Protein-inspired modified DNAzymes: dramatic effects of shortening side-chain length of 8-imidazolyl modified deoxyadenosines in selecting RNaseA mimicking DNAzymes

The discovery of imidazole/amine-functionalized DNAzymes that efficiently cleave RNA independently of divalent metal cations (M(2+)) and cofactors underscores the importance of expanding the catalytic repertoire with modified nucleosides. Considerable effort has gone into defining polymerase tolerances of various modified dNTPs for synthesizing and amplifying modified DNA. While long linkers are generally found to enhance incorporation and therefore increase sequence space, shorter linkers may reduce the entropic penalty paid for orienting catalytic functionality. Catalytic enhancement ultimately depends on both the functional group and appropriate linkage to the nucleobase. Whether a shorter linker provides enough catalytic enhancement to outweigh the cost of reduced polymerizability can only be determined by the outcome of the selection. Herein, we report the selection of DNAzyme 20-49 (Dz20-49), which depends on amine, guanidine, and imidazole-modified dNTPs. In contrast to previous selections where we used dA(ime)TP (8-(4-imidazolyl)ethylamino-2'-dATP), here we used dA(imm)TP (8-(4-imidazolyl)methylamino-2'-dATP), in which the linker arm is shortened by one methylene group. Although the most active clone, Dz20-49, was absolutely dependent on the incorporation of either dA(imm)p or dA(ime)p, it catalyzed cofactor independent self-cleavage with a rate constant of 3.1 ± 0.3 × 10(-3) min(-1), a value not dissimilar from unmodified catalysts and strikingly inferior to modified catalysts selected with dA(ime)TP. These results demonstrate that very subtle differences in modified nucleotide composition may dramatically effect DNAzyme selection.     

Peroxidase-mimicking DNAzymes for biosensing applications: a review

DNAzymes are single stranded DNA molecules that exhibit catalytic activity and are exploited in medicine, biology and material sciences. Development in this area is related to the many advantages of DNAzymes over conventional protein enzymes, such as thermal stability and simpler preparation. DNAzymes with peroxidase-like activity have recently attracted great interest. To assure such catalytic activity, oligonucleotides have to adopt a G-quadruplex structure, which can bind the hemin molecule. This system facilitates a redox reaction between the target molecule and hydrogen peroxide, which results in the appearance of an oxidized target molecule (product). DNAzymes with peroxidase-mimicking activity have great potential in bioanalytical chemistry. This review presents fundamentals concerning the design and engineering of DNAzymes with peroxidase-like activity, describes their properties and spectral characteristics and shows how DNAzymes can contribute to bioanalytical research. Examples of bioanalytical applications of DNAzymes with peroxidase-like activity include nucleic acid probes with DNAzyme labels for the detection of specific DNA sequences in colorimetric or chemiluminescent assays. Assays for telomerase or methyltransferase activity, which are potential targets in anticancer therapy, are also described in this review. Other applications include the determination of metal cations such as Ag(+), K(+), Hg(2+), Pb(2+) or Cu(2+) and amplified detection of small molecules such as adenosine, cocaine or AMP and proteins such as lysozyme or thrombin. In the last decade, DNAzymes have become part of numerous applications in many areas of science from chemistry to biology to medicine.     

Release of nitric oxide from a sol-gel hybrid material containing a photoactive manganese nitrosyl upon illumination with visible light

A polyurethane-coated sol-gel material containing the photoactive Mn nitrosyl [Mn(PaPy3)(NO)]ClO4 rapidly releases NO with high quantum efficiency when exposed to visible light of low intensity. This rigid and strongly colored hybrid material is a convenient point source of NO that can only be triggered with light. Successful delivery of NO to biological targets, such as proteins, by this material has also been demonstrated.     

Synthesis of a new photoactive nanovehicle: a nanoworm

A nanovehicle with a new photoactive moiety has been synthesized. The incorporation of the azobenzene chassis allows for potential wormlike movement accompanying the rolling behavior of the wheels. Two versions, the fullerene-wheeled and carborane-wheeled nanoworms, were synthesized to examine the solution-based photoisomerization yields of the chassis.     

Identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor

Photoactive yellow proteins (PYP) are bacterial photoreceptors with a Per-Arnt-Sim (PAS) domain fold. We report the identification of six new PYPs, thus nearly doubling the size of this protein family. This extends the taxonomic diversity of PYP-containing bacteria from photosynthetic to nonphotosynthetic bacteria, from aquatic to soil-dwelling organisms, and from Proteobacteria to Salinibacter ruber from the phylum Bacteriodetes. The new PYPs greatly increase the sequence diversity of the PYP family, reducing the most prevalent pair-wise identity from 45% to 25%. Sequence alignments and analysis indicate that all 14 PYPs share a common structure with 13 highly conserved residues that form the chromophore binding pocket. Nevertheless, the functional properties of the PYPs vary greatly--the absorbance maximum extends from 432 to 465 nm, the pK(a) of the chromophore varies from pH 2.8 to 10.2, and the lifetime of the presumed PYP signaling state ranges from 1 ms to 1 h. Thus, the PYP family offers an excellent opportunity to investigate how functional properties are tuned over a wide range, while maintaining the same overall protein structural fold. We discuss the implications of these results for structure-function relationships in the PYP family.     

