A single DNA aptamer functions as a biosensor for ricin

The use of microorganisms or toxins as weapons of death and fear is not a novel concept; however, the modes by which these agents of bioterrorism are deployed are increasingly clever and insidious. One mechanism by which biothreats are readily disseminated is through a nation's food supply. Ricin, a toxin derived from the castor bean plant, displays a strong thermostability and remains active at acidic and alkaline pHs. Therefore, the CDC has assigned ricin as a category B reagent since it may be easily amendable as a deliberate food biocontaminate. Current tools for ricin detection utilize enzymatic activity, immunointeractions and presence of castor bean DNA. Many of these tools are confounded by complex food matrices, display a limited dynamic range of detection and/or lack specificity. Aptamers, short RNA and single stranded DNA sequences, have increased affinity to their selected receptors, experience little cross-reactivity to other homologous compounds and are currently being sought after as biosensors for bacterial contaminants in food. This paper describes the selection and characterization of a single, dominant aptamer, designated as SSRA1, against the B-chain of ricin. SSRA1 displays one folding conformation that is stable across 4-63 °C (ΔG = -5.05). SSRA1 is able to concentrate at least 30 ng mL(-1) of ricin B chain from several liquid food matrices and outcompetes a currently available ELISA kit and ricin aptamer. Furthermore, we show detection of 25 ng mL(-1) of intact ricin A-B complex using SSRA1 combined with surface enhanced Raman scattering technique. Thus, SSRA1 would serve well as pre-analytical tool for processing of ricin from liquid foods to aid current diagnostics as well as a sensor for direct ricin detection.     

Aromatic foldamers as scaffolds for metal second coordination sphere design

As metalloproteins exemplify, the chemical and physical properties of metal centers depend not only on their first but also on their second coordination sphere. Installing arrays of functional groups around the first coordination sphere of synthetic metal complexes is thus highly desirable, but it remains a challenging objective. Here we introduce a novel approach to produce tailored second coordination spheres. We used bioinspired artificial architectures based on aromatic oligoamide foldamers to construct a rigid, modular and well-defined environment around a metal complex. Specifically, aza-aromatic monomers having a tethered [2Fe–2S] cluster have been synthesized and incorporated in conical helical foldamer sequences. Exploiting the modularity and predictability of aromatic oligoamide structures allowed for the straightforward design of a conical architecture able to sequester the metal complex in a confined environment. Even though no direct metal complex–foldamer interactions were purposely designed in this first generation model, crystallography, NMR and IR spectroscopy concurred to show that the aromatic oligoamide backbone alters the structure and fluxional processes of the metal cluster.

Wrapping a [2Fe–2S] metal complex in an aromatic foldamer helix is introduced as a new approach to tailor a second coordination sphere.     

Polyoxometalate-organic hybrid molecules as amphiphilic emulsion catalysts for deep desulfurization

So emulsional: Two hexavanadate-organic hybrids were synthesized and their amphiphilic properties were confirmed by forming emulsions in mixtures of water and nonpolar organic solvents, and were utilized as "emulsion catalysts" in deep desulfurization reactions (see figure). Their catalytic activities show a pH-dependent behavior, which can be explained by the size-change of emulsions and the appearance of reverse emulsions.     

NMR and UV studies of 3'-S-phosphorothiolate modified DNA in a DNA : RNA hybrid dodecamer duplex; implications for antisense drug design

High-resolution NMR spectroscopy has been used to establish the conformational consequences of the introduction of a single 3[prime or minute]-S-phosphorothiolate link in the DNA strand of a DNA : RNA hybrid. These systems are of interest as potential antisense therapeutic agents. Previous studies on similarly modified dinucleotides have shown that the conformation of the sugar to which the sulfur is attached shifts to the north (C(3[prime or minute])-endo/C(2[prime or minute])-exo). Comparisons made between NOESY cross-peak intensities, and coupling constants from PE-COSY spectra, for both non-modified and modified duplexes confirm that this conformational shift is also present in the double helical oligonucleotide system. In addition it is noted that in both the dinucleotides and the modified duplex, the conformation of the sugar ring 3[prime or minute] to the site of modification is also shifted to the north. That this pattern is observed in the small monomeric system as well as the larger double helix is suggestive of some pre-ordering of the sequences. The conclusion is supported by consideration of the (1)H chemical shifts of the heterocyclic bases near the site of the modification. The enhanced stability that these conformational changes should bring was confirmed by UV thermal melting studies. Subsequently a series of singly and doubly 3[prime or minute]-S-phosphorothiolate-modified duplexes were investigated by UV. The results are indicative of an additive effect of the modification with thermodynamic benefit being derived from alternate spacing of two modified linkers.     

