Relevant bibliographies by topics / Silicon nitride-DNA

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Silicon nitride-DNA'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Silicon nitride-DNA"

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Goto, Yusuke, Kazuma Matsui, Itaru Yanagi, and Ken-ichi Takeda. "Silicon nitride nanopore created by dielectric breakdown with a divalent cation: deceleration of translocation speed and identification of single nucleotides." Nanoscale 11, no. 30 (2019): 14426–33. http://dx.doi.org/10.1039/c9nr03563j.

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Petralia, S., T. Cosentino, F. Sinatra, M. Favetta, P. Fiorenza, C. Bongiorno, E. L. Sciuto, S. Conoci, and S. Libertino. "Silicon nitride surfaces as active substrate for electrical DNA biosensors." Sensors and Actuators B: Chemical 252 (November 2017): 492–502. http://dx.doi.org/10.1016/j.snb.2017.06.023.

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Wu, Peng, Paul Hogrebe, and David W. Grainger. "DNA and protein microarray printing on silicon nitride waveguide surfaces." Biosensors and Bioelectronics 21, no. 7 (January 2006): 1252–63. http://dx.doi.org/10.1016/j.bios.2005.05.010.

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Manning, Mary, and Gareth Redmond. "Formation and Characterization of DNA Microarrays at Silicon Nitride Substrates." Langmuir 21, no. 1 (January 2005): 395–402. http://dx.doi.org/10.1021/la0480033.

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Assad, Ossama N., Nicolas Di Fiori, Allison H. Squires, and Amit Meller. "Two Color DNA Barcode Detection in Photoluminescence Suppressed Silicon Nitride Nanopores." Nano Letters 15, no. 1 (December 22, 2014): 745–52. http://dx.doi.org/10.1021/nl504459c.

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Uplinger, James, Brian Thomas, Ryan Rollings, Daniel Fologea, David McNabb, and Jiali Li. "K+, Na+, and Mg2+on DNA translocation in silicon nitride nanopores." ELECTROPHORESIS 33, no. 23 (November 12, 2012): 3448–57. http://dx.doi.org/10.1002/elps.201200165.

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Shon, Min Ju, and Adam E. Cohen. "Nano-mechanical measurements of protein-DNA interactions with a silicon nitride pulley." Nucleic Acids Research 44, no. 1 (September 3, 2015): e7-e7. http://dx.doi.org/10.1093/nar/gkv866.

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Wang, Kai Ge, Peng Ye Wang, Shuang Lin Yue, Ai Zi Jin, Chang Zhi Gu, and Han Ben Niu. "Fabricating Nanofluidic Channels and Applying them for DNA Molecules Study." Solid State Phenomena 121-123 (March 2007): 777–80. http://dx.doi.org/10.4028/www.scientific.net/ssp.121-123.777.

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In the emerging field of nanobiotechnology, further downsizing the fluidic channels and pores to the nanometer scale are attractive for both fundamental studies and technical applications. The insulation Silicon nitride membrane nanofluidic channel arrays which have width ~50nm and depth ~80nm and length ≥20μm were created by focused-ion-beam instrument. The λ-DNA molecules were put inside nanochannels and transferred, a fluorescence microscopy was used to observe the images. Only by capillary force, λ-DNA molecules moved inside the nanochannels which dealt with activating reagent Brij aqueous solution. These scope nanostructure devices will help us study DNA transporting through a nanopore and understand more DNA dynamics characteristics.
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Pezzotti, Giuseppe, Eriko Ohgitani, Saki Ikegami, Masaharu Shin-Ya, Tetsuya Adachi, Toshiro Yamamoto, Narisato Kanamura, et al. "Instantaneous Inactivation of Herpes Simplex Virus by Silicon Nitride Bioceramics." International Journal of Molecular Sciences 24, no. 16 (August 10, 2023): 12657. http://dx.doi.org/10.3390/ijms241612657.

