Relevant bibliographies by topics / DNA Substrates

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'DNA Substrates'

Author: Grafiati
Published: 4 June 2021
Last updated: 6 September 2023

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'DNA Substrates.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Journal articles on the topic "DNA Substrates"

1

Houlston, C. E., M. Cummings, H. Lindsay, S. Pradhan, and R. L. P. Adams. "DNA substrate specificity of pea DNA methylase." Biochemical Journal 293, no. 3 (1993): 617–24. http://dx.doi.org/10.1042/bj2930617.

Full text
Abstract:
DNA methylase, present in low-salt extracts of nuclei prepared from Pisum sativum shoot tips, methylates model DNA substrates containing CNG trinucleotides or CI dinucleotides only. The binding to the hemimethylated trinucleotide substrates is very much stronger and more persistent than the binding to the unmethylated substrates or to the hemimethylated dinucleotide substrate. When the DNA concentration is limiting, the rate of methyl-group transfer with the hemimethylated CNG substrate is much greater than that with the unmethylated CNG. However, the Vmax. is similar for the two CNG substrates. On fractionation using Q-Sepharose, two peaks of activity are seen with different relative activities using the di- and trinucleotide substrates. The relative activity with these substrates changes during purification, during plant growth and on heating at 35 degrees C as well, indicating that more than one enzyme or more than one form of the enzyme may be present.
APA, Harvard, Vancouver, ISO, and other styles
2

Lu, Yue, and Piero Bianco. "High-yield purification of exceptional-quality, single-molecule DNA substrates." Journal of Biological Methods 8, no. 1 (2021): e145. http://dx.doi.org/10.14440/jbm.2021.350.

Full text
Abstract:
Single-molecule studies involving DNA or RNA, require homogeneous preparations of nucleic acid substrates of exceptional quality. Over the past several years, a variety of methods have been published describing different purification methods but these are frustratingly inconsistent with variable yields even in the hands of experienced bench scientists. To address these issues, we present an optimized and straightforward, column-based approach that is reproducible and produces high yields of substrates or substrate components of exceptional quality. Central to the success of the method presented is the use of a non-porous anion exchange resin. In addition to the use of this resin, we encourage the optimization of each step in the construction of substrates. The fully optimized method produces high yields of a hairpin DNA substrate of exceptional quality. While this substrate is suitable for single-molecule, magnetic tweezer experiments, the described method is readily adaptable to the production of DNA substrates for the majority of single-molecule studies involving nucleic acids ranging in size from 70
APA, Harvard, Vancouver, ISO, and other styles
3

Deng, Chuyun, Wanyun Ma та Jia-Lin Sun. "Fabrication of Highly Rough Ag Nanobud Substrates and Surface-Enhanced Raman Scattering ofλ-DNA Molecules". Journal of Nanomaterials 2012 (2012): 1–5. http://dx.doi.org/10.1155/2012/820739.

Full text
Abstract:
Raman scattering signals can be enhanced by several orders of magnitude on surface-enhanced Raman scattering (SERS) substrates made from noble metal nanostructures. Some SERS substrates are even able to detect single-molecule Raman signals. A novel silver nanobud (AgNB) substrate with superior SERS activity was fabricated with a solid-state ionics method. The AgNB substrate was formed by tightly collocated unidirectional 100 nm size silver buds, presenting a highly rough surface topography. Distinct SERS signals of singleλ-DNA molecules in water were detected on AgNB substrates. AgNB substrates were compared with disordered silver nanowire (AgNW) substrates manufactured by the same method through the SERS detection ofλ-DNA solutions. This original AgNB substrate provides a reliable approach towards trace analysis of biomacromolecules and promotes the utilization of the SERS technique in biomedical research.
APA, Harvard, Vancouver, ISO, and other styles
4

Hsieh, C. L., R. P. McCloskey, E. Radany, and M. R. Lieber. "V(D)J recombination: evidence that a replicative mechanism is not required." Molecular and Cellular Biology 11, no. 8 (1991): 3972–77. http://dx.doi.org/10.1128/mcb.11.8.3972-3977.1991.

Full text
Abstract:
We examined a series of extrachromosomal DNA substrates for V(D)J recombination under replicating and nonreplicating conditions. Complete and partial replications were examined by monitoring the loss of prokaryote-specific adenine methylation at 14 to 22 MboI-DpnI restriction sites (GATC) on the substrates. Some of these sites are within 2 bases of the signal sequence ends. We found that neither coding joint nor signal joint formation requires substrate replication. After ruling out replication as a substrate requirement, we determined whether replication had any effect on the efficiency of V(D)J recombination. Quantitation of V(D)J recombination efficiency on nonreplicating substrates requires some method of monitoring the entry of substrate molecules into the cells. We devised such a method by monitoring DNA repair of substrates into which we had substituted deoxyuridine for 10 to 20% of the thymidine nucleotides in the DNA. The substrates which enter the lymphoid cells were repaired efficiently in vivo by the eukaryotic uracil DNA repair system. Upon plasmid harvest, we distinguished repaired (entered) from unrepaired (not entered) plasmids by cleaving unrepaired molecules with uracil DNA glycoylase and Escherichia coli endonuclease IV in vitro. This method of monitoring DNA entry does not appear to underestimate or overestimate the amount of DNA entry. By using this method, we found no significant quantitative effect of DNA replication on V(D)J recombination efficiency.
APA, Harvard, Vancouver, ISO, and other styles
5

Hsieh, C. L., R. P. McCloskey, E. Radany, and M. R. Lieber. "V(D)J recombination: evidence that a replicative mechanism is not required." Molecular and Cellular Biology 11, no. 8 (1991): 3972–77. http://dx.doi.org/10.1128/mcb.11.8.3972.

Full text
Abstract:
We examined a series of extrachromosomal DNA substrates for V(D)J recombination under replicating and nonreplicating conditions. Complete and partial replications were examined by monitoring the loss of prokaryote-specific adenine methylation at 14 to 22 MboI-DpnI restriction sites (GATC) on the substrates. Some of these sites are within 2 bases of the signal sequence ends. We found that neither coding joint nor signal joint formation requires substrate replication. After ruling out replication as a substrate requirement, we determined whether replication had any effect on the efficiency of V(D)J recombination. Quantitation of V(D)J recombination efficiency on nonreplicating substrates requires some method of monitoring the entry of substrate molecules into the cells. We devised such a method by monitoring DNA repair of substrates into which we had substituted deoxyuridine for 10 to 20% of the thymidine nucleotides in the DNA. The substrates which enter the lymphoid cells were repaired efficiently in vivo by the eukaryotic uracil DNA repair system. Upon plasmid harvest, we distinguished repaired (entered) from unrepaired (not entered) plasmids by cleaving unrepaired molecules with uracil DNA glycoylase and Escherichia coli endonuclease IV in vitro. This method of monitoring DNA entry does not appear to underestimate or overestimate the amount of DNA entry. By using this method, we found no significant quantitative effect of DNA replication on V(D)J recombination efficiency.
APA, Harvard, Vancouver, ISO, and other styles
6

Craggs, Timothy D., Marko Sustarsic, Anne Plochowietz, et al. "Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase." Nucleic Acids Research 47, no. 20 (2019): 10788–800. http://dx.doi.org/10.1093/nar/gkz797.