Use of ferrocene scaffolds as pendant groups in hairpin-type pyrrole-imidazole polyamide molecules showing sequence-selective binding to DNA duplexes

[reaction: see text] The synthesis and properties of new conjugate molecules, Fc-PIA, composed of ferrocene (Fc) and pyrrole-imidazole polyamides (PIA) are reported. As a PIA sequence, we chose Im-Py-Im/Py-Im-Py considering its future application to the SNPs detection of genes having a GCG/CGC sequence. Two types of Fc-containing linkers, i.e., ferrocene-1,1'-dicarboxamide and ferrocenecarboxamide, were designed, and several Fc-PIPA molecules having these linkers were synthesized. Titration studies by use of circular dichroism revealed that the carboxamide-type Fc-PIA could bind to the target DNA with an association constant of 10(7) M(-1). In contrast, ferrocene dicarboxamide-type compounds have slightly weaker affinity for the target DNA. However, the affinity could be recovered by replacing one of the pyrrole residues with beta-alanine. We carried out the CV measurement and observed quasi-irreversible oxidation of the ferrocene moieties in the Fc-PIA compounds. These properties of Fc-PIA indicate the potential usefulness of these molecules in electrochemical detection of genes.     

Porphyrazines peripherally functionalized with hybrid ligands as molecular scaffolds for bimetallic metal-ion coordination

We report the synthesis and physical characterization of a new family of peripherally functionalized porphyrazine (pz) compounds, denoted 1[M1, M2], where metal ion M1 is incorporated into the pz core and metal ion M2 is bound to a salicylidene/picolinamide "hybrid" chelate built onto two nitrogen atoms attached to the pz periphery. The complexes 1[MnCl, Cu], 1[VO, Cu], and 1[Cu, Cu] have been prepared, and crystal structures show 1[MnCl, Cu] and 1[VO, Cu] to be isostructural. These complexes have been subjected to electron paramagnetic resonance and temperature-dependent magnetic susceptibility measurements. The variation of the ligand-mediated exchange splittings (delta) in these complexes is striking: delta/k(B) values for 1[MnCl, Cu] and 1[VO, Cu] are 22 and 40 K, respectively, while delta/k(B) for 1[Cu, Cu] is only 1 K. These coupling results are explained in terms of the relative orientation of the M1 and M2 orbitals and reflect the fact that the ligand set of M2 in the periphery is rotated in-plane by 45 degrees relative to the effectively coplanar pz ligand set of M1. The exchange couplings are essentially the same as those we determined for the Schiff base porphyrazines (pzs). Thus, the hybrid ligand has eliminated the dimerization found to occur when Cu(II) is bound to the periphery of bis(picolinamido) pzs and has created a more robust ligand system than the Schiff base pzs while retaining the ability they show to promote spin coupling between M1 and M2.     

Battle for the bulge: directing small molecules to DNA and RNA defects

Small molecules were tailored to specifically bind bulged DNA by complementing the geometry and nucleotide size of the bulge site. The prospect of generating small molecules that influence the secondary structure of DNA and RNA holds great promise for clinical applications.     

Hydrolytically stable octahedral silicon complexes as bioactive scaffolds: application to the design of DNA intercalators

We here introduce octahedral silicon serving as a structural center for the design of hydrolytically stable bioactive complexes as demonstrated with the generation of silicon-based high affinity DNA binders. This proof-of-principle study suggests that octahedral silicon complexes are falsely neglected, promising structural templates for widespread applications in chemical biology and medicinal chemistry.     

