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Nicholas J Turro

Publications and source records attributed to Nicholas J Turro.

At least 19 recordsLinked to original sources
PubMed2007

Photogenerated glycan arrays identify immunogenic sugar moieties of Bacillus anthracis exosporium.

Using photogenerated glycan arrays, we characterized a large panel of synthetic carbohydrates for their antigenic reactivities with pathogen-specific antibodies. We discovered that rabbit IgG antibodies elicited by Bacillus anthracis spores specifically recognize a tetrasaccharide chain that decorates the outermost surfaces of the B. anthracis exosporium. Since this sugar moiety is highly specific for the spores of B. anthracis, it appears to be a key biomarker for detection of B. anthracis spores and development of novel vaccines that target anthrax spores.

Animals↗
PubMed2006

Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators.

DNA sequencing by synthesis (SBS) on a solid surface during polymerase reaction offers a paradigm to decipher DNA sequences. We report here the construction of such a DNA sequencing system using molecular engineering approaches. In this approach, four nucleotides (A, C, G, T) are modified as reversible terminators by attaching a cleavable fluorophore to the base and capping the 3'-OH group with a small chemically reversible moiety so that they are still recognized by DNA polymerase as substrates. We found that an allyl moiety can be used successfully as a linker to tether a fluorophore to 3'-O-allyl-modified nucleotides, forming chemically cleavable fluorescent nucleotide reversible terminators, 3'-O-allyl-dNTPs-allyl-fluorophore, for application in SBS. The fluorophore and the 3'-O-allyl group on a DNA extension product, which is generated by incorporating 3'-O-allyl-dNTPs-allyl-fluorophore in a polymerase reaction, are removed simultaneously in 30 s by Pd-catalyzed deallylation in aqueous buffer solution. This one-step dual-deallylation reaction thus allows the reinitiation of the polymerase reaction and increases the SBS efficiency. DNA templates consisting of homopolymer regions were accurately sequenced by using this class of fluorescent nucleotide analogues on a DNA chip and a four-color fluorescent scanner.

Base Sequence↗
PubMed2006

Nuclear relaxation of H2 and H2@C60 in organic solvents.

The 1H nuclear spin-lattice relaxation time (T1) of H2 and H2@C60 in organic solvents varies with solvent, and it varies proportionally for H2 and for H2@C60. Since intermolecular magnetic interactions are ruled out, the solvent must influence the modulating processes of the relaxation mechanisms of H2 both in the solvent cage and inside C60. The temperature dependence of T1 also is very similar for H2 and H2@C60, T1 going through a maximum by varying the temperature in solvents which allow a wide range of temperatures to be explored. This behavior is attributed to the presence of dipolar and spin-rotation mechanisms which have an opposite dependence on temperature.

Journal Article↗
PubMed2006

Toward the syntheses of universal ligands for metal oxide surfaces: controlling surface functionality through click chemistry.

A new means for functionalizing metal oxide surfaces, specifically nanoparticles, is demostrated. This process involves the design of stable ligands that bind strongly to the surface of metal oxides and can undergo further chemical modification via click chemistry, with both small molecules as well as polymers, to yield metal oxide surfaces with tailored functionality. The nanoparticles are stable and easily dispersed in both polar and nonpolar solvents, a property that is controlled by the ligand. The resultant nanoparticles were characterized by TEM, TGA, FTIR, and NMR.

Journal Article↗
PubMed2006

Photoactive additives for cross-linking polymer films: Inhibition of dewetting in thin polymer films.

In this report, we describe a versatile photochemical method for cross-linking polymer films and demonstrate that this method can be used to inhibit thin polymer films from dewetting. A bifunctional photoactive molecule featuring two benzophenone chromophores capable of abstracting hydrogen atoms from various donors, including C-H groups, is mixed into PS films. Upon exposure to UV light, the bis-benzophenone molecule cross-links the chains presumably by hydrogen abstraction followed by radical recombination. Photoinduced cross-linking is characterized by infrared spectroscopy and gel permeation chromatography. Optical and atomic force microscopy images show that photocrosslinked polystyrene (PS) thin films resist dewetting when heated above the glass transition temperature or exposed to solvent vapor. PS films are inhibited from dewetting on both solid and liquid substrates. The effectiveness of the method to inhibit dewetting is studied as a function of the ratio of cross-linker to macromolecule, duration of exposure to UV light, film thickness, the driving force for dewetting, and the thermodynamic nature of the substrate.

