RNA interference and receptors

@article{lamanna_hydramers_2011,

title = {HYDRAmers: design, synthesis and characterization of different generation novel Hydra-like dendrons based on multifunctionalized adamantane},

author = {Giuseppe Lamanna and Julie Russier and Cécilia Ménard-Moyon and Alberto Bianco},

doi = {10.1039/c1cc11689d},

issn = {1364-548X},

year  = {2011},

date = {2011-08-01},

journal = {Chemical Communications (Cambridge, England)},

volume = {47},

number = {31},

pages = {8955--8957},

abstract = {In this communication we present a new synthetic strategy to different generation Hydra-like dendrons based on tetrafunctionalized adamantane as a building block. The novel dendrons, which we termed HYDRAmers, possess at the periphery and at the central core orthogonal protections that can be exploited for conjugation of targeting ligands, drugs and/or imaging probes.},

keywords = {Adamantane, Animals, Cell Line, Dendrimers, Drug Design, Humans, I2CT, L-Lactate Dehydrogenase, Magnetic Resonance Spectroscopy, Mice, Team-Bianco, tumor},

pubstate = {published},

tppubtype = {article}

}

@article{singh_carbon_2011,

title = {Carbon nanotube-nucleobase hybrids: nanorings from uracil-modified single-walled carbon nanotubes},

author = {Prabhpreet Singh and Francesca Maria Toma and Jitendra Kumar and V Venkatesh and Jesus Raya and Maurizio Prato and Sandeep Verma and Alberto Bianco},

doi = {10.1002/chem.201100312},

issn = {1521-3765},

year  = {2011},

date = {2011-06-01},

journal = {Chemistry (Weinheim an Der Bergstrasse, Germany)},

volume = {17},

number = {24},

pages = {6772--6780},

abstract = {Single-walled carbon nanotubes (SWCNTs) have been covalently functionalized with uracil nucleobase. The hybrids have been characterized by using complementary spectroscopic and microscopic techniques including solid-state NMR spectroscopy. The uracil-functionalized SWCNTs are able to self-assemble into regular nanorings with a diameter of 50-70 nm, as observed by AFM and TEM. AFM shows that the rings do not have a consistent height and thickness, which indicates that they may be formed by separate bundles of CNTs. The simplest model for the nanoring formation likely involves two bundles of CNTs interacting with each other via uracil-uracil base-pairing at both CNT ends. These nanorings can be envisaged for the development of advanced electronic circuits.},

keywords = {carbon, I2CT, Magnetic Resonance Spectroscopy, Molecular Structure, Nanotubes, Team-Bianco, Uracil},

pubstate = {published},

tppubtype = {article}

}

@article{marega_two-dimensional_2010,

title = {Two-dimensional diffusion-ordered NMR spectroscopy as a tool for monitoring functionalized carbon nanotube purification and composition},

author = {Riccardo Marega and Vincent Aroulmoji and Massimo Bergamin and Luigi Feruglio and Francesca Dinon and Alberto Bianco and Erminio Murano and Maurizio Prato},

doi = {10.1021/nn100257h},

issn = {1936-086X},

year  = {2010},

date = {2010-04-01},

journal = {ACS nano},

volume = {4},

number = {4},

pages = {2051--2058},

abstract = {Functionalized carbon nanotube (CNT) derivatives are currently under thorough investigation in different biomedical investigations. In this field of research, the composition of sample either in terms of covalently attached or physisorbed moieties can greatly affect the observed results and hamper the comparison between different studies. Therefore, the availability of a fast and reliable analytical technique to assess both the type of interaction (covalent vs noncovalent) and the composition of CNT conjugates is of great importance. Here we describe that the two-dimensional diffusion-ordered (DOSY) NMR spectroscopy is extremely useful to discriminate between conjugated and unconjugated polyethylene glycol groups in samples obtained by condensation with oxidized single-walled carbon nanotubes (SWNTs). This fast and nondestructive technique allows us to follow the removal of unconjugated polyethylene glycol chains during the purification. In particular, DOSY analysis reveal that about 1/3 (wt %) of the polyethylene glycol used for the condensation remained physisorbed to functionalized SWNTs after dialysis. Complete elimination of physisorbed polyethylene glycol was achieved using diafiltration.},