Microanalysis of hybrid characterization of PLA/cHA polymer scaffolds for bone regeneration

Tissue engineering uses some engineering strategies for the reconstruction and repair of the compromised tissues, among which the use of biomaterials as an alternative to conventional transplants is significant. However, not many research has been developed on the use of biopolymer nanostructure microanalysis and calcium phosphate composites of carbon apatite in PLA as scaffolds for tissue regeneration. In this work, poly (lactic acid) filaments with 5% and 20%, carbon apatite (cHA) were microanalysis to produce a 3D printing scaffold. The scaffolds were characterised by the Scanning Electron Microscope (SEM) and Energy Dispersive X-Ray (EDX) techniques, thereby making it possible to notice a good load dispersion. The microstructural analysis of the scaffolds was carried out by computerised micro-tomography to determine the roughness, morphological parameters of pore size distribution, porosity, as well as better visualisation of the distribution of particles. A computational in vitro and microanalysis tests to assess the biocompatibility viability of the PLA/cHA structure with a variation of scaffold geometry to evaluate their effects on morphological, physicochemical and mechanical properties were also carried out. The characterisation of Ca and P release assays were observed for longer incubation times and the dynamic condition control to simulate the stresses suffered by the biomaterial exerted by the flow of fluids was achieved. The results obtained indicated that the micrographs of the cross-sections of the scaffolds showed a flatness in the loaded material when compared to the 100/0 PLA. Furthermore, the apparent porosity of 5% and 20% of cHA scaffolds gave a porosity percentage of approximately 62% and 41% respectively. The reduced summit height, reduced valley depth and the percentage upper and lower bearing area difference of the samples are 16.33 nm, 9.62 nm and 75.07% respectively. The morphological characterisation surface roughness analysis and tolerance insertion gave a favourable reduced porosity result for the composite scaffolds with 5% of cHA. Hence, this work will assist biomaterial industries in the development of biomaterials which have been engineered with biological systems to meet medical purposes.     

Uracil-coumarin based hybrid molecules as potent anti-cancer and anti-bacterial agents

In the current report, we have rationally designed a series of uracil-coumarin based bifunctional molecular hybrids roped by 1,2,3-triazole moiety. The designed compounds were synthesized and tested against a panel of six human cancer cell lines namely Colo-205, MCF-7, A-549, PA-1, PC-3 and Hela cells by Sulforhodamine B assay. The results indicated that the hybrid molecules can specifically inhibit the MCF-7 cancer cell proliferation amongst which A-2 was found to be most potent hybrid (GI₅₀ = 1.55 µM) with fluorine atom as R with two carbon chain length between triazole and coumarin moieties. Cell cycle analysis revealed that A-2 significantly arrest the G2/M phase to inhibit proliferation of MCF-7 cells. Due to its mitotic arrest, A-2 was further analyzed to predict its various binding interactions within the active site of tubulin, which revealed its best binding pattern within the vinblastine binding site. In addition to this, antibacterial potential of all the synthetics was also evaluated which resulted in two hit lead molecules A-2 (MIC = 11.7 μg/mL) and A-3 (MIC = 7.23 μg/mL) that can significantly inhibit the bacterial strain Staphylococcus aureus comparable to that of standard drug levofloxacin (MIC = 3.12 μg/mL). Binding interactions within the active site of dihydrofolate reductase (DHFR) were also streamlined by using molecular docking studies. Overall studies revealed some interesting features of synthetics to be active which stated that, the compounds with electronegative atom on R and compounds with two carbon chain length between triazole and coumarin showed best results.     

RNA as multitude/RNA as one

In the configurations formed by RNA and its ions there are structural possibilities not yet realized; some are hinted at in new work on the binding of an amino acid analog.     