Cross-Linking Reagents↗
PubMed2006

Combinatorial fluorescence energy transfer molecular beacons for probing nucleic acid sequences.

We report the design, synthesis, and characterization of molecular beacons (MB) consisting of three distinct fluorophores, 6-carboxyfluorescein (Fam), N,N,N',N'-tetramethyl-6-carboxyrhodamine (Tam), and Cyanine-5 (Cy5). The primary light absorber/energy donor (Fam) is located on one terminus of the MB, whereas the primary energy acceptor/secondary donor (Tam) and secondary acceptor (Cy5) are located at the other terminus of the MB. In the absence of target DNA or RNA, the MB exists in the stem-closed form. Excitation of Fam initiates an energy transfer cascade from Fam to Tam and further to Cy5 generating unique fluorescence signatures defined as the ratio of the emission from each of the three fluorophores. This energy transfer cascade was investigated in detail by steady-state and time-resolved fluorescence spectroscopy, as well as fluorescence depolarization studies. In the presence of the complementary target DNA, the MB opened efficiently and hybridized with the target separating Fam and Tam by a large distance, so that energy transfer from Fam to Tam was blocked in the stem-open form. This opening of the MB generates a "bar code" fluorescence signature, which is different from the signature of the stem-closed MB. The fluorescence signature of this combinatorial fluorescence energy transfer MB can be tuned by variation of the spacer length between the individual fluorophores.

Base Sequence↗
PubMed2006

Phosphorylation state-responsive lanthanide peptide conjugates: a luminescence switch based on reversible complex reorganization.

[reaction: see text] A luminogenic probe for peptide dephosphorylation has been developed. It consists of a serine-/tyrosine-containing peptide modified on the N-terminus with a tryptophan residue and a DTPA chelate capable of binding Tb(3+). We propose a mechanistic model for the luminescence enhancement based on the interconversion of monomeric and dimeric lanthanide species, which is affected by the phosphorylation state of the serine or tyrosine residue. The optical switch reports effectively on phosphatase-catalyzed dephosphorylation in vitro.

Alkaline Phosphatase↗
PubMed2006

Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy.

We report here the design, synthesis and application of pyrene binary oligonucleotide probes for selective detection of cellular mRNA. The detection strategy is based on the formation of a fluorescent excimer when two pyrene groups are brought into close proximity upon hybridization of the probes with the target mRNA. The pyrene excimer has a long fluorescence lifetime (>40 ns) compared with that of cellular extracts (approximately 7 ns), allowing selective detection of the excimer using time-resolved emission spectra (TRES). Optimized probes were used to target a specific region of sensorin mRNA yielding a strong excimer emission peak at 485 nm in the presence of the target and no excimer emission in the absence of the target in buffer solution. While direct fluorescence measurement of neuronal extracts showed a strong fluorescent background, obscuring the detection of the excimer signal, time-resolved emission measurements indicated that the emission decay of the cellular extracts is approximately 8 times faster than that of the pyrene excimer probes. Thus, using TRES of the pyrene probes, we are able to selectively detect mRNA in the presence of cellular extracts, demonstrating the potential for application of pyrene excimer probes for imaging mRNAs in cellular environments that have background fluorescence.

Animals↗
PubMed2006

Synthesis of degradable model networks via ATRP and click chemistry.

A simple scheme involving atom transfer radical polymerization (ATRP) from a bifunctional initiator, conversion of the bromine end groups of the resulting telechelic polymer to azides, and cross-linking of this azido-telechelic macromonomer with multi-acetylene functionalized small molecules via copper-catalyzed azide-alkyne cycloaddition was employed to prepare the first tert-butyl acrylate model networks. This general scheme is wide in scope, enabling synthesis of model networks possessing defined pore size from any monomer polymerizable by ATRP. Introduction of an olefin moiety into the ATRP initiator enabled degradation of the materials by ozonolysis to yield star polymer products bearing three or four arms depending on which cross-linker was employed in the parent network. Size-exclusion chromatography of the ozonolysis products confirmed the pore size of the parent network and yielded insight into the number of unreacted functionalities. Model networks derived from a trifunctional alkyne were found to be more completely cross-linked than those derived from a tetrafunctional alkyne, presumably due to less steric hindrance in the former system.

Acrylates↗
PubMed2006

Design and synthesis of a photocleavable fluorescent nucleotide 3'-O-allyl-dGTP-PC-Bodipy-FL-510 as a reversible terminator for DNA sequencing by synthesis.

