1,720,954 research outputs found
G-quadruplex: a multifunction DNA structure with great potential
No full textG-quadruplex DNA has great potential for use in many biochemical applications. In the field of nucleic acid nanotechnology, G-quadruplexes can facilitate chemical reactions, mimicking the function of an enzyme when bound to hemin, collectively referred to as G-quadruplex/hemin (abbv. GQH). However, in many published studies, GQH shows unstable and inconsistent catalytic activities, especially regarding the suicide inactivation of GQH, often observed when using it as a peroxidase replacement in reactions. The unstable catalysis of GQH limits its biotechnological applications. Here, we report how varied environmental conditions and the use of different substrates influence inactivation kinetics of GQH, while posing potential solutions to improve the catalytic stability of GQH over long reaction periods. These solutions include optimization of pH condition, protection of hemin through the utilization of polyhistidine chains, and generation of H2O2 utilizing enzyme cascades. Specifically in a cascade reaction of GOx – GQH, GOx converts glucose to H2O2, which can then be utilized by GQH for oxidation of Amplex Red, rather than using high concentration of H2O2. The residual activity of GQH is more stable over time in this cascade, presumably due to the low intermediate H2O2 concentration reducing oxidative damage done to hemin. We also report and confirm previously demonstrated results of protection of hemin from damage through utilization of polypeptide-DNAzyme aggregates. Interestingly, we demonstrate a trade-off in overall initial reaction rate with long-term catalytic activity. That is, unprotected GQH had higher initial velocities at the reaction onset than protected complexes, but protected complexes significantly outperformed the unprotected DNAzyme after only 15 minutes of incubation with H2O2. Overall, our results characterize the inherent inactivation kinetics of the peroxidase-mimicking GQH DNAzyme caused by product color depletion and hemin inactivation in the presence of H2O2 across a variety of environmental conditions. We also explored potential options as detailed above to improve the stability of GQH catalysis. With these results, we hope to provide potentially useful kinetic information for future applications of GQH in biomimetic systems, DNA-based nanotechnologies, and other future applications. We also report a potentially useful future application of the GQ structure in the assembly of DNA nanowires for the efficient transfer of photon energy across nanodevices.Presented at the annual Celebration of Undergraduate Research and Creative Activity while the author was an undergraduate student at Rutgers University-Camden
Peptide-modified surfaces for enzyme immobilization.
Full text linkBACKGROUND: Chemistry and particularly enzymology at surfaces is a topic of rapidly growing interest, both in terms of its role in biological systems and its application in biocatalysis. Existing protein immobilization approaches, including noncovalent or covalent attachments to solid supports, have difficulties in controlling protein orientation, reducing nonspecific absorption and preventing protein denaturation. New strategies for enzyme immobilization are needed that allow the precise control over orientation and position and thereby provide optimized activity. METHODOLOGY/PRINCIPAL FINDINGS: A method is presented for utilizing peptide ligands to immobilize enzymes on surfaces with improved enzyme activity and stability. The appropriate peptide ligands have been rapidly selected from high-density arrays and when desirable, the peptide sequences were further optimized by single-point variant screening to enhance both the affinity and activity of the bound enzyme. For proof of concept, the peptides that bound to β-galactosidase and optimized its activity were covalently attached to surfaces for the purpose of capturing target enzymes. Compared to conventional methods, enzymes immobilized on peptide-modified surfaces exhibited higher specific activity and stability, as well as controlled protein orientation. CONCLUSIONS/SIGNIFICANCE: A simple method for immobilizing enzymes through specific interactions with peptides anchored on surfaces has been developed. This approach will be applicable to the immobilization of a wide variety of enzymes on surfaces with optimized orientation, location and performance, and provides a potential mechanism for the patterned self-assembly of multiple enzymes on surfaces
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Functionalization of gold nanoparticles with thiolated DNA