keywords = {carbon, Diffusion, I2CT, Magnetic Resonance Spectroscopy, Nanotubes, Polyethylene Glycols, Solubility, Team-Bianco, Temperature, water},

pubstate = {published},

tppubtype = {article}

}

@article{singh_synthesis_2009,

title = {Synthesis and characterization of nucleobase-carbon nanotube hybrids},

author = {Prabhpreet Singh and Jitendra Kumar and Francesca Maria Toma and Jesus Raya and Maurizio Prato and Bruno Fabre and Sandeep Verma and Alberto Bianco},

doi = {10.1021/ja905041b},

issn = {1520-5126},

year  = {2009},

date = {2009-09-01},

journal = {Journal of the American Chemical Society},

volume = {131},

number = {37},

pages = {13555--13562},

abstract = {We report the synthesis and characterization of adenine-single-walled carbon nanotube (SWCNT) hybrid materials, where for the first time nucleobases are covalently attached to the exosurface of SWCNTs. The structural properties of all hybrids have been characterized using usual spectroscopic and microscopic techniques. The degree of functional groups for functionalized SWCNTs (f-SWCNTs) 2a and 2b is one adenine group for each 26 and 37 carbon atoms, respectively. Solid-state magic angle spinning (13)C NMR spectroscopy (MAS NMR) and electrochemistry have been also applied for the characterization of these f-SWCNTs. AFM images of f-SWCNT 2b showed an interesting feature of horizontally aligned nanotubes along the surface when deposited on highly oriented pyrolytic graphite surface. Furthermore, we evaluated the coordinating ability of these hybrid materials toward silver ions, and interestingly, we found a pattern of silver nanoparticles localized over the surface of the carbon nanotube network. The presence of aligned and randomly oriented CNTs and their ability to coordinate with metal ions make this class of materials very interesting for applications in the development of novel electronic devices and as new supports for different catalytic transformations.},

keywords = {Adenine, Amides, Amines, Biosensing Techniques, carbon, Catalysis, Electrochemistry, Graphite, I2CT, Magnetic Resonance Spectroscopy, Nanotubes, Nanowires, Surface Properties, Team-Bianco},

pubstate = {published},

tppubtype = {article}

}

@article{marega_diffusion-ordered_2009,

title = {Diffusion-ordered NMR spectroscopy in the structural characterization of functionalized carbon nanotubes},

author = {Riccardo Marega and Vincent Aroulmoji and Francesca Dinon and Lisa Vaccari and Silvia Giordani and Alberto Bianco and Erminio Murano and Maurizio Prato},

doi = {10.1021/ja902728w},

issn = {1520-5126},

year  = {2009},

date = {2009-07-01},

journal = {Journal of the American Chemical Society},

volume = {131},

number = {25},

pages = {9086--9093},

abstract = {The emerging applications of functionalized carbon nanotubes (CNTs) in various research domains necessitate the use of many different analytical techniques to confirm their structural modifications in a fast and reliable manner. Thus far, NMR spectroscopy has not been among the main tools for characterization of organically modified carbon nanostructures. (1)H analysis is limited because the signals in these derivatives are typically weak and broad, resulting in uncertainties of a few parts per million, and because of the strong interference of residual solvent signals. To overcome these limitations, we investigated the applicability of proton NMR spectroscopy based on gradient-edited diffusion pulse sequences (1D diffusion-ordered spectroscopy, DOSY) in the characterization of CNT derivatives. In general, diffusion NMR experiments allow the separation of NMR signals of different species present in a mixture, according to their own diffusion coefficients, merging spectroscopy information with size analysis. In the present study, a selected set of CNT derivatives was synthesized and analyzed using 1D DOSY experiments by applying strong magnetic field gradients (up to 42.6 G cm(-1)). Colorimetric tests (i.e., Kaiser test) and TGA analysis support the NMR findings, which are related to isolated and/or bundled short SWNTs, on the basis of TEM and AFM characterization. The overall results show that the diffusion-based NMR spectroscopy is a fast and promising approach for the characterization of covalently modified CNT derivatives.},

keywords = {carbon, Diffusion, I2CT, Magnetic Resonance Spectroscopy, Nanotubes, Oxidation-Reduction, Surface Properties, Team-Bianco},