Full text
Abstract:
Abstract DNA-binding proteins utilise different recognition mechanisms to locate their DNA targets; some proteins recognise specific DNA sequences, while others interact with specific DNA structures. While sequence-specific DNA binding has been studied extensively, structure-specific recognition mechanisms remain unclear. Here, we study structure-specific DNA recognition by examining the structure and dynamics of DNA polymerase I Klenow Fragment (Pol) substrates both alone and in DNA–Pol complexes. Using a docking approach based on a network of 73 distances collected using single-molecule FRET, we determined a novel solution structure of the single-nucleotide-gapped DNA–Pol binary complex. The structure resembled existing crystal structures with regards to the downstream primer-template DNA substrate, and revealed a previously unobserved sharp bend (∼120°) in the DNA substrate; this pronounced bend was present in living cells. MD simulations and single-molecule assays also revealed that 4–5 nt of downstream gap-proximal DNA are unwound in the binary complex. Further, experiments and coarse-grained modelling showed the substrate alone frequently adopts bent conformations with 1–2 nt fraying around the gap, suggesting a mechanism wherein Pol recognises a pre-bent, partially-melted conformation of gapped DNA. We propose a general mechanism for substrate recognition by structure-specific enzymes driven by protein sensing of the conformational dynamics of their DNA substrates.
APA, Harvard, Vancouver, ISO, and other styles
7

Burke, Cassandra R., and Andrej Lupták. "DNA synthesis from diphosphate substrates by DNA polymerases." Proceedings of the National Academy of Sciences 115, no. 5 (2018): 980–85. http://dx.doi.org/10.1073/pnas.1712193115.

Full text
Abstract:
The activity of DNA polymerase underlies numerous biotechnologies, cell division, and therapeutics, yet the enzyme remains incompletely understood. We demonstrate that both thermostable and mesophilic DNA polymerases readily utilize deoxyribonucleoside diphosphates (dNDPs) for DNA synthesis and inorganic phosphate for the reverse reaction, that is, phosphorolysis of DNA. For Taq DNA polymerase, the KMs of the dNDP and phosphate substrates are ∼20 and 200 times higher than for dNTP and pyrophosphate, respectively. DNA synthesis from dNDPs is about 17 times slower than from dNTPs, and DNA phosphorolysis about 200 times less efficient than pyrophosphorolysis. Such parameters allow DNA replication without requiring coupled metabolism to sequester the phosphate products, which consequently do not pose a threat to genome stability. This mechanism contrasts with DNA synthesis from dNTPs, which yield high-energy pyrophosphates that have to be hydrolyzed to phosphates to prevent the reverse reaction. Because the last common ancestor was likely a thermophile, dNDPs are plausible substrates for genome replication on early Earth and may represent metabolic intermediates later replaced by the higher-energy triphosphates.
APA, Harvard, Vancouver, ISO, and other styles
8

Victorova, Lyubov, Vasily Sosunov, Alexander Skoblov, Alexander Shipytsin, and Alexander Krayevsky. "New substrates of DNA polymerases." FEBS Letters 453, no. 1-2 (1999): 6–10. http://dx.doi.org/10.1016/s0014-5793(99)00615-8.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Chiriboga, Matthew, Christopher M. Green, Divita Mathur, et al. "Structural and optical variation of pseudoisocyanine aggregates nucleated on DNA substrates." Methods and Applications in Fluorescence 11, no. 1 (2023): 014003. http://dx.doi.org/10.1088/2050-6120/acb2b4.

Full text
Abstract:
Abstract Coherently coupled pseudoisocyanine (PIC) dye aggregates have demonstrated the ability to delocalize electronic excitations and ultimately migrate excitons with much higher efficiency than similar designs where excitations are isolated to individual chromophores. Here, we report initial evidence of a new type of PIC aggregate, formed through heterogeneous nucleation on DNA oligonucleotides, displaying photophysical properties that differ significantly from previously reported aggregates. This new aggregate, which we call the super aggregate (SA) due to the need for elevated dye excess to form it, is clearly differentiated from previously reported aggregates by spectroscopic and biophysical characterization. In emission spectra, the SA exhibits peak narrowing and, in some cases, significant quantum yield variation, indicative of stronger coupling in cyanine dyes. The SA was further characterized with circular dichroism and atomic force microscopy observing unique features depending on the DNA substrate. Then by integrating an AlexaFluorTM 647 (AF) dye as an energy transfer acceptor into the system, we observed mixed energy transfer characteristics using the different DNA. For example, SA formed with a rigid DNA double crossover tile (DX-tile) substrate resulted in AF emission sensitization. While SA formed with more flexible non-DX-tile DNA (i.e. duplex and single strand DNA) resulted in AF emission quenching. These combined characterizations strongly imply that DNA-based PIC aggregate properties can be controlled through simple modifications to the DNA substrate’s sequence and geometry. Ultimately, we aim to inform rational design principles for future device prototyping. For example, one key conclusion of the study is that the high absorbance cross-section and efficient energy transfer observed with rigid substrates made for better photonic antennae, compared to flexible DNA substrates.
APA, Harvard, Vancouver, ISO, and other styles
10

AHN, Jinwoo, Vadim S. KRAYNOV, Xuejun ZHONG, Brian G. WERNEBURG та Ming-Daw TSAI. "DNA polymerase β: effects of gapped DNA substrates on dNTP specificity, fidelity, processivity and conformational changes1". Biochemical Journal 331, № 1 (1998): 79–87. http://dx.doi.org/10.1042/bj3310079.

Full text
Abstract:
Pre-steady-state kinetic analysis was used to compare the catalytic properties of DNA polymerase β (Pol β) for single-base gap-filling and regular duplex DNA synthesis. The rate of polymerization (kpol) and the apparent equilibrium dissociation constant of dNTP (Kd) were determined with single-nucleotide gapped DNA substrates for all four possible correct base pairs and twelve possible incorrect base pairs, and the results were compared with those obtained previously with non-gapped primer/template duplex DNA substrates. For correct dNTP incorporation, the use of single-nucleotide gapped DNA led to significant decreases in the Kd of dNTP. Although kpol was little affected, the catalytic efficiency kpol/Kd increased significantly owing to the decreases in Kd. In contrast, for incorrect dNTP incorporation, the use of single-nucleotide gapped DNA substrates did not affect the Kd of dNTP appreciably but caused the kpol (and thus kpol/Kd) for incorrect dNTP incorporation to increase. As a consequence the fidelity of Pol β was not significantly affected by the use of single-nucleotide gapped DNA substrates. In addition we show that under processive polymerization conditions the processivity of Pol β increases in the gap-filling synthesis owing to a decreased rate of DNA dissociation. Finally, with a single-nucleotide gapped DNA substrate the rate-limiting conformational change step before chemistry was also observed. However, the preceding fast conformational change observed with duplex DNA substrates was not clearly detected. A possible cause is that in the complex with the gapped DNA, the 8 kDa N-terminal domain of Pol β already exists in a closed conformation. This interpretation was supported by tryptic digestion experiments.
APA, Harvard, Vancouver, ISO, and other styles
More sources

Dissertations / Theses on the topic "DNA Substrates"

1

Riley, Jane. "The interaction of topoisomerase IV with potential DNA substrates." Thesis, University of Liverpool, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.272768.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Gössl, Illdiko Maria. "Supramolecular structures of dendronized polymers and DNA on solid substrates." [S.l.] : [s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=968755925.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Bergen, Konrad [Verfasser]. "Structural insights into DNA polymerases encountering aberrant substrates / Konrad Bergen." Konstanz : Bibliothek der Universität Konstanz, 2015. http://d-nb.info/1078230455/34.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Gössl, Illdiko Maria. "Supramolecular structures of dendronized polymers and DNA on solid substrates." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2003. http://dx.doi.org/10.18452/14893.

