Transition Metal Scaffolds as MRI Contrast Agents

Magnetic resonance imaging (MRI) is an important technique used throughout the medical field to gain improved clinical diagnostic ability. Often, different tissues can be weighted within the images if MRI contrast agents are used. Common clinical contrast agents use gadolinium to alter the T1 relaxation times of protons within surrounding tissues. Gadolinium(III), a lanthanide cation, has a grand seven unpaired electrons in its electronic configuration [Xe] 4f7. There are already a plethora of gadolinium chelate contrast agents available for medical use; however the sensitivity of these agents may be improved by increasing the rotational correlation time, tr. The goal of slower tumbling rates can be achieved by increasing their molecular weight. Thus, we propose attaching multiple gadolinium chelates to a central transition metal scaffold. The increase in molecular weight will alter the tr and improve the relaxation efficiency of the agent. These metal scaffolds will most likely include a Ru3O core

Direct Observation of Node-to-Node Communication in Zeolitic Imidazolate Frameworks

Zeolitic imidazolate frameworks (ZIFs) with open-shell transition metal nodes represent a promising class of highly ordered light harvesting antennas for photoenergy applications. However, their charge transport properties within the framework, the key criterion to achieve efficient photoenergy conversion, are not yet explored. Herein, we report the first direct evidence of a charge transport pathway through node-to-node communication in both ground state and excited state ZIFs using the combination of paramagnetic susceptibility measurements and time-resolved optical and X-ray absorption spectroscopy. These findings provide unprecedented new insights into the photoactivity and charge transport nature of ZIF frameworks, paving the way for their novel application as light harvesting arrays in diverse photoenergy conversion devices

Electrical detection of the temperature induced melting transition of a DNA hairpin covalently attached to gold interdigitated microelectrodes

The temperature induced melting transition of a self-complementary DNA strand covalently attached at the 5′ end to the surface of a gold interdigitated microelectrode (GIME) was monitored in a novel, label-free, manner. The structural state of the hairpin was assessed by measuring four different electronic properties of the GIME (capacitance, impedance, dissipation factor and phase angle) as a function of temperature from 25°C to 80°C. Consistent changes in all four electronic properties of the GIME were observed over this temperature range, and attributed to the transition of the attached single-stranded DNA (ssDNA) from an intramolecular, folded hairpin structure to a melted ssDNA. The melting curve of the self-complementary single strand was also measured in solution using differential scanning calorimetry (DSC) and UV absorbance spectroscopy. Temperature dependent electronic measurements on the surface and absorbance versus temperature values measured in solution experiments were analyzed assuming a two-state process. The model analysis provided estimates of the thermodynamic transition parameters of the hairpin on the surface. Two-state analyses of optical melting data and DSC measurements provided evaluations of the thermodynamic transition parameters of the hairpin in solution. Comparison of surface and solution measurements provided quantitative evaluation of the effect of the surface on the thermodynamics of the melting transition of the DNA hairpin

Mechanisms of base selection by human single-stranded selective monofunctional uracil-DNA glycosylase

hSMUG1 (human single-stranded selective monofunctional uracil-DNA glyscosylase) is one of three glycosylases encoded within a small region of human chromosome 12. Those three glycosylases, UNG (uracil-DNA glycosylase), TDG (thymine-DNA glyscosylase), and hSMUG1, have in common the capacity to remove uracil from DNA. However, these glycosylases also repair other lesions and have distinct substrate preferences, indicating that they have potentially redundant but not overlapping physiological roles. The mechanisms by which these glycosylases locate and selectively remove target lesions are not well understood. In addition to uracil, hSMUG1 has been shown to remove some oxidized pyrimidines, suggesting a role in the repair of DNA oxidation damage. In this paper, we describe experiments in which a series of oligonucleotides containing purine and pyrimidine analogs have been used to probe mechanisms by which hSMUG1 distinguishes potential substrates. Our results indicate that the preference of hSMUG1 for mispaired uracil over uracil paired with adenine is best explained by the reduced stability of a duplex containing a mispair, consistent with previous reports with Escherichia coli mispaired uracil-DNA glycosylase. We have also extended the substrate range of hSMUG1 to include 5-carboxyuracil, the last in the series of damage products from thymine methyl group oxidation. The properties used by hSMUG1 to select damaged pyrimidines include the size and free energy of solvation of the 5-substituent but not electronic inductive properties. The observed distinct mechanisms of base selection demonstrated for members of the uracil glycosylase family help explain how considerable diversity in chemical lesion repair can be achieved

Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines

The placement of the extreme thermophile Aquifex aeolicus in the bacterial phylogenetic tree has evoked much controversy. We investigated whether adaptations for growth at high temperatures would alter a key functional component of the replication machinery, specifically DnaG primase. Although the structure of bacterial primases is conserved, the trinucleotide initiation specificity for A. aeolicus was hypothesized to differ from other microbes as an adaptation to a geothermal milieu. To determine the full range of A. aeolicus primase activity, two oligonucleotides were designed that comprised all potential trinucleotide initiation sequences. One of the screening templates supported primer synthesis and the lengths of the resulting primers were used to predict possible initiation trinucleotides. Use of trinucleotide-specific templates demonstrated that the preferred initiation trinucleotide sequence for A. aeolicus primase was 5′-d(CCC)-3′. Two other sequences, 5′-d(GCC)-3′ and d(CGC)-3′, were also capable of supporting initiation, but to a much lesser degree. None of these trinucleotides were known to be recognition sequences used by other microbial primases. These results suggest that the initiation specificity of A. aeolicus primase may represent an adaptation to a thermophilic environment

