Molecular structure as a blueprint for supramolecular structure chemistry in confined spaces.
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Journal Article↗
Biomedical subjects
Nicholas J Turro
Publications and source records attributed to Nicholas J Turro.
157 nm pellicles (thin films) for photolithography: mechanistic investigation of the VUV and UV-C photolysis of fluorocarbons.
The use of 157 nm as the next lower wavelength for photolithography for the production of semiconductors has created a need for transparent and radiation-durable polymers for use in soft pellicles, the polymer films which protect the chip from particle deposition. The most promising materials for pellicles are fluorinated polymers, but currently available fluorinated polymers undergo photodegradation and/or photodarkening upon long term exposure to 157 nm irradiation. To understand the mechanism of the photodegradation and photodarkening of fluorinated polymers, mechanistic studies on the photolysis of liquid model fluorocarbons, including perfluorobutylethyl ether and perfluoro-2H-3-oxa-heptane, were performed employing UV, NMR, FTIR, GC, and GC/MS analyses. All hydrogen-containing compounds showed decreased photostability compared to the fully perfluorinated compounds. Irradiation in the presence of atmospheric oxygen showed reduced photostability compared to deoxygenated samples. Photolysis of the samples was performed at 157, 172, 185, and 254 nm and showed only minor wavelength dependence. Mechanisms for photodegradation of the fluorocarbons are proposed, which involve Rydberg excited states. Time-dependent density functional theory has been used to predict the excitation spectra of model compounds.
Journal Article↗
Stereoselective E/Z photoisomerization of oxazolidinone functionalized enecarbamates: direct and triplet sensitized irradiation.
Oxazolidinone-functionalized enecarbamates undergo diastereoselective E/Z photoisomerization upon direct and triplet sensitized irradiations with chiral/achiral sensitizers, showing that the enhanced product diastereoselectivity depends on the solvent and temperature.
Journal Article↗
Stereoselective photooxidation of enecarbamates: reactivity of ozone vs singlet oxygen.
[reaction: see text]. Oxazolidinone-functionalized enecarbamates show contrasting behavior upon oxidation by singlet oxygen and by ozone. The observed stereoselectivity difference indicates that the oxidation with ozone is subject to classic steric effects, whereas the very high selectivity in the photooxidation with singlet oxygen is derived from vibrational deactivation.
Journal Article↗
Investigation of the mobility of amphiphilic polymer--AOT reverse microemulsion systems using electron spin resonance.
Amphiphilic polymers can be used as tools to manipulate the behavior of reverse microemulsions. EPR spectroscopy employing the spin probe 5-doxyl stearic acid was used to study the adsorption of a comb type polymer (polymaleic anhydride octyl vinyl ether) and a diblock polymer (polybutadiene-ethylene oxide) onto reverse microemulsion droplets formed from Aerosol-OT/heptane/water. The findings indicate that the comb type polymer was adsorbed by the reverse microemulsion drops at low polymer concentrations causing a structural change of the micelle.
Journal Article↗
Design and synthesis of a 3'-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis.
DNA sequencing by synthesis (SBS) offers an approach for potential high-throughput sequencing applications. In this method, the ability of an incoming nucleotide to act as a reversible terminator for a DNA polymerase reaction is an important requirement to unambiguously determine the identity of the incorporated nucleotide before the next nucleotide is added. A free 3'-OH group on the terminal nucleotide of the primer is necessary for the DNA polymerase to incorporate an incoming nucleotide. Therefore, if the 3'-OH group of an incoming nucleotide is capped by a chemical moiety, it will cause the polymerase reaction to terminate after the nucleotide is incorporated into the DNA strand. If the capping group is subsequently removed to generate a free 3'-OH, the polymerase reaction will reinitialize. We report here the design and synthesis of a 3'-modified photocleavable fluorescent nucleotide, 3'-O-allyl-dUTP-PC-Bodipy-FL-510 (PC-Bodipy, photocleavable 4,4-difluoro-4-bora-3alpha,4alpha-diaza-s-indacene), as a reversible terminator for SBS. This nucleotide analogue contains an allyl moiety capping the 3'-OH group and a fluorophore Bodipy-FL-510 linked to the 5 position of the uracil through a photocleavable 2-nitrobenzyl linker. Here, we have shown that this nucleotide is a good substrate for a DNA polymerase. After the nucleotide was successfully incorporated into a growing DNA strand and the fluorophore was photocleaved, the allyl group was removed by using a Pd-catalyzed reaction to reinitiate the polymerase reaction, thereby establishing the feasibility of using such nucleotide analogues as reversible terminators for SBS.