Full text
Abstract:
Komplexe aus entgegengesetzt geladenen Polyelektrolyten haben sowohl in der Biologie als auch in den Materialwissenschaften eine große Bedeutung. Im Mittelpunkt des Interesses stehen besonders die Kondensation der DNA in vitro, die Struktur des Nukleosoms im Zellkern, nicht-virale Systeme zur Transfektion von DNA in Zellen oder der Vorgang der layer-by-layer Adsorption. Verschiedene Theorien befassen sich mit den treibenden Kräften solcher Komplexbildungen. Allerdings standen experimentelle Untersuchungen auf diesem Gebiet bisher noch aus. Dieser Arbeit liegt die Fragestellung zu Grunde, ob es mit Hilfe der Rasterkraftmikroskopie möglich ist, die Struktur einzelner Polyelektrolytkomplexe, bestehend aus den beiden Polyelektrolyten DNA und dendronisierten Polymer, aufzuklären und ihre Komplexbildung zu untersuchen. Die Komplexe bildeten sich in Lösung und wurden anschließend auf einer unbeschichteten oder mit positiven Polymeren beschichteten Glimmeroberfläche adsorbiert. Auf der positiv beschichteten Glimmeroberfläche hafteten DNA-dendronisierte Polymer Komplexe mit einem Ladungsverhältnis von 1:1 bis 1:0.7 (DNA:dendronisiertes Polymer). Anhand der hochaufgelösten rasterkraftmikroskopischen Aufnahmen wurde ein Modell entwickelt, das die Umwicklung der DNA um das dendronisierte Polymer beschreibt. Der DNA-DNA Abstand ergab sich zu (2.30 ± 0.27) nm für den Komplex mit DNA und zweiter Generation dendronisierter Polymere und zu (2.16 ± 0.27) nm mit vierter Generation. Die theoretische Vorhersage der Überladung der Komplexe konnte experimentell bestätigt werden. Mit Hilfe der Rasterkraftmikroskopie konnte überdies der Einfluss des Salzgehaltes der Lösung auf die Bildung der Komplexe mit DNA und zweiter Generation dendronisierter Polymere untersucht werden. Wie man anhand des Zusammenwirkens von elektrostatischen Kräften und entropischen Wechselwirkungen bei der Adsorption von Polyelektrolyten vorhersagen kann, durchlief der DNA-DNA Abstand ein Minimum bei ansteigendem Salzgehalt. Bei sehr hohem Salzgehalt (2.4 M NaCl) konnte das Ablösen der DNA von dem Komplex beobachtet werden. Die untersuchten DNA/dendroniserten Polymer Komplexe bilden ein neues Modellsystem, mit dem einzelne Polyelektrolyt-Wechselwirkungen direkt untersucht werden können. Ein Vergleich der experimentellen Daten mit den vorhandenen Theorien zeigte, dass der Prozess des Überladens weitgehend durch elektrostatische Wechselwirkung zwischen den beiden Polyelektrolyten beschrieben werden kann. Sowohl entropische Beiträge als auch die Biegeenergie der umwickelnden DNA sind vernachlässigbar. Basierend auf diesen Ergebnissen können neue Trägerstrukturen für effizientere nicht-virale DNA-Transfektionssysteme entwickelt werden.<br>Complexes of oppositely charged polyelectrolytes play an important role in both biology and material science, for instance DNA condensation in vitro, nucleosomal structure, non-viral gene transfection systems as well as layer-by-layer adsorption. Although there are theories predicting overcharging of polyelectrolyte complexes, the driving forces are still under debate and systematic experimental studies on single polyelectrolytes remain challenging. Therefore the question arose if it is possible to analyze single polyelectrolyte complexes, using DNA and dendronized polymers, with the scanning force microscope in order to investigate the complexation in detail. For the complex analysis, the polyelectrolytes were allowed to interact in solution and then to adsorb on negatively charged mica or on mica coated with a positively charged polymer. Scanning force microscopy was used to investigate the adsorbed species. DNA/dendronized polymer complexes of charge ratio of 1/1 through 1/0.7 adsorbed on mica coated with a positively charged polymer. The analysis of high resolution molecular images indicated that DNA wraps around the dendronized polymer with an estimated pitch of (2.30 ± 0.27) nm and (2.16 ± 0.27) nm for dendronized polymers of generation two and four, respectively. In the proposed model the polyelectrolyte with the smaller linear charge density is wrapped around the more highly charged dendronized polymer, resulting in a negatively overcharged complex. This overcharging is consistent within recent theories of spontaneous overcharging of complexes of one polyelectrolyte wrapping around the other. Using the complex of DNA and dendronized polymers of second generation, the influence of monovalent salt concentration on the molecular structure was studied. By increasing the salt concentration the pitch showed a minimum as predicted by the interplay of electrostatic forces and entropic interactions of polyelectrolyte adsorption. At high salt concentration (2.4 M NaCl) the release of DNA from the complex can be observed. The results showed that the DNA/dendronized polymer system can be used as a new, high potential model system to investigate single polyelectrolyte interactions. With regard to recent theories, the experimental results indicate that the overcharging of the complex is mainly driven by electrostatic forces whereas contributions of counterion entropy and bending energy seem to be negligible. This understanding may be useful for the design of single polyelectrolyte complexes for non-viral gene delivery systems and might help to optimize the transfection efficiency based on the structure of the vector system.
APA, Harvard, Vancouver, ISO, and other styles
5

Blatter, Nina [Verfasser]. "DNA Synthesis from Aberrant Substrates by KlenTaq DNA Polymerase: A Functional and Structural Analysis / Nina Blatter." Konstanz : Bibliothek der Universität Konstanz, 2013. http://d-nb.info/105832599X/34.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Ren, Ruobo. "DNA printing on polymer substrates : towards cost-effective medical diagnostic devices." Thesis, Swansea University, 2011. https://cronfa.swan.ac.uk/Record/cronfa43015.

Full text
Abstract:
DNA for sensing has a diversity o f life science applications. The aim o f this work was to explore the printing DNA onto a flexible substrate. DNA printing has a diversity of life science applications. DNA can be printed onto rigid substrates at high resolution. Printing is a candidate process for volume manufacturing. This required identification o f substrate and any surface treatment to ensure wetting and adhesion. Printing also involves matching the ink with printing process characteristics and for the purpose o f sensing, it requires the formulation o f an ink that can be printed and demonstrates suitable hybridisation characteristics. Each of these aspects was addressed within this thesis. Measurement techniques and their robustness were established as a first step. The next stage focused on determining a suitable substrate and surface treatment for immobilisation o f DNA. This was followed by an exploration o f printing processes, which include inkjet as a reference and flexography and gravure as candidates for volume printing. This work was carried out on a bench top printed, while providing a path for volume printing. The third research strand was concerned with the hybridisation of DNA formulated within an ink. A CCP (Corona treated top coated BOPP) substrate was found to enable good immobilisation o f DNA It needed to be corona treated to enhance the covalent bonding mechanism. Inkjet printing was successfully in applying out, however, within the range o f process parameters explored, neither flexography nor gravure successfully printed DNA. Further work is needed to develop them so they successfully print and could be used for volume production. An appropriate hybridisation method for DNA deposited within an ink formulation was established.
APA, Harvard, Vancouver, ISO, and other styles
7

Roewenstrunk, Julia Maria 1981. "RNF169 and RNF168 novel substrates of DYRK1A : connecting DYRK1A to DNA-damage repair." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/565442.