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Hydrolytic reactions taking place at the surface of a silicon nitride (Si3N4) bioceramic were found to induce instantaneous inactivation of Human herpesvirus 1 (HHV-1, also known as Herpes simplex virus 1 or HSV-1). Si3N4 is a non-oxide ceramic compound with strong antibacterial and antiviral properties that has been proven safe for human cells. HSV-1 is a double-stranded DNA virus that infects a variety of host tissues through a lytic and latent cycle. Real-time reverse transcription (RT)-polymerase chain reaction (PCR) tests of HSV-1 DNA after instantaneous contact with Si3N4 showed that ammonia and its nitrogen radical byproducts, produced upon Si3N4 hydrolysis, directly reacted with viral proteins and fragmented the virus DNA, irreversibly damaging its structure. A comparison carried out upon testing HSV-1 against ZrO2 particles under identical experimental conditions showed a significantly weaker (but not null) antiviral effect, which was attributed to oxygen radical influence. The results of this study extend the effectiveness of Si3N4’s antiviral properties beyond their previously proven efficacy against a large variety of single-stranded enveloped and non-enveloped RNA viruses. Possible applications include the development of antiviral creams or gels and oral rinses to exploit an extremely efficient, localized, and instantaneous viral reduction by means of a safe and more effective alternative to conventional antiviral creams. Upon incorporating a minor fraction of micrometric Si3N4 particles into polymeric matrices, antiherpetic devices could be fabricated, which would effectively impede viral reactivation and enable high local effectiveness for extended periods of time.
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Yin, Bohua, Wanyi Xie, Liyuan Liang, Yunsheng Deng, Shixuan He, Feng He, Daming Zhou, Chaker Tlili, and Deqiang Wang. "Covalent Modification of Silicon Nitride Nanopore by Amphoteric Polylysine for Short DNA Detection." ACS Omega 2, no. 10 (October 25, 2017): 7127–35. http://dx.doi.org/10.1021/acsomega.7b01245.

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Dissertations / Theses on the topic "Silicon nitride-DNA"

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Pal, Sohini. "Nanopore Based Single-molecule Sensors." Thesis, 2020. https://etd.iisc.ac.in/handle/2005/5457.

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In the past two decades nanopores have been used as highly sensitive detection systems for exploring the properties of analytes at single molecule resolution. The small dimensions of a nanopore permit the molecule of interest to be confined within it, allowing for the extraction of valuable information relating to its physical and chemical properties. Single molecule analysis, as opposed to bulk measurements does not involve ensemble averaging. Hence, short-lived states such as an intermediate configuration during a conformational change can be observed directly, while such states would be masked in the bulk assay. The main project described in this thesis involves the design and fabrication of a hybrid silicon nitride-DNA origami nanopore system for use in biosensing of proteins. We used the nanopore system to experimentally observe the effect of forces between the translocating molecule and nanopore with a focus on the electro kinetics inside the pore and escape rate problem. These are further verified by finite element simulations and MATLAB simulations which enables us to investigate the physics behind the different types of events that we observe. The key findings from this work can be summarized as follows. We report on an operating regime of this nanopore sensor, characterized by attractive interactions between the nanoparticle and the pore, where the dwell time is exponentially sensitive to the target-pore interaction. We used negatively and positively charged gold nanoparticles to control the strength of their interaction with the negatively charged silicon nitride pore. Our experiments revealed how this modulation of the electrostatic force greatly affects the ionic current with an exponential dependance of dwell times. A stochastic model is developed for analyzing this analyte-pore interaction based on the well-known Kramer’s problem of escape from a barrier.Finally, the nitride nanopore was functionalized using DNA origami with thrombin binding aptamer (TBA15), a well studied 15-mer aptamer DNA sequence that binds selectively with thrombin protein. Consistent with our previous experiment, we observed current traces with large dwell time blockades for thrombin whereas for another protein the trace contained minimal dwell time current enhancements. The presence of TBA15 aptamer increased the interaction energy between the thrombin and the nanopore resulting in a blockage with comparatively larger dwell time and enabled us in sensing thrombin at concentrations as low as 20nM. Nanopore technology will remain an important field of science in the 21st century. We believe equipped with our understanding of nanopore analysis, in future we will be able to detect and unravel important physical phenomena in the single molecule world.
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Book chapters on the topic "Silicon nitride-DNA"

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Rollings, Ryan C., David S. McNabb, and Jiali Li. "DNA Characterization with Ion Beam-Sculpted Silicon Nitride Nanopores." In Methods in Molecular Biology, 79–97. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-773-6_5.

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Conference papers on the topic "Silicon nitride-DNA"

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Dunphy, Katherine, Veljko Milanovic, Samantha Andrews, Taku Ohara, and Arun Majumdar. "Rapid Separation and Manipulation of DNA by a Ratcheting Electrophoresis Microchip (REM)." In ASME 2002 International Mechanical Engineering Congress and Exposition. ASMEDC, 2002. http://dx.doi.org/10.1115/imece2002-33564.

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The Ratcheting Electrophoresis Microchip (REM) is a microfluidic device for electrophoretic separation of biomolecules such as DNA and proteins. By using thousands of electrodes along the length of a microchannel, the REM separates molecules using low applied voltages (∼1 V) in short times (< 1 minute). This paper describes the microfabriation of the REM and initial testing results. Parallel arrays of platinum electrodes are fabricated on a silicon chip with a pitch of 10 μm. Two types of channels are fabricated: silicon nitride channels fabricated on the chip and poly(dimelthylsiloxane) (PDMS) channels fabricated separately and attached to the chip. Initial testing shows partial success with the PDMS channels and promis ing results for the silicon nitride channels.
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Kim, Min Jun, Meni Wanunu, Gautam Soni, and Amit Meller. "Nanopore Sensors for Ultra-Fast DNA Analysis." In ASME 2006 International Mechanical Engineering Congress and Exposition. ASMEDC, 2006. http://dx.doi.org/10.1115/imece2006-15571.