DNA sequencing by synthesis (SBS) using reversible fluorescent nucleotide terminators is potentially an efficient approach to address the limitations of current DNA sequencing techniques. Here, we report the design and synthesis of a 3'-O-allyl photocleavable fluorescent nucleotide analogue, 3'-O-allyl-dGTP-PC-Bodipy-FL-510, as a reversible terminator for SBS. The nucleotide is efficiently incorporated by DNA polymerase into a growing DNA strand to terminate the polymerase reaction. After that, the fluorophore is photocleaved quantitatively by irradiation at 355 nm, and the allyl group is rapidly and efficiently removed by using a Pd-catalyzed reaction under DNA-compatible conditions to regenerate a free 3'-OH group to reinitiate the polymerase reaction. Two cycles of such steps were successfully demonstrated to sequence a homopolymeric region of a DNA template, facilitating the development of SBS as a viable approach for high-throughput DNA sequencing.

Base Sequence↗
PubMed2006

Oximetry of oxygen supersaturated solutions using nitroxides as EPR probe.

The broadening of the three hyperfine EPR nitroxide lines in oxygen supersaturated solutions was examined. The solutions were supersaturated with oxygen either by thermal decomposition of 1,4-peroxy-1,4-dimethylnaphthalene or by pressurizing molecular oxygen above the sample solution. The linear relationship between the Lorentzian component of the line width and the O(2) concentration was proven to hold even when the hyperfine splitting is unresolved. In this region of line broadening, the requirement for spectral simulation is discussed.

Journal Article↗
PubMed2006

Molecular beacons with intrinsically fluorescent nucleotides.

We report the design, synthesis and characterization of a novel molecular beacon (MB-FB) which uses the fluorescent bases (FB) 2-aminopurine (AP) and pyrrolo-dC (P-dC) as fluorophores. Because the quantum yield of these FB depend on hybridization with complementary target, the fluorescent properties of MB-FB were tuned by placing the FB site specifically within the MB such that hybridization with complementary sequence switches from single strand to double strand for AP and vice versa for P-dC. The MB-FB produces a ratiometric fluorescence increase (the fluorescence emission of P-dC over that of AP in the presence and absence of complementary sequence) of 8.5 when excited at 310 nm, the maximum absorption of AP. This ratiometric fluorescence is increased to 14 by further optimizing excitation (325 nm). The fluorescence lifetime is also affected by the addition of target, producing a change in the long-lived component from 6.5 to 8.7 ns (Exc. 310 nm, Em. 450 nm). Thermal denaturation profiles monitored at 450 nm (P-dC emission) show a cooperative denaturation of the MB-FB with a melting temperature of 53 degrees C. The thermal denaturation profile of MB-FB hybridized with its target shows a marked fluorescence reduction at 53 degrees C, consistent with a transition from double stranded helix to random coil DNA.

2-Aminopurine↗
PubMed2006

Spectroscopic investigation of a FRET molecular beacon containing two fluorophores for probing DNA/RNA sequences.

We report the design, synthesis, and characterization of a molecular beacon (MB) consisting of two fluorescent dyes (Alexa 488 and RedX) for DNA and RNA analysis. In the absence of the target DNA or RNA the MB is in its stem-closed form and shows efficient energy transfer from the donor (Alexa) to the acceptor (RedX), generating mostly fluorescence from RedX. In the presence of the complementary target DNA the MB opened efficiently, hybridizes with the target DNA, and energy transfer is blocked in the stem-open form. This attachment to the target generates a fluorescence signature, which is clearly distinguishable from the fluorescence signature of the stem-closed form, allowing for ratiometric analysis of the fluorescence signal. In addition to steady-state fluorescence analysis, time resolved fluorescence (ps time range) and fluorescence depolarization studies were performed. We show that fluorescence lifetime and fluorescence depolarization measurements are useful analytical tools to optimize the MB design.

Base Sequence↗
PubMed2006

Photochemical micropatterning of carbohydrates on a surface.

