8 Matching Results

Search Results

Advanced search parameters have been applied.

New Catalytic DNA Biosensors for Radionuclides and Metal ion

Description: We aim to develop new DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides, such as uranium, technetium, and plutonium, and metal contaminants, such as lead, chromium, and mercury. The sensors will be highly sensitive and selective. They will be applied to on-site, real-time assessment of concentration, speciation, and stability of the individual contaminants before and during bioremediation, and for long-term monitoring of DOE contaminated sites. To achieve this goal, we have employed a combinatorial method called “in vitro selection” to search from a large DNA library (~ 1015 different molecules) for catalytic DNA molecules that are highly specific for radionuclides or other metal ions through intricate 3-dimensional interactions as in metalloproteins. Comprehensive biochemical and biophysical studies have been performed on the selected DNA molecules. The findings from these studies have helped to elucidate fundamental principles for designing effective sensors for radionuclides and metal ions. Based on the study, the DNA have been converted to fluorescent or colorimetric sensors by attaching to it fluorescent donor/acceptor pairs or gold nanoparticles, with 11 part-per-trillion detection limit (for uranium) and over million fold selectivity (over other radionuclides and metal ions tested). Practical application of the biosensors for samples from the Environmental Remediation Sciences Program (ERSP) Field Research Center (FRC) at Oak Ridge has also been demonstrated.
Date: March 1, 2008
Creator: Lu, Yi
Partner: UNT Libraries Government Documents Department

New Catalytic DNA Biosensors for Radionuclides and Metal ions

Description: The goals of the project are to develop new catalytic DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides and metal ions, and apply the sensors for on-site, real-time assessment of concentration, speciation and stability of the individual contaminants during and after bioremediation. A negative selection strategy was tested and validated. In vitro selection was shown to yield highly active and specific transition metal ion-dependent catalytic DNA/RNA. A fluorescence resonance energy transfer (FRET) study of in vitro selected DNA demonstrated that the trifluorophore labeled system is a simple and powerful tool in studying complex biomolecules structure and dynamics, and is capable of revealing new sophisticated structural changes. New fluorophore/quenchers in a single fluorosensor yielded improved signal to noise ratio in detection, identification and quantification of metal contaminants. Catalytic DNA fluorescent and colorimetric sensors were shown useful in sensing lead in lake water and in leaded paint. Project results were described in two papers and two patents, and won an international prize.
Date: June 1, 2002
Creator: Lu, Yi
Partner: UNT Libraries Government Documents Department

New Catalytic DNA Biosensors for Radionuclides and Metal ions

Description: In vitro selection for DNAzymes that are catalytically active with UO22+ ions as the metal cofactor has been completed. The 10th generation pool of DNA was cloned and sequenced. A total of 84 clones were sequenced and placed into families based on sequence alignments. Selected members of each family were 5-labeled with 32P and amplified using PCR. Activity assays were conducted using the isotopically labeled DNAzymes in order to determine which sequences were the most active. The secondary structures of the two most active sequences, called Clone 13 and Clone 39, were determined using the computer program Mfold. A cleavage rate of approximately 1 min-1 in the presence of 10 uM UO22+ was observed for both clones. Clone 39 was determined to be the best candidate for truncation to create a trans-cleaving DNAzyme, based on its secondary structure. An enzyme strand, called 39E, and a substrate strand, called 39DS, were designed by truncating the cis-cleaving DNAzyme. An alternative enzyme strand, called 39Ec, was also assayed with the 39DS substrate. This strand was designed so that the two binding arms were perfectly complimentary, unlike 39E, which formed three mismatched base pairs with 39DS. Both 39E and 39Ec were found to be active, with a rate of approximately 1 min-1 in the presence of 10 uM UO22+. A preliminary UO22+ binding curve was obtained for the 39Ec/39DS trans-cleaving system. The enzyme is active with UO22+ concentrations as low as 1 nM. Based on the preliminary binding curve data, the apparent UO22+ binding constant is approximately 330 nM, and kmax is approximately 1 min-1.
Date: June 1, 2005
Creator: Lu, Yi
Partner: UNT Libraries Government Documents Department

New Catalytic DNA Biosensors for Radionuclides and Metal ions

Description: The goals of the project are to develop new catalytic DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides and metal ions, and apply the sensors for on-site, real-time assessment of concentration, speciation and stability of the individual contaminants during and after bioremediation. A negative selection strategy was tested and validated. In vitro selection was shown to yield highly active and specific transition metal ion-dependent catalytic DNA/RNA. A fluorescence resonance energy transfer (FRET) study of in vitro selected DNA demonstrated that the trifluorophore labeled system is a simple and powerful tool in studying complex biomolecules structure and dynamics, and is capable of revealing new sophisticated structural changes. New fluorophore/quenchers in a single fluorosensor yielded improved signal to noise ratio in detection, identification and quantification of metal contaminants. Catalytic DNA fluorescent and colorimetric sensors were shown useful in sensing lead in lake water and in leaded paint. Project results were described in two papers and two patents, and won an international prize.
Date: June 1, 2003
Creator: Lu, Yi
Partner: UNT Libraries Government Documents Department

