Core-modified, meso-alkylidenyl porphyrins and their expanded analogues: a new family of nonplanar porphyrinoids

New core-modified, meso-alkylidenyl porphyrinoids bearing multiple exocyclic double bonds were synthesized and characterized. The synthesis was accomplished using a typical "3 + 1"-type condensation approach. Stable exocyclic tautomers bearing double bonds at the meso positions, as well the corresponding endocyclic tautomers, were isolated in the case of both thiabenziporphyrin and thiapyriporphyrin products prepared in the course of this study. On the other hand, only the exocyclic tautomer was isolated in the case of the congeneric oxapyriporphyrin and oxabenziporphyrin. Expanded analogues of the exocyclic forms of oxabenziporphyrin and thiabenziporphyrin were also isolated as minor products. A single-crystal X-ray diffraction analysis of the expanded thiabenziporphyrin (20) revealed that all four pyrrole rings displayed an inverted geometry, presumably reflecting the strong hydrogen-bonding extant between the pyrrole N-H proton and the carbonyl group of the malonate moiety in the solid state. On the other hand, the expanded oxabenziporphyrin (14) was found to possess a severely distorted geometry with only one pyrrole ring being inverted. Careful analysis of the structure revealed that the solid-state geometry of the expanded macrocycles correlates well with the internal angle defined by the 2- and 5 substituents and the centers of the furan (14) or thiophene (20) subunits.     

The components of xRNA: synthesis and fluorescence of a full genetic set of size-expanded ribonucleosides

The synthesis and properties of a full set of four benzo-expanded ribonucleosides (xRNA), analogous to A, G, C, and U RNA monomers, are described. The nucleosides are efficient fluorophores with emission maxima of 369-411 nm. The compounds are expected to be useful as RNA pathway probes and as components of an unnatural ribopolymer.     

Fluorescence of size-expanded DNA bases: reporting on DNA sequence and structure with an unnatural genetic set

We recently described the synthesis and helix assembly properties of expanded DNA (xDNA), which contains base pairs 2.4 A larger than natural DNA pairs. This designed genetic set is under study with the goals of mimicking the functions of the natural DNA-based genetic system and of developing useful research tools. Here, we study the fluorescence properties of the four expanded bases of xDNA (xA, xC, xG, xT) and evaluate how their emission varies with changes in oligomer length, composition, and hybridization. Experiments were carried out with short oligomers of xDNA nucleosides conjugated to a DNA oligonucleotide, and we investigated the effects of hybridizing these fluorescent oligomers to short complementary DNAs with varied bases opposite the xDNA bases. As monomer nucleosides, the xDNA bases absorb light in two bands: one at approximately 260 nm (similar to DNA) and one at longer wavelength ( approximately 330 nm). All are efficient violet-blue fluorophores with emission maxima at approximately 380-410 nm and quantum yields (Phifl) of 0.30-0.52. Short homo-oligomers of the xDNA bases (length 1-4 monomers) showed moderate self-quenching except xC, which showed enhancement of Phifl with increasing length. Interestingly, multimers of xA emitted at longer wavelengths (520 nm) as an apparent excimer. Hybridization of an oligonucleotide to the DNA adjacent to the xDNA bases (with the xDNA portion overhanging) resulted in no change in fluorescence. However, addition of one, two, or more DNA bases in these duplexes opposite the xDNA portion resulted in a number of significant fluorescence responses, including wavelength shifts, enhancements, or quenching. The strongest responses were the enhancement of (xG)n emission by hybridization of one or more adenines opposite them, and the quenching of (xT)n and (xC)n emission by guanines opposite. The data suggest multiple ways in which the xDNA bases, both alone and in oligomers, may be useful as tools in biophysical analysis and biotechnological applications.     

Phthaloyl group : a new amino protecting group of deoxyadenosine in oligonucleotide synthesis

A phthaloyl group has been introduced into the N⁶-amino group of deoxyadenosine $\text{via}$ silylation followed by acylation. The phthaloyl group resulted in remarkable retarding effects on depurination, while it could be removed under milder conditions than the benzoyl group. Thus, a tetradeoxyadenylate has been successfully synthesized in high yield.     