pubstate = {published},

tppubtype = {article}

}

@article{geotti-bianchini_conformationally_2009,

title = {Conformationally controlled, thymine-based alpha-nucleopeptides},

author = {Piero Geotti-Bianchini and Marco Crisma and Cristina Peggion and Alberto Bianco and Fernando Formaggio},

doi = {10.1039/b822789f},

issn = {1359-7345},

year  = {2009},

date = {2009-01-01},

journal = {Chemical Communications (Cambridge, England)},

number = {22},

pages = {3178--3180},

abstract = {Rigid peptide backbones and backbone-to-side chain H-bonds permit the design of alpha-nucleopeptides with known 3D-structure; thymine-thymine base pairing is also observed.},

keywords = {I2CT, Magnetic Resonance Spectroscopy, Oligopeptides, Protein Conformation, Team-Bianco, thymine, X-Ray Diffraction},

pubstate = {published},

tppubtype = {article}

}

@article{violette_exploring_2008,

title = {Exploring helical folding of oligoureas during chain elongation by high-resolution magic-angle-spinning (HRMAS) NMR spectroscopy},

author = {Aude Violette and Nathalie Lancelot and Alexander Poschalko and Martial Piotto and Jean-Paul Briand and Jesus Raya and Karim Elbayed and Alberto Bianco and Gilles Guichard},

doi = {10.1002/chem.200701923},

issn = {0947-6539},

year  = {2008},

date = {2008-01-01},

journal = {Chemistry (Weinheim an Der Bergstrasse, Germany)},

volume = {14},

number = {13},

pages = {3874--3882},

abstract = {The development of novel folding oligomers (foldamers) for biological and biomedical applications requires both precise structural information and appropriate methods to detect folding propensity. However, the synthesis and the systematic conformational investigation of large arrays of oligomers to determine the influence of factors, such as chain length, side chains, and surrounding environment, on secondary structure can be quite tedious. Herein, we show for 2.5-helical N,N'-linked oligoureas (gamma-peptide lineage) that the whole process of foldamer characterization can be accelerated by using high-resolution magic-angle-spinning (HRMAS) NMR spectroscopy. This was achieved by monitoring a simple descriptor of conformational homogeneity (e.g., chemical shift difference between diastereotopic main chain CH2 protons) at different stages of oligourea chain growth on a solid support. HRMAS NMR experiments were conducted on two sets of oligoureas, ranging from dimer to hexamer, immobilized on DEUSS, a perdeuterated poly(oxyethylene)-based solid support swollen in solvents of low to high polarity. One evident advantage of the method is that only minute amount of material is required. In addition, the resonance of the deuterated resin is almost negligeable. On-bead NOESY spectra of high quality and with resolution comparable to that of liquid samples were obtained for longer oligomers, thus allowing detailed structural characterization.},

keywords = {I2CT, Magnetic Resonance Spectroscopy, Molecular Structure, Solvents, Team-Bianco, Urea},

pubstate = {published},

tppubtype = {article}

}

@article{lancelot_measurement_2004,

title = {Measurement of scaled residual dipolar couplings in proteins using variable-angle sample spinning},

author = {Nathalie Lancelot and Karim Elbayed and Alberto Bianco and Martial Piotto},

doi = {10.1023/B:JNMR.0000032548.60663.1f},

issn = {0925-2738},

year  = {2004},

date = {2004-07-01},

journal = {Journal of biomolecular NMR},

volume = {29},

number = {3},

pages = {259--269},

abstract = {NMR spectra of ubiquitin in the presence of bicelles at a concentration of 25% w/v have been recorded under sample spinning conditions for different angles of rotation. For an axis of rotation equal to the magic angle, the (1)H/(15)N HSQC recorded without any (1)H decoupling in the indirect dimension corresponds to the classical spectrum obtained on a protein in an isotropic solution and allows the measurement of scalar J-couplings (1) J (NH). For an angle of rotation smaller than the magic angle, the bicelles orient with their normal perpendicular to the spinning axis, whereas for an angle of rotation greater than the magic angle the bicelles orient with their normal along the spinning axis. This bicelle alignment creates anisotropic conditions that give rise to the observation of residual dipolar couplings in ubiquitin. The magnitude of these dipolar couplings depends directly on the angle that the rotor makes with the main magnetic field. By changing this angle in a controlled manner, residual dipolar couplings can be either scaled up or down thus offering the possibility to study simultaneously a wide range of dipolar couplings in the same sample.},