Base Sequence↗
Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides.
We report four-color DNA sequencing by synthesis (SBS) on a chip, using four photocleavable fluorescent nucleotide analogues (dGTP-PC-Bodipy-FL-510, dUTP-PC-R6G, dATP-PC-ROX, and dCTP-PC-Bodipy-650) (PC, photocleavable; Bodipy, 4,4-difluoro-4-bora-3alpha,4alpha-diaza-s-indacene; ROX, 6-carboxy-X-rhodamine; R6G, 6-carboxyrhodamine-6G). Each nucleotide analogue consists of a different fluorophore attached to the 5 position of the pyrimidines and the 7 position of the purines through a photocleavable 2-nitrobenzyl linker. After verifying that these nucleotides could be successfully incorporated into a growing DNA strand in a solution-phase polymerase reaction and the fluorophore could be cleaved using laser irradiation ( approximately 355 nm) in 10 sec, we then performed an SBS reaction on a chip that contains a self-priming DNA template covalently immobilized by using 1,3-dipolar azide-alkyne cycloaddition. The DNA template was produced by PCR, using an azido-labeled primer, and the self-priming moiety was attached to the immobilized DNA template by enzymatic ligation. Each cycle of SBS consists of the incorporation of the photocleavable fluorescent nucleotide into the DNA, detection of the fluorescent signal, and photocleavage of the fluorophore. The entire process was repeated to identify 12 continuous bases in the DNA template. These results demonstrate that photocleavable fluorescent nucleotide analogues can be incorporated accurately into a growing DNA strand during a polymerase reaction in solution and on a chip. Moreover, all four fluorophores can be detected and then efficiently cleaved using near-UV irradiation, thereby allowing continuous identification of the DNA template sequence. Optimization of the steps involved in this SBS approach will further increase the read-length.
Base Sequence↗
Two-photon induced uncaging of a reactive intermediate. Multiphoton in situ detection of a potentially valuable label for biological applications.
[reaction: see text] Two-photon induced Wolff rearrangement of a terphenyl diazoketone 1 was achieved by using focused laser pulses of 532 nm from a Q-switched Nd:YAG laser. The nonfluorescent terphenyl diazoketone 1 was transformed into a fluorescent ester derivative 4, which can be detected in situ using the focused laser pulses at 532 nm. Laser power dependence studies show that the Wolff rearrangement is induced by two-photon absorption of the terphenyl diazoketone 1, but suggests that more than two photons of 532 nm are involved (a multiphoton process) in excitation of the ester derivative 4.
Diazomethane↗
Direct measurement of the singlet oxygen lifetime in zeolites by near-IR phosphorescence.
Time-resolved near-IR phosphorescence spectroscopy was employed to determine the lifetime of singlet oxygen in Y-zeolites and porous silica and it was found to depend strongly on the alumina content of the zeolite.
Luminescent Measurements↗
Reversible surface oxidation and efficient luminescence quenching in semiconductor single-wall carbon nanotubes.
We have investigated reversible single-wall carbon nanotube (SWNT) oxidation by quantitative analysis of the oxide-induced absorption bleaching and luminescence quenching at low pH. These data, in combination with DFT structure calculations, suggest that the nanotube oxide is a 1,4-endoperoxide. At low pH, the endoperoxide protonates to create a hydroperoxide carbocation, introducing a hole in the SWNT valence band. Nanotube luminescence is extremely sensitive to quenching by hole-doping, while the absorption is relatively robust.
Journal Article↗
Interactions of dendrimers with selected amino acids and proteins studied by continuous wave EPR and Fourier transform EPR.