Full text
Abstract:
Gene dosage alterations of the kinase DYRK1A are linked to disease in humans. To better understand DYRK1A activities an interactome analysis was performed. RNF169, an E3-ubiquitin ligase key component of the cellular response to double-strand breaks (DSBs), was found as a top nuclear interactor. The functional characterization of this interaction has uncovered that a dedicated motif in the non-catalytic N-terminus of DYRK1A is responsible of the direct interaction with RNF169 and that this interaction is essential for the recruitment of DYRK1A to DSBs. Using a combination of mass spectrometry analysis, mutagenesis, and in vitro kinase assays several DYRK1A-dependent phosphosites have been identified in RNF169 and its paralog RNF168. Reporter-cell assays and IRIF analysis showed that DYRK1A silencing perturbs the DSB-repair pathways. In agreement, DYRK1A knockdown leads to increased radiation sensitivity. All together, the data suggest a role for DYRK1A in DSB-repair that might involve the phosphorylation of RNF168 and RNF169.<br>Alteraciones de la dosis génica de la quinasa DYRK1A son causantes de enfermedad en humanos. Para profundizar en las actividades biológicas de DYRK1A, se ha realizado un estudio de interactoma, en el que RNF169, elemento clave en la respuesta al daño al DNA causado por roturas de doble cadena, se reveló como uno de los principales interactores. La interacción DYRK1A-RNF169 es directa y responsable de la localización de DYRK1A en el DNA en respuesta al daño. La combinación de espectrometría de masas, mutagénesis y ensayos quinasa ha permitido identificar varios residuos fosforilados por DYRK1A en RNF169 y en su parálogo RNF168, que actúa en el mismo proceso. El silenciamiento de DYRK1A causa alteraciones en los mecanismos de respuesta al daño y las células presentan un aumento de la sensibilidad a la radiación. Estos resultados permiten sugerir que DYRK1A puede ser un nuevo regulador de la respuesta al daño al DNA.
APA, Harvard, Vancouver, ISO, and other styles
8

Baker, Bryan Alexander. "Employing double-stranded DNA probes on colloidal substrates for competitive hybridization events." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/33922.

Full text
Abstract:
The study of the DNA has found application beyond our understanding of its cellular function and into a variety of materials assembly and nucleic acid detection systems. The current research investigates double-stranded DNA probes in both a colloidal particle assembly and fluorescent assay format utilizing competitive hybridization events. In both contexts, the affinity of the dsProbes is tuned by the sequence design parameters of duplex length and complementarity. These systems were incubated with nucleic acid targets of interest and, based on the mechanism of competitive hybridization, were responsive to the presence of a high affinity competitive target. In the case of the particle assemblies, incubation with the competitive target resulted in observable disassembly of particle structures. In the case of fluorescently labeled dsProbes, incubation with competitive targets resulted in a quantifiable loss of fluorescence as determined by flow cytometry. Utilizing the fluorescently labeled dsProbe system, the kinetics of competitive hybridization was characterized for nucleic acid targets of varying specificity and strand context. The results indicate promise for the development of the competitive hybridization approach in nucleic acid detection systems providing advantages over current single-stranded probe designs. By utilizing a fluorescently labeled dsProbe approach, it is unnecessary to chemically modify the target of interest to impart a signaling mechanism. Additionally, as the process of competitive hybridization of dsProbes with targets of interest is an affinity driven process, discrimination of targets based on specificity is decoupled from standard measures such as elevated temperature protocols, an important step in translating nucleic acid technologies from the controlled laboratory environment to field applications.
APA, Harvard, Vancouver, ISO, and other styles
9

Tapp, Maeling Janelle Nicole. "Competition-induced selection of ligands for the screening of DNA aptamers for gold substrates." Diss., Georgia Institute of Technology, 2015. http://hdl.handle.net/1853/54851.

Full text
Abstract:
This dissertation presents the development of an alternative aptamer screening process, Competition-Induced Selection of Ligands (CISL), and its use in screening for ssDNA aptamers for gold substrates. Gold substrates are presented as the nonnucleotide target for implementing CISL as a novel aptamer screening approach. Chapter 1 provides an overview of the in vitro selection of oligonucleotide aptamers, the polymerase chain reaction that is a key step in the aptamer screening process, the synthesis and properties of gold nanoparticles and the biomolecule-mediated formation of inorganic nanoparticles. Chapter 2 presents the goals and objectives of this thesis along with an organizational overview of the dissertation. Chapter 3 describes the experimental techniques and optimizations pertinent to the development of the CISL aptamer screening process. Chapter 4 investigates the effects of various nucleic acid additions during the seed-mediated growth of gold nanoparticles. Chapter 5 discusses the use of CISL in screening for ssDNA aptamer candidates for spherical gold nanoparticles (AuNPs) and the primary and secondary structure analysis of identified sequences. Chapter 6 presents the use of CISL in screening for ssDNA aptamer candidates for planar gold substrates (PlanarAu) and also includes primary and secondary structure analysis of identified sequences accompanied with an incubation study to provide a “frequency” ranking of aptamers as adsorbate species on PlanarAu. Chapter 7 offers concluding remarks and ideas for future expansion and applications of this work.
APA, Harvard, Vancouver, ISO, and other styles
10

Grealy, Alicia Catherine. "New approaches to ancient DNA: using novel substrates to characterise DNA preservation and past biodiversity in warm-climate ecosystems." Thesis, Curtin University, 2016. http://hdl.handle.net/20.500.11937/51741.

Full text
Abstract:
Retrieving ancient DNA (aDNA) from fossils in warm, tropical environments remains a challenge. This thesis describes the development and application of next generation sequencing technologies in the search for warm-climate aDNA. Methods to extract, enrich and sequence aDNA from fossil ‘bulk bone’ and avian eggshell are successfully explored from sites in Australia and Madagascar. Collectively, the research provides new insights into past biodiversity and evolutionary processes in climates not previously considered conducive to DNA preservation.
APA, Harvard, Vancouver, ISO, and other styles
More sources

Books on the topic "DNA Substrates"

1

Day, Philip John Royle. The development of strategies for the reversible immobilisation of oligonucleotides for hybridisation and as substrates to initiate DNA synthesis. University of Birmingham, 1995.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
2

Motor speech disorders: Substrates, differential diagnosis, and management. Mosby, 1995.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
3

Motor speech disorders: Substrates, differential diagnosis, and management. 2nd ed. Elsevier Mosby, 2005.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
4

Duffy, Joseph R. Motor speech disorders: Substrates, differential diagnosis, and management. 2nd ed. Elsevier Mosby, 2004.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
5

Keim, Celia D. Post Translational Regulation of AID Targeting to Both Strands of a Transcribed DNA Substrate. [publisher not identified], 2012.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
6

Narlikar, A. V., and Y. Y. Fu, eds. Oxford Handbook of Nanoscience and Technology. Oxford University Press, 2017. http://dx.doi.org/10.1093/oxfordhb/9780199533053.001.0001.