keywords = {anisotropy, I2CT, Magnetic Resonance Spectroscopy, Magnetics, Models, Phospholipid Ethers, Proteins, Statistical, Team-Bianco, Temperature, ubiquitin},

pubstate = {published},

tppubtype = {article}

}

@article{cornet_refined_1995,

title = {Refined three-dimensional solution structure of insect defensin A},

author = {B Cornet and J M Bonmatin and Charles Hetru and Jules A Hoffmann and M Ptak and F Vovelle},

issn = {0969-2126},

year  = {1995},

date = {1995-05-01},

journal = {Structure},

volume = {3},

number = {5},

pages = {435--448},

abstract = {BACKGROUND: Insect defensin A is a basic 4 kDa protein secreted by Phormia terranovae larvae in response to bacterial challenges or injuries. Previous biological tests suggest that the bacterial cytoplasmic membrane is the target of defensin A. The structural study of this protein is the first step towards establishing a structure-activity relationship and forms the basis for understanding its antibiotic activity at the molecular level. RESULTS: We describe a refined model of the three-dimensional structure of defensin A derived from an extensive analysis of 786 inter-proton nuclear Overhauser effects. The backbone fold involves an N-terminal loop and an alpha-helical fragment followed by an antiparallel beta-structure. The helix and the beta-structure are connected by two of the three disulphide bridges present in defensin A, forming a so-called 'cysteine-stabilized alpha beta' (CS alpha beta) motif. The N-terminal loop, which is locally well defined, can occupy different positions with respect to the other moieties of the molecule. CONCLUSIONS: The CS alpha beta motif, which forms the core of the defensin A structure, appears to be a common organization for several families of small proteins with toxic properties. The distribution of amino acid side chains in the protein structure creates several hydrophobic or hydrophilic patches. This leads us to propose that the initial step in the action of positively charged defensin A molecules with cytoplasmic membranes may involve interactions with acidic phospholipids.},

keywords = {Amino Acid, Animals, Bacteriolysis, Chemistry, Defensins, Diptera, Gram-Positive Bacteria, hoffmann, Hydrogen Bonding, Insect Hormones, M3i, Magnetic Resonance Spectroscopy, Models, Molecular, Physical, Physicochemical Phenomena, Protein Conformation, Recombinant Proteins, Sequence Homology, Solutions, Structure-Activity Relationship},

pubstate = {published},

tppubtype = {article}

}

@article{bonmatin_two-dimensional_1992,

title = {Two-dimensional 1H NMR study of recombinant insect defensin A in water: resonance assignments, secondary structure and global folding},

author = {J M Bonmatin and J L Bonnat and X Gallet and F Vovelle and M Ptak and Jean-Marc Reichhart and Jules A Hoffmann and E Keppi and M Legrain and T Achstetter},

issn = {0925-2738},

year  = {1992},

date = {1992-01-01},

journal = {J. Biomol. NMR},

volume = {2},

number = {3},

pages = {235--256},

abstract = {A 500 MHz 2D 1H NMR study of recombinant insect defensin A is reported. This defense protein of 40 residues contains 3 disulfide bridges, is positively charged and exhibits antibacterial properties. 2D NMR maps of recombinant defensin A were fully assigned and secondary structure elements were localized. The set of NOE connectivities, 3JNH-alpha H coupling constants as well as 1H/2H exchange rates and delta delta/delta T temperature coefficients of NH protons strongly support the existence of an alpha-helix (residues 14-24) and of an antiparallel beta-sheet (residues 27-40). Models of the backbone folding were generated by using the DISMAN program and energy refined by using the AMBER program. This was done on the basis of: (i) 133 selected NOEs, (ii) 21 dihedral restraints from 3JNH-alpha H coupling constants, (iii) 12 hydrogen bonds mostly deduced from 1H/2H exchange rates or temperature coefficients, in addition to 9 initial disulfide bridge covalent constraints. The two secondary structure elements and the two bends connecting them involve approximately 70% of the total number of residues, which impose some stability in the C-terminal part of the molecule. The remaining N-terminal fragment forms a less well defined loop. This spatial organization, in which a beta-sheet is linked to an alpha-helix by two disulfide bridges and to a large loop by a third disulfide bridge, is rather similar to that found in scorpion charybdotoxin and seems to be partly present in several invertebrate toxins.},