Simple ethers as models of sugar molecules in calculations of vertical excitation energies of DNA and RNA nucleosides

The ribose and deoxyribose molecules of RNA and DNA nucleosides are substituted with simple model compounds 1-methoxy-2-ethanol and 1-methoxypropane to mimic the effect of binding to sugars on the vertical excitation energies of purine and pyrimidine bases. The (R)-1-methoxy-2-ethanol, CH(3)OC*HCH(2)OH, for model ribose nucleosides and (R)-1-methoxypropane, CH(3)OC*HC(2)H(5), for model deoxyribose nucleosides have minimal structural characteristics of ribose and deoxyribose molecules when attached to nucleic acid purine and pyrimidine bases. The bases are attached to the C1 carbon atom designated by the asterisk. The vertical excitation energies of these model nucleosides are calculated with the time-dependent density functional theory method at the B3LYP level with 6-311++G(d,p) and aug-cc-pVDZ basis sets. The attachment of the ether molecules qualitatively and quantitatively modifies the excited state energy levels of the model nucleosides when compared to the free bases. These changes can affect the deexcitation mechanisms for photoexcited nucleosides.     

Homogeneous organic/inorganic hybrid scaffolds with high osteoinductive activity for bone tissue engineering

Composite scaffolds of polymers/β-tricalcium phosphate (TCP) have been widely used for bone regeneration due to the combination of osteoinductivity of TCP and mechanical properties of the polymers. However, the difference in surface properties of the two material causes composite has poor uniformity and weak two-phase interaction, resulting in poor TCP release and weak new bone-forming ability. In this research, a TCP sol was developed to replace traditional TCP nanoparticles for the preparation of homogeneous polycaprolactone (PCL)/TCP sol nanofibrous scaffolds. It was found that compared with TCP nanoparticles, TCP sol homogeneously distributed in PCL nanofibers, and greatly improved the hydrophilicity, biodegradability, and mechanical properties of the scaffolds. It is also confirmed that loading TCP sol promoted the formation of bone-like apatite on the surface of the scaffolds. Biological experiments showed that all scaffolds supported rat bone marrow mesenchymal stem cells (rBMSCs) proliferation, especially scaffolds loaded with TCP sol. The increase in alkaline phosphatase activity and collagen production, enhanced calcium deposition, and up-regulation of osteocalcin expression demonstrated that the loading TCP sol expanded an advantage of scaffolds in promoting rBMSCs osteogenic differentiation, suggesting it dramatically improved the osteoinductive activity of PCL/TCP hybrid system and had a great potential application in bone regeneration.     

Synthesis of novel scaffolds based on thiazole or triazolothiadiazine linked to benzofuran or benzo[d]thiazole moieties as new hybrid molecules

Abstract

A synthesis of novel hybrid molecules containing thiazole or bis(thiazoles) each bearing benzofuran and/or benzo[d]thiazole moieties by the reaction of the appropriate thioamide derivatives with the corresponding bis-bromoacetyl derivatives is reported. Mono- and bis(triazolothiadiazine) derivatives based on benzofuran or benzo[d]thiazole moieties were also synthesized in good yields by the reaction of the appropriate bis(bromoacetyl) derivatives with each of 4-amino-5-mercapto-1,2,4-triazoles and their corresponding bis-derivatives.     

Chemoinformatics methods for systematic comparison of molecules from natural and synthetic sources and design of hybrid libraries

Until recently, the field of diversity and library design has more or less ignored natural products as a compound source. This is probably due to at least two reasons. First, combinatorial and reaction-based approaches have been major focal points in the early days of computational library design. In addition, a widespread view is that natural products are often highly complex and not amenable to medicinal chemistry efforts. This contribution introduces recent computational approaches to systematically analyze natural molecules and bridge the gap between natural products and synthetic chemistry programs. Large scale comparisons of natural and synthetic molecules are discussed as well as studies designed to identify `synthetic mimics' of natural products with specific activity. In addition, a concept for the design of natural/synthetic hybrid libraries is introduced. Although research in this area is still in its early stages, an important lesson to be learned from computational analyses is that there is no need to a priori `shy away' from natural products as a source for molecular design.     

