Relevant bibliographies by topics / Nanoscale ‘On-Surface’ Nucleic Acid Detection

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Academic literature on the topic 'Nanoscale ‘On-Surface’ Nucleic Acid Detection'

Author: Grafiati
Published: 7 September 2023

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Journal articles on the topic "Nanoscale ‘On-Surface’ Nucleic Acid Detection"

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Ying, Yiwen, Qian Tang, Da Han, and Shan Mou. "Nucleic Acid Nanotechnology for Diagnostics and Therapeutics in Acute Kidney Injury." International Journal of Molecular Sciences 23, no. 6 (March 13, 2022): 3093. http://dx.doi.org/10.3390/ijms23063093.

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Acute kidney injury (AKI) has impacted a heavy burden on global healthcare system with a high morbidity and mortality in both hospitalized and critically ill patients. However, there are still some shortcomings in clinical approaches for the disease to date, appealing for an earlier recognition and specific intervention to improve long-term outcomes. In the past decades, owing to the predictable base-pairing rule and highly modifiable characteristics, nucleic acids have already become significant biomaterials for nanostructure and nanodevice fabrication, which is known as nucleic acid nanotechnology. In particular, its excellent programmability and biocompatibility have further promoted its intersection with medical challenges. Lately, there have been an influx of research connecting nucleic acid nanotechnology with the clinical needs for renal diseases, especially AKI. In this review, we begin with the diagnostics of AKI based on nucleic acid nanotechnology with a highlight on aptamer- and probe-functionalized detection. Then, recently developed nanoscale nucleic acid therapeutics towards AKI will be fully elucidated. Furthermore, the strengths and limitations will be summarized, envisioning a wiser and wider application of nucleic acid nanotechnology in the future of AKI.
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Prilepskii, Artur Y., Arseniy Y. Kalnin, Anna F. Fakhardo, Elizaveta I. Anastasova, Daria D. Nedorezova, Grigorii A. Antonov, and Vladimir V. Vinogradov. "Cationic Magnetite Nanoparticles for Increasing siRNA Hybridization Rates." Nanomaterials 10, no. 6 (May 27, 2020): 1018. http://dx.doi.org/10.3390/nano10061018.

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An investigation of the interaction principles of nucleic acids and nanoparticles is a priority for the development of theoretical and methodological approaches to creating bionanocomposite structures, which determines the area and boundaries of biomedical use of developed nanoscale devices. «Nucleic acid—magnetic nanoparticle» type constructs are being developed to carry out the highly efficient detection of pathogens, create express systems for genotyping and sequencing, and detect siRNA. However, the data available on the impact of nanoparticles on the behavior of siRNA are insufficient. In this work, using nanoparticles of two classical oxides of inorganic chemistry (magnetite (Fe3O4) and silica (SiO2) nanoparticles), and widely used gold nanoparticles, we show their effect on the rate of siRNA hybridization. It has been determined that magnetite nanoparticles with a positive charge on the surface increase the rate of siRNA hybridization, while negatively charged magnetite and silica nanoparticles, or positively charged gold nanoparticles, do not affect hybridization rates (HR).
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Dragomir, Isabela S., Alina Asandei, Irina Schiopu, Ioana C. Bucataru, Loredana Mereuta, and Tudor Luchian. "The Nanopore-Tweezing-Based, Targeted Detection of Nucleobases on Short Functionalized Peptide Nucleic Acid Sequences." Polymers 13, no. 8 (April 9, 2021): 1210. http://dx.doi.org/10.3390/polym13081210.

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The implication of nanopores as versatile components in dedicated biosensors, nanoreactors, or miniaturized sequencers has considerably advanced single-molecule investigative science in a wide range of disciplines, ranging from molecular medicine and nanoscale chemistry to biophysics and ecology. Here, we employed the nanopore tweezing technique to capture amino acid-functionalized peptide nucleic acids (PNAs) with α-hemolysin-based nanopores and correlated the ensuing stochastic fluctuations of the ionic current through the nanopore with the composition and order of bases in the PNAs primary structure. We demonstrated that while the system enables the detection of distinct bases on homopolymeric PNA or triplet bases on heteropolymeric strands, it also reveals rich insights into the conformational dynamics of the entrapped PNA within the nanopore, relevant for perfecting the recognition capability of single-molecule sequencing.
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Datar, Ram, Seonghwan Kim, Sangmin Jeon, Peter Hesketh, Scott Manalis, Anja Boisen, and Thomas Thundat. "Cantilever Sensors: Nanomechanical Tools for Diagnostics." MRS Bulletin 34, no. 6 (June 2009): 449–54. http://dx.doi.org/10.1557/mrs2009.121.