Porphyrin Interactions with Wild Type and Mutant Mouse Ferrochelatase

Description: Ferrochelatase (EC 4.99.1.1), the terminal enzyme of the heme biosynthetic pathway, catalyzes Fe<sup>2+</sup> chelation into protoporphyrin IX. Resonance Raman and W-visible absorbance spectroscopes of wild type and engineered variants of murine ferrochelatase were used to examine the proposed structural mechanism for iron insertion into protoporphyrin by ferrochelatase. The recombinant variants (i.e., H207N and E287Q) are enzymes in which the conserved amino acids histidine-207 and glutamate-287 of murine ferrochelatase were substituted with asparagine and glutamine, respectively. Both of these residues are at the active site of the enzyme as deduced from the Bacillus subtilis ferrochelatase three-dimensional structure. Addition of free base or metalated porphyrins to wild type ferrochelatase and H207N variant yields a quasi 1:1 complex, possibly a monomeric protein-bound species. In contrast, the addition of porphyrin (either free base or metalated) to E287Q is sub-stoichiometric, as this variant retains bound porphyrin in the active site during isolation and purification. The specificity of porphyrin binding is confirmed by the narrowing of the structure-sensitive resonance Raman lines and the vinyl vibrational mode. Resonance Raman spectra of free base and metalated porphyrins bound to the wild type ferrochelatase indicate a nonplanar distortion of the porphyrin macrocycle, although the magnitude of the distortion cannot be determined without first defining the specific type of deformation. Significantly, the extent of the nonplanar distortion varies in the case of H207N- and E287Q-bound porphyrins. In fact, resonance Raman spectral decomposition indicates a homogeneous ruffled distortion for the nickel protoporphyrin bound to the wild type ferrochelatase, whereas both a planar and ruffled conformations are present for the H207N-bound porphyrin. Perhaps more revealing is the unusual resonance , 3 Raman spectrum of the endogenous E287Q-bound porphyrin, which has the structure-sensitive lines greatly upshifted relative to those of the free base protoporphyrin in solution. This could be interpreted as an equilibrium ...
Date: May 19, 1999
Creator: Ferreira, Gloria C.; Franco, Ricardo; Lu, Yi; Ma, Jian-Guo & Shelnutt, John A.
Partner: UNT Libraries Government Documents Department

Calcium-Dependent Conformation of a Heme and Fingerprint Peptide of the Di-Heme Cytochrome c Peroxidase from Paracoccus Pantotrophus

Description: The structural changes in the heme macrocycle and substituents caused by binding of Ca{sup 2+} to the diheme cytochrome c peroxidase from Paracoccuspantotrophus were clarified by resonance Raman spectroscopy of the inactive filly oxidized form of the enzyme. The changes in the macrocycle vibrational modes are consistent with a Ca{sup 2+}-dependent increase in the out-of-plane distortion of the low-potential heme, the proposed peroxidatic heme. Most of the increase in out-of-plane distortion occurs when the high affinity site I is occupied, but a small further increase in distortion occurs when site II is also occupied by Ca{sup 2+}or Mg{sup 2+}. This increase in the heme distortion also explains the red shift in the Soret absorption band that occurs upon Ca{sup 2+} binding. Changes also occur in the low frequency substituent modes of the heme, indicating that a structural change in the covalently attached fingerprint pentapeptide of the LP heme occurs upon CM{sup 2+} binding to site I. These structural changes, possibly enhanced in the semi-reduced form of the enzyme, may lead to loss of the sixth ligand at the peroxidatic heme and activation of the enzyme.
Date: December 18, 2000
Creator: PAULETA,SOFIA R.; LU,YI; GOODHEW,CELIA F.; MOURA,ISABEL; PETTIGREW,GRAHAM W. & SHELNUTT,JOHN A.
Partner: UNT Libraries Government Documents Department

Heme Distortions in Sperm-Whale Carbonmonoxy Myoglobin: Correlations between Rotational Strengths and Heme Distortions in MD-Generated Structures

Description: The authors have investigated the effects of heme rotational isomerism in sperm-whale carbonmonoxy myoglobin using computational techniques. Several molecular dynamics simulations have been performed for the two rotational isomers A and B, which are related by a 180{degree} rotation around the {alpha}-{gamma} axis of the heme, of sperm-whale carbonmonoxy myoglobin in water. Both neutron diffraction and NMR structures were used as starting structures. In the absence of an experimental structure, the structure of isomer B was generated by rotating the heme in the structure of isomer A. Distortions of the heme from planarity were characterized by normal coordinate structural decomposition and by the angle of twist of the pyrrole rings from the heme plane. The heme distortions of the neutron diffraction structure were conserved in the MD trajectories, but in the NMR-based trajectories, where the heme distortions are less well defined, they differ from the original heme deformations. The protein matrix induced similar distortions on the heroes in orientations A and B. The results suggest that the binding site prefers a particular macrocycle conformation, and a 180{degree} rotation of the heme does not significantly alter the protein's preference for this conformation. The intrinsic rotational strengths of the two Soret transitions, separated according to their polarization in the heme plane, show strong correlations with the ruf-deformation and the average twist angle of the pyrrole rings. The total rotational strength, which includes contributions from the chromophores in the protein, shows a weaker correlation with heme distortions.
Date: July 13, 2000
Creator: KIEFL,CHRISTOPH; SCREERAMA,NARASIMHA; LU,YI; QIU,YAN; SHELNUTT,JOHN A. & WOODY,ROBERT W.
Partner: UNT Libraries Government Documents Department