SNP assay to detect the ‘Hyuuga’ red-brown lesion resistance gene for Asian soybean rust

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi Syd., has the potential to become a serious threat to soybean, Glycine max L. Merr., production in the USA. A novel rust resistance gene, Rpp?(Hyuuga), from the Japanese soybean cultivar Hyuuga has been identified and mapped to soybean chromosome 6 (Gm06). Our objectives were to fine-map the Rpp?(Hyuuga) gene and develop a high-throughput single nucleotide polymorphism (SNP) assay to detect this ASR resistance gene. The integration of recombination events from two different soybean populations and the ASR reaction data indicates that the Rpp?(Hyuuga) locus is located in a region of approximately 371 kb between STS70887 and STS70923 on chromosome Gm06. A set of 32 ancestral genotypes which is predicted to contain 95% of the alleles present in current elite North American breeding populations and the sources of the previously reported ASR resistance genes (Rpp1, Rpp2, Rpp3, Rpp4, Rpp5, and rpp5) were genotyped with five SNP markers. We developed a SimpleProbe assay based on melting curve analysis for SNP06-44058 which is tighly linked to the Rpp?(Hyuuga) gene. This SNP assay can differentiate plants/lines that are homozygous/homogeneous or heterozygous/heterogeneous for the resistant and susceptible alleles at the Rpp?(Hyuuga) locus

Identifying Fishes through DNA Barcodes and Microarrays

Background: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings: This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of ‘‘DNA barcoding’’ and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the ‘‘position of label’’ effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (.90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance: Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products

Investigating the Coordination Chemistry of Tetrathiooxalate

Transition metal complexes with bridging ligands containing sulfur and carbon are commonplace in molecular electronics. Tetrathiooxalate (C2S42-; tto) has redox properties which allow it to store electrons, which could provide useful functionality in molecular circuitry. To date, there are only a handful of molecular complexes with tto due to difficulties in synthesizing and utilizing this ligand. Our research investigates tto as a bridging ligand and alkylated derivatives of tto as terminal ligands. The reaction of tto with dichloro(p-cymene) ruthenium(II) dimer at low temperature gives insoluble green microcrystals which have been characterized by IR spectroscopy, SEM/EDS, and XRD. We believe that the insolubility may arise from the lability of the p-cymene ligands giving rise to polymers of ruthenium metal centers bridged by tto ligands. To find a solution to this issue, we have been investigating the trispyrazolylborate (Tp) ligand since it is negatively charged and might prove to be less labile. We have made attempts to coordinate the Tp ligand to Co(II), and future work will involve trying to bridge two Co(II) centers with tto. Alkylation of tto with hexyl bromide and benzyl bromide results in a mixture of products. The NMR spectra of the purified products revealed unexpected anisotropies, which were hypothesized to be due to the formation of cis/trans conformers. Coordinate scans for dimethyltetrathiooxalate using the Gaussian computational engine do not support this hypothesis. A competing alternative hypothesis is that a hetero Diels-Alder dimerization reaction produces multiple constitutional isomers

Coprecipitation and Hydrothermal Synthesis of Doped Hydroxyapatite Nanoparticles

Our goal is to create a nanoparticle scaffold that has multimodal imaging capabilities. We are using hydroxyapatite as the basis of the scaffold due to its stability in biological conditions and lack of toxicity. Following coprecipitation and hydrothermal techniques from the literature, we have synthesized hydroxyapatite nanoparticles doped with europium, gadolinium and terbium. The nanoparticles have been characterized with SEM/ EDS, P-XRD, and DLS. In another approach to make MRI active scaffolds, we are currently working towards modifying the surface of the particles with iron oxide, and building nanoparticles with iron oxide cores. Further, we have modified the surface of these hydroxyapatite nanoparticles using alendronate, a bisphosphonate with the goal of attaching targeting peptides and zirconium ions to the nanoparticles. In collaboration with the Lapi research team at University of Alabama, these particles will be labeled with peptides targeting somatostatin receptors and radioactive 89Zr for PET/SPECT imaging of tumors

Gadolinium-doped Hydroxyapatite Nanoparticles as Scaffolds for Multimodal Imaging

Multimodal imaging agents are beneficial to medical imaging and research because they combine strengths of individual modalities. Nanoparticles provide an excellent scaffold to combine different imaging agents into one entity. Following a literature precedent, we have synthesized gadolinium-doped hydroxyapatite nanoparticles for magnetic resonance imaging. We have characterized these particles using SEM/EDS. Further, we have investigated modification of the surface of these hydroxyapatite nanoparticles using a phosphate-labeled dye. Current goals are to further characterize the size, structure, and composition of these nanoparticles