Peripherally metalated secoporphyrazines: a new generation of photoactive pigments

Base-catalyzed cross condensation of dipropylmaleonitrile 1 with bis(dimethylamino)maleonitrile 2 in an equimolar ratio afforded the porphyrazines 3a, 4a, 5a, 6a and 7a. Subsequent demetalation of 5a with TFA followed by remetalation with Zn(OAc)(2) gave ligand 5c in good yield. Compound 5c was, in turn, selectively oxidized and further peripherally functionalized using Pt(PhCN)(2)Cl(2) and PdCl(2) to yield the novel seco solitaire porphyrazines 10a and 10b. The photophysical profiles of the seco solitaire porphyrazines 10a and 10b were evaluated by means of absorption, emission, and transient absorption spectroscopy. The new pigments 10a and 10b were found to be photochemically more stable than the solitaire complexes 3d and 3e and mediated the generation of singlet oxygen with quantum yields of 0.59 and 0.45, respectively.     

p-Carborane: a new cage spacer for photoactive metal polypyridine dyads

The first example of a binuclear ruthenium complex involving the p-carborane framework in the bridging ligand is reported. The bridging ligand is a symmetric linear array comprising a central p-carborane unit, two p-phenylene spacers, and two 5-yl-2,2'-bipyridine coordinating units. A homobinuclear Ru(II) complex, with 2,2'-bipyridine as peripheral ligands, was synthesized and characterized. The Ru(II)-Ru(III) mixed-valence species, obtained by partial oxidation, has been investigated with steady-state and time-resolved techniques in CH3CN. The rate of photoinduced electron transfer is 2.3 x 10(8) s(-1).     

60]Fullerene: a versatile photoactive core for dendrimer chemistry

Owing to their special photophysical properties, fullerene derivatives are good candidates to demonstrate dendritic effects. In particular, the triplet lifetimes of a C(60) core can be used to evaluate its degree of isolation from external contacts. On the other hand, the fullerene core can act as a terminal energy receptor in dendrimer-based light-harvesting systems. When a fullerodendrimer is further functionalized with a suitable electron donor, it may exhibit the essential features of a multicomponent artificial photosynthetic system in which photoinduced energy transfer from the antenna to the C(60) core is followed by electron transfer.     

Visible light induced regioselective C5 halogenation of 8-aminoquinolines with 1,3-dihalo-5,5-dimethylhydantoin in continuous flow

An efficient and convenient method for remote C5 halogenation of 8-aminoquinoline derivatives was developed in continuous flow at room temperature. This method employed inexpensive 1,3-dibromo-5,5-dimethylhydantoin (DBDMH) and 1,3-dichlro-5,5-dimethylhydantoin (DCDMH) as halogenation reagents and visible light to catalyze the reaction. The reaction is scalable to gram-scale and proceeded with air and moisture tolerance, good functional group compatibility, and outstanding site selectivity, providing a new pathway for C5 halogenation of 8-aminoquinolines.     

Cyclic disulfide C8 iminoporfiromycin: nucleophilic activation of a porfiromycin

The clinical success of mitomycin C (1) and its associated toxicities and resistance have led to efforts to prepare semisynthetic analogues (i.e., KW-2149 (3), BMS-181174 (4)) that have improved pharmacological profiles. In this study, we report the preparation and evaluation of the novel 7-N-(1'-amino-4',5'-dithian-2'-yl)porfiromycin C(8) cyclized imine (6) and its reference compound, 7-N-(1'-aminocyclohex-2'-yl)porfiromycin C(8) cyclized imine (13). Porfiromycin 6 contains a disulfide unit that, upon cleavage, may provide thiol(s) that affect drug reactivity. We demonstrated that phosphines dramatically accelerated 6 activation and solvolysis in methanolic solutions ("pH 7.4") compared with 13. Porfiromycins 6 and 13 efficiently cross-linked EcoRI-linearized pBR322 DNA upon addition of Et3P. We found enhanced levels of interstrand cross-link (ISC) adducts for 6 and 13 compared with porfiromycin (7) and that 6 was more efficient than 13. The large Et3P-mediated rate enhancements for the solvolysis of 6 compared with 13 and a N(7)-substituted analogue of 1, and the increased levels of ISC adducts for 6 compared with 13 and 7 are attributed to a nucleophile-assisted disulfide cleavage process that permits porfiromycin activation and nucleophile (MeOH, DNA) adduction. The in vitro antiproliferative activities of 6 and 13 using the A549 tumor cell line (lung adenocarcinoma) were determined under aerobic and hypoxic conditions and then compared with 7. Both 6 and 13 were more cytotoxic than 7, with 13 being more potent than 6. The C(8) iminoporfiromycins 6 and 13 displayed anticancer profiles similar to 3.     