Toward a novel series of furanopyrimidine nucleoside analogues

Based on an unusual furanose ring opening of 1,2-O-isopropylidene pentofuranoside derivatives, a preparation scheme of a new series of furanopyrimidine nucleoside analogues has been devised.     

A set of nonpolar thymidine nucleoside analogues with gradually increasing size

[structure: see text] We describe a series of nonpolar nucleoside analogues having similar shapes and gradually increasing size. The structure of the nucleobase thymine was mimicked with toluene derivatives, replacing O2/O4 with hydrogen, fluorine, chlorine, bromine, and iodine. Glycosidic bonds were formed by reactions of lithiated 2,4-dihalotoluenes with a deoxyribonolactone derivative. Structural analysis by NMR showed similar conformations across the series. The compounds are useful for study of the biological recognition of nucleotides and nucleic acids.     

22]Porphyrin-(3.1.1.3), a new vinylogous expanded porphyrin system

Acid-catalyzed condensation of a pyrrole bisacrylaldehyde with a tripyrrane, followed by oxidation with ferric chloride, gave a [22]porphyrin-(3.1.1.3). This stretched macrocycle shows a strong diamagnetic ring current by (1)H NMR spectroscopy and gives red-shifted porphyrin-like UV-vis spectra; coordination with palladium(II) induces an EZ isomerization to accommodate the metal cation while retaining highly diatropic characteristics. [structure: see text]     

Toward a designed, functioning genetic system with expanded-size base pairs: solution structure of the eight-base xDNA double helix

We describe the NMR-derived solution structure of the double-helical form of a designed eight-base genetic pairing system, termed xDNA. The benzo-homologous xDNA design contains base pairs that are wider than natural DNA pairs by ca. 2.4 A (the width of a benzene ring). The eight component bases of this xDNA helix are A, C, G, T, xA, xT, xC, and xG. The structure was solved in aqueous buffer using 1D and 2D NMR methods combined with restrained molecular dynamics. The data show that the decamer duplex is right-handed and antiparallel, and hydrogen-bonded in a way analogous to that of Watson-Crick DNA. The sugar-phosphate backbone adopts a regular conformation similar to that of B-form DNA, with small dihedral adjustments due to the larger circumference of the helix. The grooves are much wider and more shallow than those of B-form DNA, and the helix turn is slower, with ca. 12 base pairs per 360 degrees turn. There is an extensive intra- and interstrand base stacking surface area, providing an explanation for the greater stability of xDNA relative to natural DNA. There is also evidence for greater motion in this structure compared to a previous two-base-expanded helix; possible chemical and structural reasons for this are discussed. The results confirm paired self-assembly of the designed xDNA system. This suggests the possibility that other genetic system structures besides the natural one might be functional in encoding information and transferring it to new complementary strands.     

Inverted sapphyrin: a new family of doubly N-confused expanded porphyrins

The synthesis of an inverted, methoxylated sapphyrin derivative is described. This system, wherein inversion of pyrrolic nitrogen atoms is configurationally enforced via the use of a 3,3'-bipyrrolic precursor, displays what is best described as "weak aromaticity" as judged from its spectroscopic features and supporting theoretical calculations.     