Full text
Abstract:
This Handbook presents important developments in the field of nanoscience and technology, focusing on the advances made with a host of nanomaterials including DNA and protein-based nanostructures. Topics include: optical properties of carbon nanotubes and nanographene; defects and disorder in carbon nanotubes; roles of shape and space in electronic properties of carbon nanomaterials; size-dependent phase transitions and phase reversal at the nanoscale; scanning transmission electron microscopy of nanostructures; the use of microspectroscopy to discriminate nanomolecular cellular alterations in biomedical research; holographic laser processing for three-dimensional photonic lattices; and nanoanalysis of materials using near-field Raman spectroscopy. The volume also explores new phenomena in the nanospace of single-wall carbon nanotubes; ZnO wide-bandgap semiconductor nanostructures; selective self-assembly of semi-metal straight and branched nanorods on inert substrates; nanostructured crystals and nanocrystalline zeolites; unusual properties of nanoscale ferroelectrics; structural, electronic, magnetic, and transport properties of carbon-fullerene-based polymers; fabrication and characterization of magnetic nanowires; and properties and potential of protein-DNA conjugates for analytic applications.
APA, Harvard, Vancouver, ISO, and other styles
7

Lachmann, Robin H., and Nigel Manning. Trimethylaminuria. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199972135.003.0064.

Full text
Abstract:
Trimethylaminuria (TMAU) or “Fish Odor Syndrome” is a disorder caused by increased concentrations of the volatile amine trimethylamine (TMA) in body fluids resulting in an unpleasant odor. The excess TMA may occur either due to deficient hepatic oxidation (primary) or increased bacterial generation (secondary). Testing urine for TMA concentration is the first line of investigation, preferably following a dietary load of a TMA precursor such as choline. Measurement of TMA and TMA-oxide are used as a guide to determine a primary or secondary cause, which can be confirmed by DNA analysis. FMO3 deficiency may have further clinical consequences due to the wide range of substrates oxidized by the enzyme including many drugs. Treatment of both primary and secondary TMAU relies on restriction of dietary precursors of TMA, antibiotic-based reduction of gut flora, and odor chelators. Riboflavin may also benefit some patients.
APA, Harvard, Vancouver, ISO, and other styles
8

Motor Speech Disorders: Substrates, Differential Diagnosis, and Management. Mosby, 2015.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
9

Motor Speech Disorders: Substrates, Differential Diagnosis, and Management. Elsevier - Health Sciences Division, 2012.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
10

Makroinvertebrata sungai di hutan pendidikan dan penelitian biologi UNAND Padang dan kolonisasinya pada substrat buatan. Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Andalas, 1999.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
More sources

Book chapters on the topic "DNA Substrates"

1

Spears, Jessica L., Kirk W. Gaston, and Juan D. Alfonzo. "Analysis of tRNA Editing in Native and Synthetic Substrates." In RNA and DNA Editing. Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-018-8_13.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Liaqat, Anam, Maksim V. Sednev, and Claudia Höbartner. "In Vitro Selection of Deoxyribozymes for the Detection of RNA Modifications." In Ribosome Biogenesis. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_10.

Full text
Abstract:
AbstractDeoxyribozymes are artificially evolved DNA molecules with catalytic abilities. RNA-cleaving deoxyribozymes have been recognized as an efficient tool for detection of modifications in target RNAs and provide an alternative to traditional and modern methods for detection of ribose or nucleobase methylation. However, there are only few examples of DNA enzymes that specifically reveal the presence of a certain type of modification, including N6-methyladenosine, and the knowledge about how DNA enzymes recognize modified RNAs is still extremely limited. Therefore, DNA enzymes cannot be easily engineered for the analysis of desired RNA modifications, but are instead identified by in vitro selection from random DNA libraries using synthetic modified RNA substrates. This protocol describes a general in vitro selection stagtegy to evolve new RNA-cleaving DNA enzymes that can efficiently differentiate modified RNA substrates from their unmodified counterpart.
APA, Harvard, Vancouver, ISO, and other styles
3

Sagner, Gregor. "DIG DNA Sequencing with Chemiluminescent or Dye Substrates." In Nonradioactive Analysis of Biomolecules. Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-642-57206-7_59.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Wilson, Stuart M. "Novel Applications of PCR Through the Use of DNA Substrates." In Methods in Molecular Biology. Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-944-4_17.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Beloglazova, Natalia, Sofia Lemak, Robert Flick, and Alexander F. Yakunin. "Analysis of Nuclease Activity of Cas1 Proteins Against Complex DNA Substrates." In Methods in Molecular Biology. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2687-9_16.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Pegg, Anthony E., and M. Eileen Dolan. "Investigation of Sequence Specificity in DNA Alkylation and Repair Using Oligodeoxynucleotide Substrates." In DNA Repair Mechanisms and Their Biological Implications in Mammalian Cells. Springer US, 1989. http://dx.doi.org/10.1007/978-1-4684-1327-4_5.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Chen, Shu-Hui. "Microchip Electrophoresis for DNA Separation by Wire-Imprinted Microchannels on PMMA Substrates." In Methods in Molecular Biology. Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-426-1_1.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Yadav, Janardan, Prem Narayan Yadav, Edward Arnold, Swamy Laxminarayan, and Mukund J. Modak. "Molecular modeling of the interactions between Escherichia coli DNA polymerase I and substrates." In Proteins. Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-010-9063-6_49.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Cowart, Dominique A., Katherine R. Murphy, and C. H. Christina Cheng. "Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction." In Methods in Molecular Biology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2313-8_11.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

O’Donnell, Kerry, Imana Laraba, and David M. Geiser. "Pure Culture and DNA Sequence-Based Identification of Fusarium from Symptomatic Plants and Diverse Substrates." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1795-3_1.

Full text
APA, Harvard, Vancouver, ISO, and other styles

Conference papers on the topic "DNA Substrates"

1

"Activity of DNA glycosylases on non-canonical DNA substrates." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-346.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Chippada, Uday, Xue Jiang, Michelle Previtera, et al. "Alteration of Fibroblast Cell Behavior due to Contraction of Substrate." In ASME 2010 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2010. http://dx.doi.org/10.1115/sbc2010-19507.

