of the β-D -deoxyribose rings. At the first stage, the full screening of atomic partial charges was assumed. The structures of the calculated B and the A forms of DNA are characterized by low energy and absence of short contacts; the dihedral angles are near the average values in the monomers. With the typical energy difference of 3–5 kcal/mol nucleotide pairs in all cases, the B form is more preferable as compared to the A form. At the final step the effect of the Coulomb term is evaluated for poly(dA)·poly(dT) using various values of the effective dielectric constant (? = 28, 24, 20, 18, 14, 12, 10, 8, 6, 4, and 1). If ? ?24, the energy optimization leads A to B. We discuss the stereochemical details of the intermediate conformations on the A–B path and hypothesize the nature of stability of the A and the B forms and the mechanism of the A–B transition.     

Apolar carbohydrates as DNA capping agents

Mono- and disaccharides have been shown to stack on top of DNA duplexes stabilizing sequences with terminal C-G base pairs. Here we present an apolar version of glucose and cellobiose as new capping agents that stack on DNA increasing considerably its stability with respect to their natural polyhydroxylated mono- and disaccharide DNA conjugates.     

DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes

We have previously reported DNA triplexes containing the unnatural base triad G-PPI·C3, in which PPI is an indole-fused cytosine derivative incorporated into DNA duplexes and C3 is an abasic site in triplex-forming oligonucleotides (TFOs) introduced by a propylene linker. In this study, we developed a new unnatural base triad A-ψ·C(R1) where ψ and C(R1) are base moieties 2'-deoxypseudouridine and 5-substituted deoxycytidine, respectively. We examined several electron-withdrawing substituents for R1 and found that 5-bromocytosine (C(Br)) could selectively recognize ψ. In addition, we developed a new PPI derivative, PPI(Me), having a methyl group on the indole ring in order to achieve selective triplex formation between DNA duplexes incorporating various Watson-Crick base pairs, such as T-A, C-G, A-ψ, and G-PPI(Me), and TFOs containing T, C, C(Br), and C3. We studied the selective triplex formation between these duplexes and TFOs using UV-melting and gel mobility shift assays.     

Eight new limonoids from Turraea pubescens

Eight new ring B-seco limonoids, turrapubesic acids A-C (1-3) and turrapubesins C-G (4-8), along with turraflorin E and isoazadironolide were isolated from the twigs and leaves of Turraea pubescens. Turrapubesic acids A-C (1-3) are a group of ring B-seco limonoid 17-carboxylic acids with a new C₂₃ skeleton, and turrapubesin C (4) incorporates an unprecedented 1,30-oxygen bridge. The structures including absolute stereochemistry of 1-8 were established on the basis of extensive NMR spectroscopic analysis and CD study. The cytotoxicity of the isolates against the P-388 and A-549 cells was evaluated.     

Three-Dimensional DNA Crystals with pH-Responsive Noncanonical Junctions

Three-dimensional (3D) DNA crystals have been envisioned as programmable biomaterial scaffolds for creating ordered arrays of biological and nonbiological molecules. Despite having excellent programmable properties, the linearity of the Watson-Crick B-form duplex imposes limitations on 3D crystal design. Predictable noncanonical base pairing motifs have the potential to serve as junctions to connect linear DNA segments into complex 3D lattices. Here, we designed crystals based on a template structure with parallel-stranded noncanonical base pairs. Depending on pH, the structures we determined contained all but one or two of the designed secondary structure interactions. Surprisingly, a conformational change of the designed Watson-Crick duplex region resulted in crystal packing differences between the predicted and observed structures. However, the designed noncanonical motif was virtually identical to the template when crystals were grown at pH 5.5, highlighting the motif's predictability. At pH 7.0 we observed a structurally similar variation on this motif that contains a previously unobserved C-G?G-C quadruple base pair. We demonstrate that these two variants can interconvert in crystallo in response to pH perturbations. This study spotlights several important considerations in DNA crystal design, describes the first 3D DNA lattice composed of A-DNA helical sheets, and reveals a noncanonical DNA motif that has adaptive features that may be useful for designing dynamic crystals or biomaterial assemblies.     

Synthesis,Base Pairing,and Structural Transitions of Oligodeoxyribonucleotides Containing 8-Aza-2′-deoxyguanosine

The synthesis of oligonucleotides containing 8-aza-2′-deoxyguanosine (z⁸G_d; 1 ) or its N⁸-regioisomer z⁸G_d^* ( 2 ) instead of 2′-deoxyguanosine (G_d) is described. For this purpose, the NH₂ group of 1 and 2 was protected with a (dimethylamino)methylidene residue (→ 5, 6 ), a 4,4′-dimethoxytrityl group was introduced at 5′-OH (→ 7, 8 ), and the phosphonates 3a and 4 as well as the phosphoramidite 3b were prepared. These building blocks were used in solid-phase oligonucleotide synthesis. The oligonucleotides were characterized by enzymatic hydrolysis and melting curves (T_m values). The thermodynamic data of the oligomers 12–15 indicate that duplexes were stabilized when 1 was replacing G_d. The aggregation of d(T-G-G-G-G-T) ( 18 ) was studied by RP 18 HPLC, gel electrophoresis and CD spectroscopy and compared with that of oligonucleotides containing an increasing number of z⁸G_d residues instead of G_d. Similarly to [d(C-G)]₃ ( 12a ), the hexamer d(C-z⁸G-C-z⁸G-C-G) ( 14 ) underwent salt-dependent B-Z transition.     