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We have developed novel approaches for ultra-fast DNA analysis by measuring of an ionic current blockage and parallel optical readout of DNA translocation through single nanopores and nanopore arrays. Parallelism is achieved by the fabrication of high density solid-state arrays of single nanometer resolution pores and simultaneous optical readout of DNA translocation. Optical readout in arrays circumvents the direct electrical addressing of each pore. We will present new nanofabrication techniques to create nanoscale pores in 50 nm thick silicon nitride membrane using transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) and discuss our progress towards ultra-fast DNA sequencing.
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Yue, Min, Jeanne C. Stachowiak, Henry Lin, Kenneth Castelino, Ram Datar, Karolyn Hansen, Thomas Thundat, Arup Chakraborty, Richard J. Cote, and Arun Majumdar. "Nanomechanical Sensor Array for Detection of Biomolecular Bindings: Toward a Label-Free Clinical Assay for Serum Tumor Markers." In ASME 2004 3rd Integrated Nanosystems Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/nano2004-46034.

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A label-free technique capable of rapidly screening human blood samples simultaneously for multiple serum tumor markers would enable accurate and cost-effective diagnosis of cancer before physiological symptoms appear. Recently, microfabricated, bimaterial cantilever sensors have been demonstrated to detect DNA hybridization and antigen-antibody binding at clinically relevant concentrations. Cantilever sensors deflect measurably under the surface stress resulting when biomolecules immobilized on one surface of the sensor interact with their binding partners [1]. We present an array of cantilever sensors (silicon nitride with a gold coated surface) capable of simultaneously interrogating 100 different biomolecular interactions.
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Huang, Yong, and Boris Rubinsky. "A Microfabricated Chip for the Study of Cell Electroporation." In ASME 2000 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2000. http://dx.doi.org/10.1115/imece2000-2233.

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Abstract It has been observed that when certain electrical potentials are applied across a cell they can induce the formation of pores in the cell membrane and consequently increase the permeability of the cell to macromolecules. This phenomenon is known as electroporation. Since the first report on gene transfer by electroporation1, it has become a standard method for introduction of macromolecules into cells2 3 4. Currently, electroporation is normally done in batches of cells between electrodes and there is little control over the permeabilization of individual cells. Therefore, it is very difficult to study the fundamental biophysics of cell membrane electro-permeabilization and to design optimal electroporation protocols for individual cells2 3 . Although the biophysics of electroporation are still not fully understood, indirect evidence shows that micro aqueous pores with diameters of tens to hundreds of angstroms are created in the cell membrane due to the electrical field induced structural rearrangement of the lipid bilayer5. It occurred to us that if electroporation induces pores in the cell membrane, then in a state of electroporation, a measurable current should flow through the individual cell. From this idea, we have developed a new micro-electroporation technology that employs a “bionic” chip to study and control the electroporation process in individual cells. The micro-electroporation chip, shown schematically in Figure 1, is designed and fabricated using standard silicon microfabrication technology. Each chip is a three-layer device that consists of two translucent poly silicon electrodes and a silicon nitride membrane, which all together form two fluid chambers. The two chambers are interconnected only through a micro hole through the dielectric silicon nitride membrane. In a typical process, the two chambers are filled with conductive solutions and one chamber contains biological cells. Individual cells can be captured in the micro hole and thus incorporated into the electrical circuit between the two electrodes of the chip. When the cell is in its normal state no current flows through the insulating lipid bilayer and consequently between the electrodes. However, when the electrical potential across the electrodes is sufficient to induce electroporation, a measurable current will flow through the pores of the cell membrane and between the electrodes. Measuring the currents through the bionic chip in real time will reveal the information of the state of electropermeabilization in cell membrane. The breakdown potential of irreversible electroporation, the most critical parameter in electroporation process, can be detected by analyzing current signals as well. Figure 2 illustrates a typical electrical signature in an irreversible electroporation process. Once the target cell is electroporated by the application of sufficient electroporation electrical potentials, macromolecules that are normally impermeant to cell membrane can be uploaded into the cell. Figure 3 shows how a cell entrapped in a hole is loaded during electroporation with a fluorescent die. With the ability to manipulate individual cells and detect the electrical potentials that induce electroporation in each cell, the chip can be used to study the fundamental biophysics of membrane electropermeabilization on the single cell level and in biotechnology, for controlled introduction of macromolecules, such as DNA fragments, into individual cells. We anticipate that this new technology will change the way in which electroporation is done and will provide key understanding of the biophysical processes that lead to cell electroporation. This paper will discuss the design, fabrication of the micro-electroporation chip, the experiment system as well as experiments carried out to precisely detect the parameters of electroporation of individual biological cells.
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