Toward a new generation of therapeutics

Scientific evidence in the prevention and treatment of various disorders is accumulating regarding probiotics. The health benefits supported by adequate clinical data include increased resistance to infectious disease, decreased duration of diarrhea, management of inflammatory bowel disease, reduction of serum cholesterol, prevention of allergy, modulation of cytokine gene expression, and suppression of carcinogen production. Recent ventures in metabolic engineering and heterologous protein expression have enhanced the enzymatic and immunomodulatory effects of probiotics and, with time, may allow more active intervention among critical care patients. In addition, a number of approaches are currently being explored, including the physical and chemical protection of cells, to increase probiotic viability and its health benefits. Traditional immobilization of probiotics in gel matrices, most notably calcium alginate and κ-carrageenan, has frequently been employed, with noted improvements in viability during freezing and storage. Conflicting reports exist, however, on the protection offered by immobilization from harsh physiologic environments. An alternative approach, microencapsulation in “artificial cells,” builds on immobilization technologies by combining enhanced mechanical stability of the capsule membrane with improved mass transport, increased cell loading, and greater control of parameters. This review summarizes the current clinical status of probiotics, examines the promises and challenges of current immobilization technologies, and presents the concept of artificial cells for effective delivery of therapeutic bacterial cells.     

Toward breast cancer resistance protein (BCRP) inhibitors: design, synthesis of a series of new simplified fumitremorgin C analogues

In this study, we report the design and synthesis of a series of new simplified fumitremorgin C analogues. The preliminary biological study indicated some of these simplified fumitremorgin C might be developed into breast cancer resistance inhibitors.     

Synthesis of a new alkynylated deoxyadenosine phosphoramidite for the click reaction-mediated DNA labeling

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A series of nonpolar thymidine analogues of increasing size: DNA base pairing and stacking properties

[reaction: see text] We describe the properties in DNA of a set of five nonpolar nucleoside mimics in which shape is similar but size is increased gradually. The compounds vary in the size of their exocyclic substituents, which range from hydrogen to iodine, and are designed to test the steric effects of nucleosides, nucleotides, and DNA in biological systems in a systematic way. We describe the conversion of toluene, 2,4-difluorotoluene, 2,4-dichlorotoluene, 2,4-dibromotoluene, and 2,4-diiodotoluene deoxyribosides into suitably protected phosphoramidite derivatives and their incorporation into synthetic DNAs. Studies of their behavior in the context of hexamer and dodecamer duplexes were carried out, with comparison to natural thymine. Thermal melting data with compounds in 5' dangling positions showed that all five compounds stack more strongly than thymine, and all the dihalo-substituted cases stack more strongly than the unsubstituted toluene case. Stacking correlated with surface area and hydrophobicity, both of which increase across the series. In base-pairing studies, all five compounds showed destabilized pairing opposite natural bases (relative to thymine-adenine pairing), as expected. Notably, pairing among the nonpolar base analogues was considerably more stable, and some of the pairs involving the largest analogues showed stability equal to that of a natural thymine-adenine pair. The results establish the base pairing properties of a potentially useful new series of biochemical probes for DNA-protein interactions and also identify a set of new, stable hydrophobic base pairs for designed genetic pairing systems.     

Isoxazolidine analogues of pseudouridine: a new class of modified nucleosides

A new class of modified C-nucleosides has been synthesized according to the 1,3-dipolar cycloaddition methodology. The obtained compounds are structurally related to natural pseudouridine, where the sugar moiety is replaced by an isoxazolidine ring. Different experimental conditions, and the effect of additives on the cycloaddition process, have been examined; the best results were obtained when the cycloaddition reaction was performed under microwave irradiation     

Two versatile routes towards Cerpegin and analogues: applications of a one pot reaction to new analogues of Cerpegin

Simple and efficient routes to the natural alkaloid Cerpegin and new analogues are described herein. In a first approach, we extend the scope of a one pot three steps reaction, which permits the synthesis of new analogues of Cerpegin, substituted in different ways. In a second line of approach, we present an unprecedented synthesis of Cerpegin and analogues where methylfuranones are condensed with dimethylformamide diethylacetal (DMFDEA) to yield enaminolactone esters, which react easily with various primary amines affording Cerpegin and new analogues. We applied this second approach to the synthesis of new bis-Cerpegins and N-amino-Cerpegins. Most of the syntheses are performed under environmental friendly conditions.     