Engineering artificial redox chains by molecular 'Lego'

This work reports on a novel approach for building artificial redox chains: the molecular 'Lego' approach. This exploits the scaffold of natural redox proteins by fusing together functional protein modules with the desired properties. The molecular 'Lego' mimics the natural molecular evolution that proceeded by modular assembly of genes/DNA segments. Non-physiological electron transfer partners, flavodoxin (fld) and cytochrome c553 (c553) from Desulfovibrio vulgaris and the haem domain of P450 BM3 (BMP) from Bacillus megaterium have been used as building blocks in different combinations to build artificial redox chains. The kinetic characterization of the electron transfer (ET) between the separate building blocks has been carried out. Under pseudo-first order conditions, a limiting ET rate, klim, of 0.48 +/- 0.05 s-1 and 43.77 +/- 2.18 s-1 and an apparent binding constant, Kapp, of 21 +/- 6 microM and 1.23 +/- 0.32 microM have been found for the fld/c553 and fld/BMP redox pairs, respectively. These results show that fld can be used as a module for transferring electrons to c553 and BMP. A 3D model of the fld/c553 and fld/BMP complexes was used to guide the construction of covalently linked assemblies via engineered disulfide bridges or by fusion of the relevant genes via an engineered loop. The first approach led to the construction, expression and characterization of the S35C and S64C mutants of fld and M23C and G51C mutants of c553. Although the redox potentials of the separate mutants were found to be the same as those of recombinant wild type proteins (-408 mV for the semiquinone/hydroquinone couple of fld and +32 mV for the c553), the c553 homo-dimers M23C-M23C and G51C-G51C were found to have redox potentials of +88 and +105 mV, respectively. These differences have been analysed in terms of exposure of the haem cofactors to the solvent, and these lead to some interesting questions on the redox potentials of the transient redox complexes in physiological systems. The fld-c553 S64C-M23C and S35C-M23C chimeras were constructed, expressed and purified but the FMN was found to be destabilised resulting in the apo-form of these proteins. The gene fusion strategy was used to produce covalently linked assemblies of both fld-c553 and fld-BMP. The former was expressed using a seven amino acid (GPGPGPG) loop linking the C-terminus of fld to the N-terminus of c553. The fld-BMP fusion protein was successfully expressed by using the naturally occurring loop of the P450 BM3 (residues 471-479) to link the BMP domain at the N-terminus with fld domain at the C-terminus. This fusion was found to be correctly folded and functional. Efficient ET from the FMN to the haem domain (370 s-1) was also found to be in the same region of the physiological redox partners (250 s-1). This work demonstrates the feasibility of the molecular 'Lego' approach in generating functional multi-domain proteins with designed properties, beyond the restrictions imposed by the naturally occurring protein domains.     

Structure of the lipid A of Bordetella hinzii ATCC 51730

Bordetella hinzii has recently been isolated from immunocompromised human hosts. The structure of the lipid A of its endotoxin was investigated using chemical analyses, nuclear magnetic resonnance (NMR), gas liquid chromatography/mass spectrometry (GC/MS), plasma desorption mass spectrometry (PDMS) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The lipid A contains the classical bisphosphorylated beta-(1-->6)-linked D-glucosamine disaccharide with hydroxytetradecanoic acid (C14OH) in amide linkages. The lipid A components of B. pertussis, B. bronchiseptica, and B. parapertussis all differ in their acylation pattern but share a residue of tetradecanoyl-3-hydroxytetradecanoic acid in amide linkage at the C-2' position. However, in the B. hinzii species, the tetradecanoic acid (C14) is stoichiometrically replaced by a 2-hydroxytetradecanoic acid (2-C14OH). In the few reported examples of a hydroxylated fatty acid in this position, the substitutions were only partial. The B. hinzii lipid A differs from that of B. pertussis also by replacement of the hydroxydecanoic acid (C10OH) by hydroxydodecanoic acid (C12OH) and by the presence of a hexadecanoic acid (C16) to give a sixth fatty acid. The lipid A was heterogeneous, being composed of three major molecular species: tetra-, penta- and hexaacylated. The fatty acids in ester linkage were localized by PDMS of the native and alkali-treated lipid A. The lipid A components isolated from the O-chain-linked lipopolysaccharides (LPSs) were shown to be more acylated than those from the O-chain-free LPSs.