Full text
Abstract:
Many researchers have utilized hydrogels as substrates for cell attachment. The stiffness of these substrates has been found to influence the cellular behavior such as morphology, proliferation, growth and differentiation. Lo et al. deformed polyacrylamide substrates with a blunted microneedle and observed the movement of NIH 3T3 fibroblasts. In both pulling and pushing, the cells reversed their direction and moved away from the needle. This shows that cellular behavior is also affected by stretching the underlying substrates. In a previous study, Lin et al. have demonstrated the ability to contract DNA-crosslinked polyacrylamide hydrogels (‘DNA gels’ in short) by addition of crosslinks. Jiang et al. have utilized these DNA gels as substrates to observe the cellular responses of L929 and GFP fibroblasts to both static and dynamic substrate compliances.
APA, Harvard, Vancouver, ISO, and other styles
3

Bergen, Konrad, Holger Busskamp, Anna-Lena Steck, Samra Obeid, Karin Betz, and Andreas Marx. "DNA polymerases in action with modified substrates." In XVIth Symposium on Chemistry of Nucleic Acid Components. Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2014. http://dx.doi.org/10.1135/css201414101.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Becerril, Héctor A. "Micromachined Substrates for Molecular Follow-Up in DNA-Templated Nanofabrication." In DNA-BASED MOLECULAR ELECTRONICS: International Symposium on DNA-Based Molecular Electronics. AIP, 2004. http://dx.doi.org/10.1063/1.1805376.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Mathur, Divita, William P. Klein, Hieu Bui, et al. "Competitive binding of gold nanospheres and nanorods on DNA origami substrates." In Colloidal Nanoparticles for Biomedical Applications XV, edited by Marek Osiński and Antonios G. Kanaras. SPIE, 2020. http://dx.doi.org/10.1117/12.2545953.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Charlot, Benoit, Roland Teissier, and Etienne Schwob. "Micro and nanostructured substrates for DNA fibers combing by forced dewetting." In 2015 Symposium on Design, Test, Integration and Packaging of MEMS/MOEMS (DTIP). IEEE, 2015. http://dx.doi.org/10.1109/dtip.2015.7160967.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Lee, Tae Yoon, Dimistris E. Nikitopoulos, Daniel S. Park, Steven A. Soper, and Michael C. Murphy. "Design and Fabrication of a Ligase Detection Reaction (LDR) Microchip With an Integrated Passive Micromixer." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-42216.

Full text
Abstract:
The ligase detection reaction (LDR) is a technique that can distinguish low-abundant mutant DNAs from wild-type DNAs. LDR is usually carried out on DNAs amplified using the polymerase chain reaction (PCR). In the realization of modular microfluidic systems, the DNA output of the PCR handed off to the LDR chip needs to be mixed with LDR reagents before continuing the reaction. Polymer, continuous flow ligase detection reaction (CFLDR) devices with integrated passive micromixers, were designed, fabricated and tested. The devices each consisted of: a passive mixer for mixing a PCR sample, a cocktail of primers, and ligase, an enzyme of DNA; an incubator channel (95°C) for preheating the mixture; and a thermal cycling channel for the LDR. The devices were produced by hot embossing polycarbonate (PC) substrates with brass mold inserts manufactured by micro-milling. Experiments using food dyes showed that the appropriate mixture concentrations were delivered to the preheating channel in both the pulling and pushing modes.
APA, Harvard, Vancouver, ISO, and other styles
8

Corrigan, Timothy D., Matthew Kessinger, Jesse Kidd, David Neff, Masudur Rahman, and Michael L. Norton. "Fluorescence of quantum dots on e-beam patterned and DNA origami substrates." In SPIE Sensing Technology + Applications, edited by Nibir K. Dhar and Achyut K. Dutta. SPIE, 2015. http://dx.doi.org/10.1117/12.2180638.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Ye, Yun, April K. Y. Wong, and Ulrich J. Krull. "Potential for optical DNA biosensors and biochips based on a GaAs substrates." In Photonics North 2005, edited by Warren C. W. Chan, Kui Yu, Ulrich J. Krull, Richard I. Hornsey, Brian C. Wilson, and Robert A. Weersink. SPIE, 2005. http://dx.doi.org/10.1117/12.628713.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Carpignano, F., J. A. Grant-Jacob, J. Lamb, K. Pechstedt, W. S. Brocklesby, and T. Melvin. "Direct detection of DNA on gold structured planar substrates by Raman microscopy." In 2014 Fotonica AEIT Italian Conference on Photonics Technologies (Fotonica AEIT). IEEE, 2014. http://dx.doi.org/10.1109/fotonica.2014.6843930.

Full text
APA, Harvard, Vancouver, ISO, and other styles

Reports on the topic "DNA Substrates"

1

Anderson, C. W., M. A. Connelly, H. Zhang, et al. The human DNA-activated protein kinase, DNA-PK: Substrate specificity. Office of Scientific and Technical Information (OSTI), 1994. http://dx.doi.org/10.2172/113929.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Elbaum, Michael, and Peter J. Christie. Type IV Secretion System of Agrobacterium tumefaciens: Components and Structures. United States Department of Agriculture, 2013. http://dx.doi.org/10.32747/2013.7699848.bard.

Full text
Abstract:
Objectives: The overall goal of the project was to build an ultrastructural model of the Agrobacterium tumefaciens type IV secretion system (T4SS) based on electron microscopy, genetics, and immunolocalization of its components. There were four original aims: Aim 1: Define the contributions of contact-dependent and -independent plant signals to formation of novel morphological changes at the A. tumefaciens polar membrane. Aim 2: Genetic basis for morphological changes at the A. tumefaciens polar membrane. Aim 3: Immuno-localization of VirB proteins Aim 4: Structural definition of the substrate translocation route. There were no major revisions to the aims, and the work focused on the above questions. Background: Agrobacterium presents a unique example of inter-kingdom gene transfer. The process involves cell to cell transfer of both protein and DNA substrates via a contact-dependent mechanism akin to bacterial conjugation. Transfer is mediated by a T4SS. Intensive study of the Agrobacterium T4SS has made it an archetypal model for the genetics and biochemistry. The channel is assembled from eleven protein components encoded on the B operon in the virulence region of the tumor-inducing plasmid, plus an additional coupling protein, VirD4. During the course of our project two structural studies were published presenting X-ray crystallography and three-dimensional reconstruction from electron microscopy of a core complex of the channel assembled in vitro from homologous proteins of E. coli, representing VirB7, VirB9, and VirB10. Another study was published claiming that the secretion channels in Agrobacterium appear on helical arrays around the membrane perimeter and along the entire length of the bacterium. Helical arrangements in bacterial membranes have since fallen from favor however, and that finding was partially retracted in a second publication. Overall, the localization of the T4SS within the bacterial membranes remains enigmatic in the literature, and we believe that our results from this project make a significant advance. Summary of achievements : We found that polar inflations and other membrane disturbances relate to the activation conditions rather than to virulence protein expression. Activation requires low pH and nutrient-poor medium. These stress conditions are also reflected in DNA condensation to varying degrees. Nonetheless, they must be considered in modeling the T4SS as they represent the relevant conditions for its expression and activity. We identified the T4SS core component VirB7 at native expression levels using state of the art super-resolution light microscopy. This marker of the secretion system was found almost exclusively at the cell poles, and typically one pole. Immuno-electron microscopy identified the protein at the inner membrane, rather than at bridges across the inner and outer membranes. This suggests a rare or transient assembly of the secretion-competent channel, or alternatively a two-step secretion involving an intermediate step in the periplasmic space. We followed the expression of the major secreted effector, VirE2. This is a single-stranded DNA binding protein that forms a capsid around the transferred oligonucleotide, adapting the bacterial conjugation to the eukaryotic host. We found that over-expressed VirE2 forms filamentous complexes in the bacterial cytoplasm that could be observed both by conventional fluorescence microscopy and by correlative electron cryo-tomography. Using a non-retentive mutant we observed secretion of VirE2 from bacterial poles. We labeled the secreted substrates in vivo in order detect their secretion and appearance in the plant cells. However the low transfer efficiency and significant background signal have so far hampered this approach.
APA, Harvard, Vancouver, ISO, and other styles
3

Devol, Allan H. Tracing Substrate Utilization by Specific Marine Sedimentary Microorganisms Using DNA Hybridization-Capture Technology. Defense Technical Information Center, 2002. http://dx.doi.org/10.21236/ada402393.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Barkan, Alice, and Zach Adam. The Role of Proteases in Regulating Gene Expression and Assembly Processes in the Chloroplast. United States Department of Agriculture, 2003. http://dx.doi.org/10.32747/2003.7695852.bard.