A photoactive isoprenoid diphosphate analogue containing a stable phosphonate linkage: synthesis and biochemical studies with prenyltransferases

A number of biochemical processes rely on isoprenoids, including the post-translational modification of signaling proteins and the biosynthesis of a wide array of compounds. Photoactivatable analogues have been developed to study isoprenoid utilizing enzymes such as the isoprenoid synthases and prenyltransferases. While these initial analogues proved to be excellent structural analogues with good cross-linking capability, they lack the stability needed when the goals include isolation of cross-linked species, tryptic digestion, and subsequent peptide sequencing. Here, the synthesis of a benzophenone-based farnesyl diphosphate analogue containing a stable phosphonophosphate group is described. Inhibition kinetics, photolabeling experiments, as well as X-ray crystallographic analysis with a protein prenyltransferase are described, verifying this compound as a good isoprenoid mimetic. In addition, the utility of this new analogue was explored by using it to photoaffinity label crude protein extracts obtained from Hevea brasiliensis latex. Those experiments suggest that a small protein, rubber elongation factor, interacts directly with farnesyl diphosphate during rubber biosynthesis. These results indicate that this benzophenone-based isoprenoid analogue will be useful for identifying enzymes that utilize farnesyl diphosphate as a substrate.     

The EQCM: electrogravimetry with a light touch

In its simplest manifestation, the electrochemical quartz crystal microbalance (EQCM) is a relatively new device for executing a classical technique, electrogravimetry. The advantages it brought were in situ applicability (notwithstanding prior misconceptions regarding damping by a contacting fluid), exceptional sensitivity and dynamic capability, thereby permitting real-time monitoring of changes in surface populations of species during electrochemically driven processes. The basis of the method relies on the storage and dissipation of energy injected into the interfacial region by a high frequency (megahertz) acoustic wave; the latter is generated by a piezoelectric (generally quartz) resonator. From modest early aspirations, largely associated with the deposition/dissolution of simple adsorbates and thin metal films, the technique has expanded in three strategic respects: materials, phenomena and methodology. In the first instance, extension to thick electroactive films (notably metal oxides and polymers) has generated considerable insight. Second, the sensitivity of the EQCM to viscoelastic phenomena, stress and interfacial slip has been recognized. Considerable attention has been given to viscoelastic processes in redox and conducting polymers: these have been parameterized in terms of shear moduli, whose variation with polymer structure and imposed conditions provides insight into polymer dynamics. Procedures exist for characterizing film stress in harder materials, but this is less well exploited. Interfacial slip remains a poorly understood area. Third, application in the context of diverse electrochemical control functions and integration with other in situ techniques provide many as yet unexploited opportunities. The extent to which these are realised will probably depend on the level of interpretation of the resultant data, which presently underuses the library of modelling protocols available.     

Synthesis of a C8 oxygenated pyranonaphthoquinone: a useful precursor to dimeric pyranonaphthoquinones

The synthesis of a pyranonaphthoquinone bearing an oxygenated substituent at C8 is reported. The oxygen substituent at C8 provides a key functionality for use as a homocoupling precursor for the synthesis of a dimeric pyranonaphthoquinone.     

Rhodium-Catalyzed C8-Alkenylation of Isoquinolones with Maleimides

An efficient Rh(III)-catalyzed C−H alkenylation of N-protected isoquinolone with maleimides is reported. The carbonyl group of isoquinolone acts as an inherent directing group. Various N-substituents in the maleimide, including alkyl, aryl, and even H and −OH, were well tolerated under the developed reaction condition. This protocol showed broad substrate scope, good selectivity, and excellent yields. Hammett plot is also drawn to check the effect of substituents on the reaction progress.     