Bismethylene triphosphate nucleotides of uridine 4-phosphate analogues: a new class of anionic pyrimidine nucleotide analogues

Cytidine-5'-triphosphate synthase (CTPS) catalyzes the formation of cytidine triphosphate (CTP) from glutamine, uridine 5'-triphosphate (UTP), and adenosine 5'-triphosphate (ATP). This reaction proceeds via formation of the high-energy intermediate UTP-4-phosphate (UTP-4-P). Stable analogues of UTP-4-P may be potent inhibitors of CTPS and useful as lead structures for the development of anticancer and antiviral agents. Several bismethylene triphosphate (BMT) nucleotides of uridine 4-phosphate (U-4-P) analogues have been prepared. A key step was the selective methanolysis, with the aid of a tin catalyst, of the 5' ester moiety of 2',3',5'-tri-O-acetyl or tri-O-benzoyl U-4-P analogues. We believe this represents the first general approach to the selective cleavage of 5' benzoyl esters in benzoylated nucleosides. Mitsunobu coupling of these 5'-deprotected U-4-P analogues to an unsymmetrical, protected BMT bearing a free phosphonic acid moiety at one of the terminal positions gave fully protected BMT-U-4-P analogues. Global deprotection of these species was achieved using TMSBr followed by treatment with NH4OH-MeOH or NH4OH-pyridine. The resulting BMT nucleotides represent a new class of anionic pyrimidine nucleotide analogues.     

Synthesis and properties of a new family of cyclodextrin analogues

The chemical synthesis of a series of cyclic oligosaccharides built up from (14)-linked alternatingD– andl-pyranosidic units is described for the first time. Key intermediates employed were disaccharides representing minimal repeating units. These disaccharides (monomers) have been prepared in specifically modified forms so that they bear both glycosyl donor (cyanoethylidene group) and glycosyl acceptor (trityloxy group) functions. Polycondensation-cyclisation of these disaccharide monomers, catalysed by TrC1O₄ under normal conditions of dilution, has led to series of homologous cyclic oligosaccharides with an even number of sugar residues (6, 8, 10, 12,etc.) in each case. Cyclic hexa- and octa-saccharides, based onl-rhamnose andD-mannose as the alternating monosaccharides units, have been deprotected to produce analogues of - and -cyclodextrins (CDs) and the X-ray crystal structure of the cyclic octasaccharide has been determined.     

Rigid, conjugated, fluoresceinated thymidine triphosphates: syntheses and polymerase mediated incorporation into DNA analogues

Syntheses of a unique set of energy transfer dye labeled nucleoside triphosphates, compounds 1-3, are described. Attempts to prepare these compounds were only successful if the triphosphorylation reaction was performed before coupling the dye to the nucleobase, and not the other way around. Compounds were prepared as both the 2'-deoxy (a) and 2',3'-dideoxy- (b) forms. They feature progressively longer rigid conjugated linkers connecting the nucleobase and the hydroxyxanthone moiety. UV spectra of the parent nucleosides 12-14 show that as the length of the linker increases so does the absorption of the donor in the 320-330 nm region, but with relatively little red-shift of the maxima. Fluorescence spectra of the same compounds show that radiation in the 320-330 nm region results in predominant emission from the fluorescein. When the linker is irradiated at 320 nm, the only significant emission observed corresponds to the hydroxyxanthone part of the molecules at 520 nm; this corresponds to an effective Stokes' shift of 200 nm. As the absorption at 320-330 nm by the linker increases with length, so does the intensity of the fluorescein emission. A gel assay was used to gauge relative incorporation efficiencies of compounds 1-3, dTTP, ddTTP, and 6-TAMRA-ddTTP. Throughout, the thermostable polymerase TaqFS was used, as it is the one most widely applied in high throughput DNA sequencing. This assay showed that only compounds 3 were incorporated efficiently; these have the longest linkers. Of these, the 2'-deoxy nucleoside 3 a was incorporated and did not prevent the polymerase from extending the chain further. The 2',3'-dideoxy nucleoside 3 b was incorporated only about 430 times less efficiently than ddTTP under the same conditions, and caused chain termination. The implications of these studies on modified sequencing protocols are discussed.