In this report, we demonstrate a versatile method for the immobilization and patterning of unmodified carbohydrates onto glass substrates. The method employs a novel self-assembled monolayer to present photoactive phthalimide chromophores at the air-monolayer interface. Upon exposure to UV radiation, the phthalimide end-groups graft to surface-adsorbed carbohydrates, presumably by a hydrogen abstraction mechanism followed by radical recombination to form a covalent bond. Immobilized carbohydrate thin films are evidenced by fluorescence, ellipsometry and contact-angle measurements. Surface micropatterns of mono-, oligo-, and polysaccharides are generated by exposure through a contact photomask and are visualized by condensing water onto the surface. The efficiency of covalent coupling is dependent on the thermodynamic state of the surface. The amount of surface-grafted carbohydrate is enhanced when carbohydrate surface interactions are increased by the incorporation of amine-terminated molecules into the monolayer. Glass substrates modified with mixed monolayers of this nature are used to construct carbohydrate microarrays by spotting the carbohydrates with a robot and subsequently illuminating them with UV light to covalently link the carbohydrates. Surface-immobilized polysaccharides display well-defined antigenic determinants for antibody recognition. We demonstrate, therefore, that this novel technology combines the ability to create carbohydrate microarrays using the current state-of-the-art technology of robotic microspotting and the ability to control the shape of immobilized carbohydrate patterns with a spatial resolution defined by the UV wavelength and a shape defined by a photomask.

Carbohydrates↗
PubMed2005

Light-switching excimer probes for rapid protein monitoring in complex biological fluids.

Quantitative protein bioanalysis in complex biological fluids presents considerable challenges in biological studies and disease diagnosis. The major obstacles are the background signals from both the probe and the biological fluids where the proteins reside. We have molecularly engineered light-switching excimer aptamer probes for rapid and sensitive detection of a biomarker protein, platelet-derived growth factor (PDGF). Labeled with one pyrene at each end, the aptamer switches its fluorescence emission from approximately 400 nm (pyrene monomer) to 485 nm (pyrene excimer) upon PDGF binding. This fluorescence wavelength change from monomer to excimer emission is a result of aptamer conformation rearrangement induced by target binding. The excimer probe is able to effectively detect picomolar PDGF in homogeneous solutions. Because the excimer has a much longer fluorescence lifetime (approximately 40 ns) than that of the background (approximately 5 ns), time-resolved measurements were used to eliminate the biological background. We thus were able to detect PDGF in a cell sample quantitatively without any sample pretreatment. This molecular engineering strategy can be used to develop other aptamer probes for protein monitoring. Combined with lifetime-based measurements and molecular engineering, light-switching excimer aptamer probes hold great potential in protein analysis for biomedical studies.

Body Fluids↗
PubMed2005

Chemically induced dynamic electron polarization generated through the interaction between singlet molecular oxygen and nitroxide radicals.

An absorptive chemically induced dynamic electron polarization (CIDEP) was generated by the quenching of singlet oxygen by nitroxide radicals (TEMPO derivatives). The spin polarization decay time of the nitroxide (measured by time-resolved EPR) correlates with the lifetime of singlet oxygen (measured by singlet oxygen phosphorescence spectroscopy). In addition, a deuterium isotope effect on the spin polarization decay time was observed, a signature of singlet oxygen involvement. With use of isotope labeled nitroxides (15N, 14N), the relative spin polarization efficiencies of TEMPO, 4-oxo-TEMPO, and 4-hydroxy-TEMPO by singlet oxygen were determined. The relative spin polarization efficiencies (per quenching event) decrease in the order 4-hydroxy-TEMPO > TEMPO > 4-oxo-TEMPO, whereas an opposite trend was observed for the total quenching rate constants of singlet oxygen by the nitroxides where the order is 4-hydroxy-TEMPO < TEMPO < 4-oxo-TEMPO.

Journal Article↗
PubMed2005

Conformational changes of pyrene-labeled polyelectrolytes with pH: effect of hydrophobic modifications.

Structural changes of pyrene-labeled and unlabeled poly(maleic acid/octyl vinyl ether) (PMAOVE) and poly(maleic acid/methyl vinyl ether) (PMAMVE) with changes in pH have been investigated in this study. The changes in the photophysical properties of pyrene are interpreted to investigate uncoiling or swelling of the polymeric chains with pH. The vibrational fine structure of the pyrene fluorescence (I(3)/I(1)) and the ratio between excimer and monomer fluorescence (I(e)/I(m)) of both pyrene-labeled and unlabeled PMAMVE and PMAOVE suggest that, at pH 4, the polymers are in the coiled form and PMAOVE forms hydrophobic nanodomains. An increase in pH ionizes a number of COOH groups on both PMAMVE and PMAOVE, which leads to the stretching or swelling of the polymers.

Hydrogen-Ion Concentration↗