Interactions of polyamidoamine dendrimers, termed Gn, where n indicates the generation (=number of amidoamine layers), at different protonation levels with selected amino acids and proteins have been investigated by means of continuous wave electron paramagnetic resonance (cw-EPR) and pulsed-EPR (electron spin-echo = ESE) analyses. A low-generation dendrimer (G2) and a high-generation one (G6) were labeled with nitroxides for the EPR measurements. Gly, Glu, Arg, and Leu were selected as representative of neutral(zwitterionic)-polar, acidic, basic, and low-polar amino acids, respectively. The water-soluble proteins alpha-chymotrypsin and albumin were selected on the basis of a basic and an acidic isoelectric point, respectively. The cw-EPR spectra were analyzed by computing the line shapes to extract information about the dendrimer-biomolecule interactions. In general, dendrimers at a high protonation level interact stronger with amino acids than those at a low level of protonation. However, even for highly protonated dendrimers, a synergistic effect between hydrophilic and hydrophobic interactions promoted the formation of stable Gn-amino acid adducts, as demonstrated by the enhanced interactions with Leu. As expected from acid-base interactions, stable adducts were formed between Arg and highly protonated dendrimers and between Glu and low level protonated dendrimers. The relatively strong dendrimer interactions with the protein chymotrypsin and the poor interactions of dendrimers with albumin demonstrated that the protonated amino groups of the dendrimers are predominantly involved in the interactions with these proteins and indicated a significant role in the interactions with the dendrimers of the hydrophobic external residues of chymotrypsin. Computer-aided analysis of the ESE experiments was consistent with the cw-EPR results and supported the conclusion of a partial complexation of the nitroxides of the dendrimer with Leu and alpha-chymotrypsin.
Albumins↗
Stereocontrol within confined spaces: enantioselective photooxidation of enecarbamates inside zeolite supercages.
Dye-exchanged Y zeolite is shown to be an effective medium to control the stereoselectivity in the photooxygenation of chiral oxazolidinone-functionalized Z/E-1 enecarbamates. An enantioselectivity (ee) as high as 80% was observed in the methyldesoxybenzoin (MDB) product, obtained in the methylene-blue-exchanged NaY zeolite at room temperature. The efficacy of the asymmetric induction in the MDB product depends on the Z/E geometry of the alkene, the Z-isomer being more effective than the corresponding E-isomer. The stereoselectivity is rationalized in terms of conformational effects through cationic interactions between the zeolite and the substrate.
Journal Article↗
Temperature and solvent control of the stereoselectivity in the reactions of singlet oxygen with oxazolidinone-substituted enecarbamates.
Oxazolidinone-functionalized enecarbamates react stereoselectively with singlet oxygen to give methyldesoxybenzoin (MDB) in moderate to high enantiomeric excess. The stereochemical outcome depends on the E/Z substrate geometry, temperature, and solvent variables. The analysis of the differential activation parameters suggests a large contribution from the entropy term in determining the enantioselectivity. We demonstrate the utility of the temperature and solvent variables in determining the degree of the photochemical kinetic resolution of the enecarbamates; for example, in the photooxygenation at -70 degrees C in methanol, MDB may be obtained in methanol.
Benzoin↗
Porphyrins as photosensitizers to enhance night vision.
Relative bleaching rates of bovine rhodopsin (rod outer segments) in the presence and absence of seven porphyrins and methylene blue were measured under exposure to lambdamax = 675 nm light, using UV-vis spectroscopy. Rate enhancements on the order of up to three times compared to the bleaching of rhodopsin alone where observed. Fluorescence measurements and other data suggests that the porphyrins act as photosensitizers and excite the visual pigment via electron or triplet state energy transfer. These mechanisms suggest that rhodopsin possesses a pocket, proximal to the Schiff base so that porphyrins act as photosensitizers.
Animals↗
Photochemistry of A1E, a retinoid with a conjugated pyridinium moiety: competition between pericyclic photooxygenation and pericyclization.
The photochemistry of the retinoid analogue A1E shows an oxygen and solvent dependence. Irradiation of A1E with visible light (lambda(irr) = 425 nm) in methanol solutions resulted in pericyclization to form pyridinium terpenoids. Although the quantum yield for this cyclization is low (approximately 10(-4)), nevertheless the photochemical transformation occurs with quantitative chemical yield with remarkable chemoselectivity and diastereoselectivity. Conversely, irradiation of A1E under the same irradiation conditions in air-saturated carbon tetrachloride or deuterated chloroform produced a cyclic 5,8-peroxide as the major product. Deuterium solvent effects, experiments utilizing endoperoxide, phosphorescence, and chemiluminescence quenching studies strongly support the involvement of singlet oxygen in the endoperoxide formation. It is proposed that, upon irradiation, in the presence of oxygen, A1E acts as a sensitizer for generation of singlet oxygen from triplet oxygen present in the solution; the singlet oxygen produced reacts with A1E to produce cyclic peroxide. Thus, the photochemistry of A1E is characterized by two competing reactions, cyclization and peroxide formation. The dominant reaction is determined by the concentration of oxygen, the concentration of A1E, and the lifetime of singlet oxygen in the solvent employed. If the lifetime of singlet oxygen in a given solvent is long enough, then oxidation (peroxide formation) is the major reaction. If the singlet oxygen produced is quenched by the protonated solvent molecules faster than singlet oxygen reacts with A1E, then cyclization dominates.