Near-infrared light activated release of nitric oxide from designed photoactive manganese nitrosyls: strategy, design, and potential as NO donors

Two new manganese complexes derived from the pentadentate ligand N,N-bis(2-pyridylmethyl)amine-N-ethyl-2-quinoline-2-carboxamide, PaPy2QH, where H is dissociable proton), namely, [Mn(PaPy2Q)(NO)]ClO4 (2) and [Mn(PaPy2Q)(OH)]ClO4 (3), have been synthesized and structurally characterized. The Mn(III) complex [Mn(PaPy2Q)(OH)]ClO4 (3), though insensitive to dioxygen, reacts with nitric oxide (NO) to afford the nitrosyl complex [Mn(PaPy2Q)(NO)]ClO4 (2) via reductive nitrosylation. This diamagnetic {Mn-NO}6 nitrosyl exhibits nuNO at 1725 cm-1 and is highly soluble in water, with lambdamax at 500 and 670 nm. Exposure of solutions of 2 to near-infrared (NIR) light (810 nm, 4 mW) results in bleaching of the maroon solution and detection of free NO by an NO-sensitive electrode. The quantum yield of 2 (Phi = 0.694 +/- 0.010, lambdairr = 550 nm, H2O) is much enhanced over the first generation {Mn-NO}6 nitrosyl derived from analogous polypyridine ligand, namely, [Mn(PaPy3)(NO)]ClO4 (1, Phi = 0.385 +/- 0.010, lambdairr = 550 nm, H2O), reported by this group in a previous account. Although quite active in the visible range (500-600 nm), 1 exhibits very little photoactivity under NIR light. Both 1 and 2 have been incorporated into sol-gel (SG) matrices to obtain nitrosyl-polymer composites 1.SG and 2.SG. The NO-donating capacities of the polyurethane-coated hybrid materials 1.HM and 2.HM have been determined. 2.HM has been used to transfer NO to reduced myoglobin with 780 nm light. The various strategies for synthesizing photosensitive metal nitrosyls have been discussed to establish the merits of the present approach. The results of the present study confirm that proper ligand design is a very effective way to isolate photoactive manganese nitrosyls that could be used to deliver NO to biological targets under the control of NIR light.     

A new photoactive and highly soluble C(60)-TTF-C(60) dimer: charge separation and recombination

The covalent linkage of two [60]fullerene cores to a tetrathiafulvalene (TTF) donor affords a soluble and photoactive C(60)-TTF-C(60) triad. Spectroscopic and photophysical characterization of the C(60)-TTF-C(60) triad are given. Although the cyclic voltammetry measurements reveal no notable interaction between the chromophores in the ground state, photophysical data show that in the excited state an intramolecular electron transfer, evolving from the TTF donor to the singlet state of C(60), prevails, yielding a long-lived charge separated radical pair.     

Deprotonation of Coordinated Phosphanes in a Rhenium Complex: CC Coupling with Diimine Coligands

The reaction of fac‐[Re(bipy)(CO)₃(PMe₃)][OTf] (bipy=2,2′‐bipyridine) with KN(SiMe₃)₂ affords two neutral products: cis,trans‐[Re(bipy)(CO)₂(CN)(PMe₃)], and a thermally unstable compound, which features a new C?C bond between a P‐bonded methylene group (from methyl group deprotonation) and the C6 position of bipy. The solid‐state structures of more stable 1,2‐bis[(2,6‐diisopropylphenyl)imino]acenaphthene analogs, resulting from the deprotonation of PMe₃, PPhMe₂, and PPh₂Me ligands, are determined by X‐ray diffraction.     

Synthesis and properties of a microtube photocatalyst with photoactive inner surface and inert outer surface

Synthesis of a photocatalyst with a novel particle form, its photoactivity, and the degradation of polyvinyl alcohol containing the photocatalyst were studied in detail. A microtube photocatalyst with titanium dioxide particles supported on the inner surface of the microtube was synthesized by adding fine titanium dioxide particles in the formation process of basic magnesium carbonate microtube. The photoactivity of the microtube photocatalyst was confirmed from the decomposition of 2-propanol under blacklight irradiation. Moreover, the microtube photocatalyst was found to cause no degradation of polyvinyl alcohol, whereas, it decomposed 2-propanol with its photoactivity when impregnated in a polyvinyl alcohol foam. This fact was considered to be derived from the unique structure of the microtube photocatalyst, which has a photoactive inner surface with titanium dioxide and an inert outer surface of basic magnesium carbonate.     

Total synthesis of (+)-discodermolide: an improved endgame exploiting a Still-Gennari-type olefination with a C1-C8 beta-ketophosphonate fragment

[structure: see text] An improved, third-generation, total synthesis of (+)-discodermolide, a potent microtubule-stabilizing anticancer agent of marine sponge origin, is achieved in 11.1% yield over 21 steps. Key steps include a Still-Gennari HWE olefination, performed using NaH as the base, between C1-C8 beta-ketophosphonate 7 and C9-C24 aldehyde 8, introducing the (8Z)-alkene with 10:1 selectivity, and K-Selectride reduction of the derived enone 16, installing the (7S)-configuration.