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AbstractCantilever sensors have attracted considerable attention over the last decade because of their potential as a highly sensitive sensor platform for high throughput and multiplexed detection of proteins and nucleic acids. A micromachined cantilever platform integrates nanoscale science and microfabrication technology for the label-free detection of biological molecules, allowing miniaturization. Molecular adsorption, when restricted to a single side of a deformable cantilever beam, results in measurable bending of the cantilever. This nanoscale deflection is caused by a variation in the cantilever surface stress due to biomolecular interactions and can be measured by optical or electrical means, thereby reporting on the presence of biomolecules. Biological specificity in detection is typically achieved by immobilizing selective receptors or probe molecules on one side of the cantilever using surface functionalization processes. When target molecules are injected into the fluid bathing the cantilever, the cantilever bends as a function of the number of molecules bound to the probe molecules on its surface. Mass-produced, miniature silicon and silicon nitride microcantilever arrays offer a clear path to the development of miniature sensors with unprecedented sensitivity for biodetection applications, such as toxin detection, DNA hybridization, and selective detection of pathogens through immunological techniques. This article discusses applications of cantilever sensors in cancer diagnosis.
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Koehne, Jessica E., Hua Chen, Alan M. Cassell, Qi Ye, Jie Han, Meyya Meyyappan, and Jun Li. "Miniaturized Multiplex Label-Free Electronic Chip for Rapid Nucleic Acid Analysis Based on Carbon Nanotube Nanoelectrode Arrays." Clinical Chemistry 50, no. 10 (October 1, 2004): 1886–93. http://dx.doi.org/10.1373/clinchem.2004.036285.

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Abstract Background: Reducing cost and time is the major concern in clinical diagnostics, particularly in molecular diagnostics. Miniaturization technologies have been recognized as promising solutions to provide low-cost microchips for diagnostics. With the recent advancement in nanotechnologies, it is possible to further improve detection sensitivity and simplify sample preparation by incorporating nanoscale elements in diagnostics devices. A fusion of micro- and nanotechnologies with biology has great potential for the development of low-cost disposable chips for rapid molecular analysis that can be carried out with simple handheld devices. Approach: Vertically aligned multiwalled carbon nanotubes (MWNTs) are fabricated on predeposited microelectrode pads and encapsulated in SiO2 dielectrics with only the very end exposed at the surface to form an inlaid nanoelectrode array (NEA). The NEA is used to collect the electrochemical signal associated with the target molecules binding to the probe molecules, which are covalently attached to the end of the MWNTs. Content: A 3 × 3 microelectrode array is presented to demonstrate the miniaturization and multiplexing capability. A randomly distributed MWNT NEA is fabricated on each microelectrode pad. Selective functionalization of the MWNT end with a specific oligonucleotide probe and passivation of the SiO2 surface with ethylene glycol moieties are discussed. Ru(bpy)2+-mediator-amplified guanine oxidation is used to directly measure the electrochemical signal associated with target molecules. Summary: The discussed MWNT NEAs have ultrahigh sensitivity in direct electrochemical detection of guanine bases in the nucleic acid target. Fewer than ∼1000 target nucleic acid molecules can be measured with a single microelectrode pad of ∼20 × 20 μm2, which approaches the detection limit of laser scanners in fluorescence-based DNA microarray techniques. MWNT NEAs can be easily integrated with microelectronic circuitry and microfluidics for development of a fully automated system for rapid molecular analysis with minimum cost.
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Lee, Keum-Ju, Hye-Mi So, Byoung-Kye Kim, Do Won Kim, Jee-Hwan Jang, Ki-Jeong Kong, Hyunju Chang, and Jeong-O. Lee. "Single Nucleotide Polymorphism Detection Using Au-Decorated Single-Walled Carbon Nanotube Field Effect Transistors." Journal of Nanomaterials 2011 (2011): 1–8. http://dx.doi.org/10.1155/2011/105138.

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We demonstrate that Au-cluster-decorated single-walled carbon nanotubes (SWNTs) may be used to discriminate single nucleotide polymorphism (SNP). Nanoscale Au clusters were formed on the side walls of carbon nanotubes in a transistor geometry using electrochemical deposition. The effect of Au cluster decoration appeared as hole doping when electrical transport characteristics were examined. Thiolated single-stranded probe peptide nucleic acid (PNA) was successfully immobilized on Au clusters decorating single-walled carbon nanotube field-effect transistors (SWNT-FETs), resulting in a conductance decrease that could be explained by a decrease in Au work function upon adsorption of thiolated PNA. Although a target single-stranded DNA (ssDNA) with a single mismatch did not cause any change in electrical conductance, a clear decrease in conductance was observed with matched ssDNA, thereby showing the possibility of SNP (single nucleotide polymorphism) detection using Au-cluster-decorated SWNT-FETs. However, a power to discriminate SNP target is lost in high ionic environment. We can conclude that observed SNP discrimination in low ionic environment is due to the hampered binding of SNP target on nanoscale surfaces in low ionic conditions.
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Ghosal, Souvik, Sagar Bag, and Sudipta Bhowmik. "Unravelling the Drug Encapsulation Ability of Functional DNA Origami Nanostructures: Current Understanding and Future Prospects on Targeted Drug Delivery." Polymers 15, no. 8 (April 12, 2023): 1850. http://dx.doi.org/10.3390/polym15081850.