Preparation and characterization of bacterial cellulose/heparin hybrid nanofiber for potential vascular tissue engineering scaffolds

Blending two polymers is a common and effective way to develop a new material with combinations of properties not possessed by individual polymers and to overcome some limitations of individual components. This study aimed at developing a novel scaffold to mimic natural extracellular matrix (ECM) and to promote blood compatibility. Heparin (Hep) and bacterial cellulose (BC), for the first time, were hybridized to prepare a novel class of nanofibrous scaffold for vascular tissue engineering by the co‐synthesis process. The morphology of Hep–BC hybrid nanofiber was observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The hybrid was further characterized by Fourier transform infrared spectroscopy (FTIR), X‐ray photoelectron spectroscopy (XPS), and X‐ray diffraction (XRD). The results show that hybridizing heparin brings anticoagulant sulfate groups into BC nanofiber and that Hep–BC nanofiber has a different structure in comparison to pristine BC. This work paves a new way of improving anticoagulant property of tissue engineered vessels other than coating process. Copyright © 2010 John Wiley & Sons, Ltd.     

Hexakis-adducts of [60]fullerene as molecular scaffolds of polynuclear spin-crossover molecules

A family of hexakis-substituted [60]fullerene adducts endowed with the well-known tridentate 2,6-bis(pyrazol-1-yl)pyridine (bpp) ligand for spin-crossover (SCO) systems has been designed and synthesized. It has been experimentally and theoretically demonstrated that these molecular scaffolds are able to form polynuclear SCO complexes in solution. UV-vis and fluorescence spectroscopy studies have allowed monitoring of the formation of up to six Fe(ii)–bpp SCO complexes. In addition, DFT calculations have been performed to model the different complexation environments and simulate their electronic properties. The complexes retain SCO properties in the solid state exhibiting both thermal- and photoinduced spin transitions, as confirmed by temperature-dependent magnetic susceptibility and Raman spectroscopy measurements. The synthesis of these complexes demonstrates that [60]fullerene hexakis-adducts are excellent and versatile platforms to develop polynuclear SCO systems in which a fullerene core is surrounded by a SCO molecular shell.

Polynuclear spin-crossover molecules showing both thermal and photoinduced spin transitions have been prepared using a [60]fullerene hexakis-adduct endowed with Fe(ii) complexes of tridentate 2,6-bis(pyrazol-1-yl)pyridine (bpp) ligand.     

Two-dimensional scaffolds for the parallel alignment of rod-shaped conjugated molecules

Described is a method for creating two-dimensional, ordered arrays of linear, conjugated organic molecules on polyimide scaffolds. Key to the design was the enforcement of consecutive 90 degrees twist angles along the polyimide backbone. Rod molecules that are templated by such scaffolds are held parallel and in the same plane and have optical properties that are similar to those of monomeric analogues. As supporting evidence for the structures of the polymers, a series of model compounds were synthesized and characterized by X-ray crystallography. The polymeric materials are soluble and have been characterized by 1H NMR, 13C NMR, MALDI-TOF, and UV-vis spectroscopy.     

NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes.

The first structure of a 2'-deoxy-2'-fluoro-D-arabinose nucleic acid (2'F-ANA)/RNA duplex is presented. We report the structural characterization by NMR spectroscopy of a small hybrid hairpin, r(GGAC)d(TTCG)2'F-a(GTCC), containing a 2'F-ANA/RNA stem and a four-residue DNA loop. Complete (1)H, (13)C, (19)F, and (31)P resonance assignments, scalar coupling constants, and NOE constraints were obtained from homonuclear and heteronuclear 2D spectra. In the chimeric duplex, the RNA strand adopts a classic A-form structure having C3' endo sugar puckers. The 2'F-ANA strand is neither A-form nor B-form and contains O4' endo sugar puckers. This contrasts strongly with the dynamic sugar conformations previously observed in the DNA strands of DNA/RNA hybrid duplexes. Structural parameters for the duplex, such as minor groove width, x-displacement, and inclination, were intermediate between those of A-form and B-form duplexes and similar to those of DNA/RNA duplexes. These results rationalize the enhanced stability of 2'F-ANA/RNA duplexes and their ability to elicit RNase H activity. The results are relevant for the design of new antisense drugs based on sugar-modified nucleic acids.