Full text
Abstract:
Chloroplasts house many biochemical processes that are essential for plant viability. Foremost, among these is photosynthesis, which requires the protein-rich thylakoid membrane system. The activation of chloroplast genes encoding thylakoid membrane proteins and the targeting and assembly of these proteins together with their nuclear-encoded partners are essential for the elaboration of the thylakoid membrane. Several nuclear-encoded proteins that regulate chloroplast gene expression and that mediate the targeting of proteins to the thylakoid membrane have been identified in recent years, and many more remain to be discovered. The abundance of such proteins is critical and is likely to be determined to a significant extent by their stability, which in turn, is influenced by chloroplast protease activities. The primary goal of this project was to link specific proteases to specific substrates, and in particular, to specific regulatory and assembly proteins. We proposed a two-pronged approach, involving genetic analysis of the consequences of the mutational loss of chloroplast proteases, and biochemical analysis of the degradation pathways of specific proteins that have been shown to control chloroplast gene expression. Our initial bioinformatic analysis of chloroplast proteases allowed us to identify the set of pro teases that is targeted to the chloroplast. We used that information to recover three Arabidopsis mutants with T - DNA insertions in specific chloroplast protease genes. We carried out the first analysis of the stability of a regulator of chloroplast gene expression (CRS2), and found that the protein is much less stable than are typical components of the photosynthetic apparatus. Genetic reagents and analytical methods were developed that have set the stage for a rapid advancement of our understanding of chloroplast proteolysis. The results obtained may be useful for manipulating the expression of transgenes in the chloroplast and for engineering plants whose photosynthetic activity is optimized under harsh environmental conditions.
APA, Harvard, Vancouver, ISO, and other styles
5

Wilson, Thomas E., Avraham A. Levy, and Tzvi Tzfira. Controlling Early Stages of DNA Repair for Gene-targeting Enhancement in Plants. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7697124.bard.

Full text
Abstract:
Gene targeting (GT) is a much needed technology as a tool for plant research and for the precise engineering of crop species. Recent advances in this field have shown that the presence of a DNA double-strand break (DSB) in a genomic locus is critical for the integration of an exogenous DNA molecule introduced into this locus. This integration can occur via either non-homologous end joining (NHEJ) into the break or homologous recombination (HR) between the broken genomic DNA and the introduced vector. A bottleneck for DNA integration via HR is the machinery responsible for homology search and strand invasion. Important proteins in this pathway are Rad51, Rad52 and Rad54. We proposed to combine our respective expertise: on the US side, in the design of zincfinger nucleases (ZFNs) for the induction of DNA DSBs at any desired genomic locus and in the integration of DNA molecules via NHEJ; and on the Israeli side in the HR events, downstream of the DSB, that lead to homology search and strand invasion. We sought to test three major pathways of targeted DNA integration: (i) integration by NHEJ into DSBs induced at desired sites by specially designed ZFNs; (ii) integration into DSBs induced at desired sites combined with the use of Rad51, Rad52 and Rad54 proteins to maximize the chances for efficient and precise HR-mediated vector insertion; (iii) stimulation of HR by Rad51, Rad52 and Rad54 in the absence of DSB induction. We also proposed to study the formation of dsT-DNA molecules during the transformation of plant cells. dsT-DNA molecules are an important substrate for HR and NHEJ-mediatedGT, yet the mode of their formation from single stranded T-DNA molecules is still obscure. In addition we sought to develop a system for assembly of multi-transgene binary vectors by using ZFNs. The latter may facilitate the production of binary vectors that may be ready for genome editing in transgenic plants. ZFNs were proposed for the induction of DSBs in genomic targets, namely, the FtsH2 gene whose loss of function can easily be identified in somatic tissues as white sectors, and the Cruciferin locus whose targeting by a GFP or RFP reporter vectors can give rise to fluorescent seeds. ZFNs were also proposed for the induction of DSBs in artificial targets and for assembly of multi-gene vectors. We finally sought to address two important cell types in terms of relevance to plant transformation, namely GT of germinal (egg) cells by floral dipping, and GT in somatic cells by root and leave transformation. To be successful, we made use of novel optimized expression cassettes that enable coexpression of all of the genes of interest (ZFNs and Rad genes) in the right tissues (egg or root cells) at the right time, namely when the GT vector is delivered into the cells. Methods were proposed for investigating the complementation of T-strands to dsDNA molecules in living plant cells. During the course of this research, we (i) designed, assembled and tested, in vitro, a pair of new ZFNs capable of targeting the Cruciferin gene, (ii) produced transgenic plants which expresses for ZFN monomers for targeting of the FtsH2 gene. Expression of these enzymes is controlled by constitutive or heat shock induced promoters, (iii) produced a large population of transgenic Arabidopsis lines in which mutated mGUS gene was incorporated into different genomic locations, (iv) designed a system for egg-cell-specific expression of ZFNs and RAD genes and initiate GT experiments, (v) demonstrated that we can achieve NHEJ-mediated gene replacement in plant cells (vi) developed a system for ZFN and homing endonuclease-mediated assembly of multigene plant transformation vectors and (vii) explored the mechanism of dsTDNA formation in plant cells. This work has substantially advanced our understanding of the mechanisms of DNA integration into plants and furthered the development of important new tools for GT in plants.
APA, Harvard, Vancouver, ISO, and other styles
6

Palhares Neto, Luiz, Leilane Gomes, José Marangon, Genilton Santos, and Cecílio Caldeira Júnior. Protocolo de micropropagação de Cattleya milleri, espécie endêmica do quadrilátero ferrífero criticamente ameaçada de extinção. ITV, 2022. http://dx.doi.org/10.29223/prod.tec.itv.ds.2022.12.palharesneto.