Cyclization↗
Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry.
DNA sequencing by synthesis on a solid surface offers new paradigms to overcome limitations of electrophoresis-based sequencing methods. Here we report DNA sequencing by synthesis using photocleavable (PC) fluorescent nucleotides [dUTP-PC-4,4-difluoro-4-bora-3 alpha,4 alpha-diaza-s-indacene (Bodipy)-FL-510, dCTP-PC-Bodipy-650, and dUTP-PC-6-carboxy-X-rhodamine (ROX)] on a glass chip constructed by 1,3-dipolar azide-alkyne cycloaddition coupling chemistry. Each nucleotide analogue consists of a different fluorophore attached to the base through a PC 2-nitrobenzyl linker. We constructed a DNA microarray by using the 1,3-dipolar cycloaddition chemistry to site-specifically attach azido-modified DNA onto an alkyne-functionalized glass chip at room temperature under aqueous conditions. After verifying that the polymerase reaction could be carried out successfully on the above-described DNA array, we then performed a sequencing reaction on the chip by using a self-primed DNA template. In the first step, we extended the primer using DNA polymerase and dUTP-PC-Bodipy-FL-510, detected the fluorescent signal from the fluorophore Bodipy-FL-510, and then cleaved the fluorophore using 340 nm UV irradiation. This process was followed by extension of the primer with dCTP-PC-Bodipy-650 and the subsequent detection of the fluorescent signal from Bodipy-650 and its photocleavage. The same procedure was also performed by using dUTP-PC-ROX. The entire process was repeated five times by using the three fluorescent nucleotides to identify 7 bases in the DNA template. These results demonstrate that the PC nucleotide analogues can be incorporated accurately into a growing DNA strand during polymerase reaction on a chip, and the fluorophore can be detected and then efficiently cleaved using near-UV irradiation, thereby allowing the continuous identification of the template sequence.
Alkynes↗
Enecarbamates as selective substrates in oxidations: chiral-auxiliary-controlled mode selectivity and diastereoselectivity in the [2+2] cycloaddition and ene reaction of singlet oxygen and in the epoxidation by DMD and mCPBA.
The stereochemical course of the oxidation of chiral oxazolidinone-substituted enecarbamates has been studied for singlet oxygen ((1)O(2)), dimethyldioxirane (DMD), and m-chloroperbenzoic acid (mCPBA) by examining of the special structural and stereoelectronic features of the enecarbamates. Valuable mechanistic insight into these selective oxidations is gained. Whereas the R(1) substituent on the chiral auxiliary is responsible for the steric shielding of the double bond and determines the sense of the pi-facial diastereoselectivity, structural characteristic such as the Z/E configuration and the nature of the R(2) group on the double bond are responsible for the extent of the diastereoselectivity. Stereoelectronic steering by the vinylic nitrogen functionality controls the mode selectivity (ene reaction vs [2+2] cycloaddition) in the case of (1)O(2).
Journal Article↗
Design and synthesis of a photocleavable biotinylated nucleotide for DNA analysis by mass spectrometry.
We report here the design, synthesis and evaluation of a novel photocleavable (PC) biotinylated nucleotide analog, dUTP-PC-Biotin, for DNA polymerase extension reaction to isolate DNA products for mass spectrometry (MS) analysis. This nucleotide analog has a biotin moiety attached to the 5-position of 2'-deoxyribouridine 5'-triphosphate via a photocleavable 2-nitrobenzyl linker. We have demonstrated that dUTP-PC-Biotin can be faithfully incorporated by the DNA polymerase Thermo Sequenase into the growing DNA strand in a DNA polymerase extension reaction and that its incorporation does not hinder the addition of the subsequent nucleotide. Therefore, the DNA extension fragments generated by using the dUTP-PC-Biotin can be efficiently isolated by a streptavidin-coated surface and recovered by near-UV light irradiation at room temperature in mild condition for further analysis without using any chemicals or heat. Single and multiple primer extension reactions were performed using the dUTP-PC-Biotin to generate DNA products for MALDI-TOF MS analysis. Such nucleotide analogs that carry a biotin and a photocleavable linker will allow the isolation and purification of DNA products under mild conditions for MS-based genetic analysis by DNA sequencing or multiplex single nucleotide polymorphism (SNP) detection. Furthermore, these nucleotide analogs should also be useful in isolating DNA-protein complexes under non-denaturing conditions.
Biotin↗