No full textNanotechnology has been rapidly advancing in recent decades, and nanoparticles, particularly gold nanoparticles, have contributed significantly to technological developments in various fields such as modern pharmaceuticals, materials manufacturing, electronics, and medicine. While bare gold nanoparticles have limitations in biochemical systems, loading DNA on their surface has created a highly stable and specific nanomaterial with diverse functionalization options. Conjugating gold nanoparticles with DNA is a complex process that can be achieved through the salt-aging method, the Rapid Modification at Low pH (RMLP) method, and the freeze-thaw method. In this thesis, we compare the procedures and efficiency of these three methods, examining the recovery yield, DNA to GNP ratios, and DLS images for size changes. We study the stability and efficiency of DNA-modified gold nanoparticles using gel electrophoresis and by assessing stability against salt-triggered aggregation. Additionally, we investigate FRET and fluorescence quenching properties of gold nanoparticles by probe DNA-DNA hybridization of DNA-loaded gold nanoparticles. The stability and conjugation efficiency of gold nanoparticles are essential for their successful application in nanotechnology, and understanding these factors is vital for future developments in this field. DNA-functionalized gold nanoparticles have unique properties that make them suitable for various applications, including biosensing, diagnostics, bioimaging, and drug delivery.These nanoparticles can also be used to develop plasmonically-triggered platforms for DNA-based molecular switches, which can open new avenues for molecular signaling and biosensing.M.S.Includes bibliographical reference
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Co-aggregation studies of nucleic acid nanostructures with tetracycline molcules
No full textBiological systems have evolved complex macromolecular nanostructures to carry out cellular functions with high specificity and efficiency, such as mitochondrial electron transport chains, polymerase and transcription cofactors and light-harvesting antenna in photosynthesis. These organized nanostructures are formed inside cells by spontaneous self-assembly of individual molecular components. In the past few decades, researchers have taken advantage of the self-assembly of nucleic acids to construct various 1D – 3D nanostructures. Self-assembled DNA nanostructures have an inherent advantage of generating programmable nanostructures with controllable parameters of dimension, structural hierarchy and nanometer precision, which can be used for mediating drug release. In this thesis, we have studied single- or double-stranded DNA molecules for forming nanoparticles with minocycline (MH) in the presence of magnesium ions (bridging effect) and π-π stacking interaction. We evaluated multi-dimensional DNA nanostructures (e.g. ssDNA, dsDNA, DNA origami) to load and release MH with sufficient dose during an interval of two weeks. The entrapment efficiency of MH and iii DNA was found to depend on the Mg2+ concentration, DNA length, and types of DNA (i.e. as a function of nitrogen bases). The molecule ssDNA with length > 11-nucleotide (nt) was found to form aggregates with MH in the presence of Mg2+. The titration of Mg2+ concentration showed that the maximum particle formation yield was reached at ~ 4 mM. ssDNA also showed higher dimensional aggregate formation yield than dsDNA, due to the flexible structure of ssDNA allowing more aggregation with MH and Mg2+. In collaboration with Drexel University, we have applied DNA-Mg2+-MH particles to agarose gel encapsulation and release for maintaining the activity of MH during a long period release. This DNA-mediated MH release could be potentially used in the future spinal cord therapy for localized delivery of MH at the injury site.M.S.Includes bibliographical referencesby Nouf Alzahran
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Developing dna-mediated proximity assembly circuit for actuating biochemical reactions and molecular sensing
No full textLife functions are regulated by numerous biochemical reactions occurring in cells. Mimicry of this regulation of biochemical reactions in a non-living system can be found useful in many applications. Recently, self-assembled DNA nanostructures have been developed to organize the assembly of biomolecular components and to regulate the components’ interactions and reactions. These discoveries are promising to have a revolutionary impact on medical diagnostics and therapeutics.
This dissertation presents a novel DNA-mediated proximity assembly circuit (DPAC) of biochemical reactions. The assembly circuit is regulated by a DNA logic-AND-gate module, which is comprised of a DNA hairpin-locked catalytic cofactor and a toehold or an aptamer. Targets of nucleic acids, small molecules, or proteins trigger the conformational switch of DPAC by dynamic mechanisms of toehold-mediated strand displacement or aptamer switch and exposes the cofactor. When enzyme/cofactor pair actuates a reaction, colorimetric or fluorescence signals are produced and detected.
DPAC can be optimized to detect a wide range of biotargets. The molecular sensing of adenosine and COVID-19 virus is explored. After optimization, DPAC can be transferred to a paper-based assay and be used for point-of-care diagnostics. This idea and the commercialization potential of this technology was explored through participation in the Innovation Corps program by the National Science Foundation.Ph.D.Includes bibliographical reference
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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