Full text
Abstract:
A espécie Cattleya milleri é uma orquídea endêmica dos Campos Rupestres Ferruginosos do Quadrilátero Ferrífero em Minas Gerais. Esta espécie é atualmente classificada como criticamente ameaçada de extinção sobretudo devido a restrição geográfica de sua ocorrência, degradação de seu habitat natural e reduzidas populações naturais. O estabelecimento de métodos de propagação e cultivo que possibilitem a rápida multiplicação desta espécie é etapa crucial para a conservação ex situ e também para o enriquecimento em áreas naturais e a manutenção da espécie em seu habitat. A micropropagação ou a propagação in vitro consiste na multiplicação em larga escala de plantas através do cultivo de células, tecidos, órgãos ou a planta inteira em meio nutritivo sob condições controladas de temperatura e luminosidade. As etapas da micropropagação são constantemente ajustadas de acordo com as necessidades das diferentes espécies. Diante disso, o objetivo do relatório foi descrever as etapas desenvolvidas para estabelecer o protocolo de micropropagação de C. milleri. O protocolo estabelecido foi dividido em quatro etapas: (1) coleta e assepsia do material vegetal, (2) estabelecimento e desenvolvimento in vitro, (3) aclimatização e rustificação e (4) reintrodução e monitoramento das mudas. Sementes de C. milleri foram retiradas de cápsulas maduras e transferidas para seringas. As seringas contendo as sementes foram preenchidas totalmente com a solução de hipoclorito de sódio (NaClO) a 0,3%. Após 12 minutos, em câmara de fluxo laminar, aproximadamente 1 mL da solução contendo as sementes foi adicionada em potes contendo 22 mL do meio de cultivo previamente esterilizado. O meio utilizado foi composto de sacarose (15g/L), fertilizante B&amp;G® (3mL/L), carvão ativado (1,5g/L) e ágar nutriente (5g/L). A germinação foi observada em quase todas as sementes inoculadas, tendo início aos 25 dias. O processo de propagação in vitro de C. milleri teve duração de 18 meses, com dois episódios de repicagem durante esse período. As plantas responderam positivamente as condições in vitro, apresentando crescimento satisfatório da parte aérea e de raízes. Na etapa de aclimatização, as plantas enraizadas tiveram suas raízes lavadas e foram transplantadas para embalagens plásticas contendo musgo chileno e fragmentos de isopor. Após 450 dias de cultivo em estufa coberta com sombrite 80 (80% de interceptação) foi observada uma reduzida mortalidade de mudas. Posteriormente, plantas aclimatadas foram transplantadas para recipientes contendo substrato natural (contendo canga granular) e cultivadas em estufa com sombrite 80 e posteriormente em sombrite 50, onde permaneceram por 1.095 dias. Ao final da etapa de rustificação foram obtidas aproximadamente 3.000 mudas de C. milleri aptas para o plantio em ambiente natural. A reintrodução destas mudas ocorreu através do plantio das mudas na Serra da Calçada (MG). O monitoramento das plantas ocorre mensalmente com a quantificação das mudas sobreviventes. Após 2 anos de acompanhamento observou-se baixa taxa de mortalidade (-30%) e crescimento satisfatório das plantas. O processo de monitoramento continuará sendo realizado com o objetivo de avaliar os processos de floração e frutificação e recrutamento de novas plantas. Os resultados obtidos evidenciam que a técnica de propagação in vitro é uma alternativa viável para a produção em larga escala de mudas de qualidade da espécie C. milleri. Uma vez que esta é uma espécie criticamente ameaçada de extinção, a reintrodução de plantas em ambiente natural contribui para o enriquecimento das populações existentes e, consequentemente, a conservação da espécie em seu ambiente natural. Uma próxima etapa importante será avaliar a diversidade genética da espécie para determinação das matrizes prioritárias para propagação
APA, Harvard, Vancouver, ISO, and other styles
7

Guy, Charles, Gozal Ben-Hayyim, Gloria Moore, Doron Holland, and Yuval Eshdat. Common Mechanisms of Response to the Stresses of High Salinity and Low Temperature and Genetic Mapping of Stress Tolerance Loci in Citrus. United States Department of Agriculture, 1995. http://dx.doi.org/10.32747/1995.7613013.bard.

Full text
Abstract:
The objectives that were outlined in our original proposal have largely been achieved or will be so by the end of the project in February 1995 with one exception; that of mapping cold tolerance loci based on the segregation of tolerance in the BC1 progeny population. Briefly, our goals were to 1) construct a densely populated linkage map of the citrus genome: 2) map loci important in cold and/or salt stress tolerance; and 3) characterize the expression of genes responsive to cold land salt stress. As can be seen by the preceding listing of accomplishments, our original objectives A and B have been realized, objective C has been partially tested, objective D has been completed, and work on objectives E and F will be completed by the end of 1995. Although we have yet to map any loci that contribute to an ability of citrus to maintain growth when irrigated with saline water, our very encouraging results from the 1993 experiment provides us with considerable hope that 1994's much more comprehensive and better controlled experiment will yield the desired results once the data has been fully analyzed. Part of our optimism derives from the findings that loci for growth are closely linked with loci associated with foliar Cl- and Na+ accumulation patterns under non-salinization conditions. In the 1994 experiment, if ion exclusion or sequestration traits are segregating in the population, the experimental design will permit their resolution. Our fortunes with respect to cold tolerance is another situation. In three attempts to quantitatively characterize cold tolerance as an LT50, the results have been too variable and the incremental differences between sensitive and tolerant too small to use for mapping. To adequately determine the LT50 requires many plants, many more than we have been able to generate in the time and space available by making cuttings from small greenhouse-grown stock plants. As it has turned out, with citrus, to prepare enough plants needed to be successful in this objective would have required extensive facilities for both growing and testing hardiness which simply were not available at University of Florida. The large populations necessary to overcome the variability we encountered was unanticipated and unforeseeable at the project's outset. In spite of the setbacks, this project, when it is finally complete will be exceedingly successful. Listing of Accomplishments During the funded interval we have accomplished the following objectives: Developed a reasonably high density linkage map for citrus - mapped the loci for two cold responsive genes that were cloned from Poncirus - mapped the loci for csa, the salt responsive gene for glutathione peroxidase, and ccr a circadian rhythm gene from citrus - identified loci that confer parental derived specific DNA methylation patterns in the Citrus X Poncirus cross - mapped 5 loci that determine shoot vigor - mapped 2 loci that influence leaf Na+ accumulation patterns under non-saline conditions in the BC1 population - mapped 3 loci that influence leaf Na+ accumulation paterns during salt sress - mapped 2 loci that control leaf Cl- accumulation patterns under non-saline conditions - mapped a locus that controls leaf Cl- accumulation patterns during salt stress Screened the BC1 population for growth reduction during salinization (controls and salinized), and cold tolerance - determined population variation for shoot/root ratio of Na+ and Cl- - determined levels for 12 inorganic nutrient elements in an effort to examine the influence of salinization on ion content with emphasis on foliar responses - collected data on ion distribution to reveal patterns of exclusion/sequestration/ accumulation - analyzed relationships between ion content and growth Characterization of gene expression in response to salt or cold stress - cloned the gene for the salt responsive protein csa, identified it as glutathione peroxidase, determined the potential target substrate from enzymatic studies - cloned two other genes responsive to salt stress, one for the citrus homologue of a Lea5, and the other for an "oleosin" like gene - cold regulated (cor) genes belonging to five hybridization classes were isolated from Poncirus, two belonged to the group 2 Lea superfamily of stress proteins, the others show no significant homology to other known sequences - the expression of csa during cold acclimation was examined, and the expression of some of the cor genes were examined in response to salt stress - the influence of salinization on cold tolerance has been examined with seedling populations - conducted protein blot studies for expression of cold stress proteins during salt stress and vice versa
APA, Harvard, Vancouver, ISO, and other styles
You might also be interested in the extended bibliographies on the topic 'DNA Substrates' for particular source types:
Journal articles Dissertations / Theses Books
We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!

To the bibliography