keywords = {Animals, Defensins, hoffmann, Hydrogen, Insect Hormones, insects, M3i, Magnetic Resonance Spectroscopy, Models, Molecular, Protein Conformation, Recombinant Proteins, reichhart, Saccharomyces cerevisiae, Thermodynamics},

pubstate = {published},

tppubtype = {article}

}

@article{debono_a21978c_1987,

title = {A21978C, a complex of new acidic peptide antibiotics: isolation, chemistry, and mass spectral structure elucidation},

author = {M Debono and M Barnhart and C B Carrell and Jules A Hoffmann and J L Occolowitz and B J Abbott and D S Fukuda and R L Hamill and K Biemann and W C Herlihy},

issn = {0021-8820},

year  = {1987},

date = {1987-01-01},

journal = {J. Antibiot.},

volume = {40},

number = {6},

pages = {761--777},

abstract = {A21978C, produced by Streptomyces roseosporus, NRRL 11379, is a complex of new acidic lipopeptolide antibiotics which inhibits Gram-positive bacteria. HPLC separation of the various components from the purified complex resulted in the isolation of A21978C1, -C2 and -C3 (major components) and -C4, -C5, and -C0 (minor components). Each of these components was fermented with cultures of Actinoplanes utahensis (NRRL 12052) to give the identical inactive peptide ("A21978C nucleus") by removal of the fatty acid acyl groups from the N-terminus. This peptide was composed of 13 amino acids: L-kynurenine, L-threo-3-methylglutamic acid, L-asparagine, L-aspartic acid (3 residues), glycine (2 residues), L-tryptophan, L-ornithine, D-alanine, D-serine and L-threonine. The amino acid sequence was determined using a combination of the Edman degradation and gas chromatography mass spectrum (GC-MS) analysis of appropriately derivatized peptides obtained from partial hydrolysis. Each major component was shown to be acylated with a branched chain fatty acid at the N-terminus and the structure of this fatty acid was determined by 1H NMR and mass spectral methods. A structure for A21978C was assigned on the basis of this degradative and physico-chemical information.},

keywords = {Acylation, Amino Acids, Anti-Bacterial Agents, Chemical Phenomena, Chemistry, Chromatography, Cyclic, Fatty Acids, Gas Chromatography-Mass Spectrometry, High Pressure Liquid, hoffmann, Hydrolysis, M3i, Magnetic Resonance Spectroscopy, Mass Spectrometry, Molecular Conformation, Peptides, Spectrophotometry, Streptomyces},

pubstate = {published},

tppubtype = {article}

}

@article{hetru_ecdysone_1985,

title = {Ecdysone conjugates: isolation and identification},

author = {Charles Hetru and B Luu and Jules A Hoffmann},

issn = {0076-6879},

year  = {1985},

date = {1985-01-01},

journal = {Meth. Enzymol.},

volume = {111},

pages = {411--419},

keywords = {Animals, Bombyx, Chromatography, Ecdysone, Helix (Snails), High Pressure Liquid, hoffmann, Insect Hormones, M3i, Magnetic Resonance Spectroscopy, Mass Spectrometry, Spectrophotometry, Structure-Activity Relationship},

pubstate = {published},

tppubtype = {article}

}

@article{tsoupras_isolation_1982,

title = {Isolation and identification of three ecdysteroid conjugates with a C-20 hydroxy group in eggs of Locusta migratoria},

author = {G Tsoupras and B Luu and Jules A Hoffmann},

issn = {0039-128X},

year  = {1982},

date = {1982-11-01},

journal = {Steroids},

volume = {40},

number = {5},

pages = {551--560},

abstract = {Three ecdysteroids conjugates with a hydroxy group at C-20 were isolated from developing eggs of locusta migratoria and identified as 22-phosphate conjugates of 2-deoxy-20-hydroxy-ecdysone, 20-hydroxyecdysone and 20-hydroxyecdysone acetate.},

keywords = {Animals, Chromatography, Ecdysone, Ecdysterone, Female, Grasshoppers, High Pressure Liquid, hoffmann, M3i, Magnetic Resonance Spectroscopy, Ovum, Phosphates, Spectrophotometry, Ultraviolet},

pubstate = {published},

tppubtype = {article}

}