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Rapid breakthroughs in nucleic acid nanotechnology have always driven the creation of nano-assemblies with programmable design, potent functionality, good biocompatibility, and remarkable biosafety during the last few decades. Researchers are constantly looking for more powerful techniques that provide enhanced accuracy with greater resolution. The self-assembly of rationally designed nanostructures is now possible because of bottom-up structural nucleic acid (DNA and RNA) nanotechnology, notably DNA origami. Because DNA origami nanostructures can be organized precisely with nanoscale accuracy, they serve as a solid foundation for the exact arrangement of other functional materials for use in a number of applications in structural biology, biophysics, renewable energy, photonics, electronics, medicine, etc. DNA origami facilitates the creation of next-generation drug vectors to help in the solving of the rising demand on disease detection and therapy, as well as other biomedicine-related strategies in the real world. These DNA nanostructures, generated using Watson–Crick base pairing, exhibit a wide variety of properties, including great adaptability, precise programmability, and exceptionally low cytotoxicity in vitro and in vivo. This paper summarizes the synthesis of DNA origami and the drug encapsulation ability of functionalized DNA origami nanostructures. Finally, the remaining obstacles and prospects for DNA origami nanostructures in biomedical sciences are also highlighted.
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Huang, Kun, Feray Demirci, Mona Batish, Wayne Treible, Blake C. Meyers, and Jeffrey L. Caplan. "Quantitative, super-resolution localization of small RNAs with sRNA-PAINT." Nucleic Acids Research 48, no. 16 (July 27, 2020): e96-e96. http://dx.doi.org/10.1093/nar/gkaa623.

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Abstract Small RNAs are non-coding RNAs that play important roles in the lives of both animals and plants. They are 21- to 24-nt in length and ∼10 nm in size. Their small size and high diversity have made it challenging to develop detection methods that have sufficient resolution and specificity to multiplex and quantify. We created a method, sRNA-PAINT, for the detection of small RNAs with 20 nm resolution by combining the super-resolution method, DNA-based points accumulation in nanoscale topography (DNA-PAINT), and the specificity of locked nucleic acid (LNA) probes for the in situ detection of multiple small RNAs. The method relies on designing probes to target small RNAs that combine DNA oligonucleotides (oligos) for PAINT with LNA-containing oligos for hybridization; therefore, we developed an online tool called ‘Vetting & Analysis of RNA for in situ Hybridization probes’ (VARNISH) for probe design. Our method utilizes advances in DNA-PAINT methodologies, including qPAINT for quantification, and Exchange-PAINT for multiplexing. We demonstrated these capabilities of sRNA-PAINT by detecting and quantifying small RNAs in different cell layers of early developmental stage maize anthers that are important for male sexual reproduction.
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Valenti, Giovanni, Sara Rebeccani, Alessandra Zanut, Massimo Marcaccio, and Francesco Paolucci. "(Invited) Ingenious Nanomaterials for Ultrasensitive ECL." ECS Meeting Abstracts MA2022-01, no. 53 (July 7, 2022): 2221. http://dx.doi.org/10.1149/ma2022-01532221mtgabs.

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The impact of nanotechnology and nanosystems on analytical science is hardly overlooked. In the search for ever-increasing sensitivity in biomedical sensors, nanoparticles have been playing a unique role as, e.g., ultrabright labels in clinical analysis (markers, tumor cells, and pharmaceuticals) and in the detection of pathogenic microorganisms, toxic agents, and pesticides in the environmental field and food products. Coupling such nanosystems with electrochemiluminescence (ECL), which naturally brings improved signal-to-noise ratio compared to photoluminescence, with minimized effects due to light scattering and luminescence background, has brought about new systems and strategies for analytes determination, even in very complex matrices, such as urine, blood or lysate. Among the several nanosystems, dye-doped silica nanoparticles (DDSNs) have proved as very promising and versatile nanomaterials in ECL-based bioanalytical platforms. The increase of the number of complexes active in the generation of the ECL signals together with an even larger increase in the signal stability, represents in fact a promising strategy towards ultrasensitive ECL. Approaches based on ECL generation on the nanoscale using luminophore-reporter-modified DNA-based nanoswitches (i.e., molecular beacon) has been additionally investigated and, in this context, the development of innovative amplification-free detection methods represents a significant breakthrough compared to existing PCR-based methodologies, allowing the integration of nucleic acid detection on portable and low-cost sensor devices, and enabling the massive diagnostic screening.
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Campuzano, Susana, Maria Gamella, Verónica Serafín, María Pedrero, Paloma Yáñez-Sedeño, and José Manuel Pingarrón. "Biosensing and Delivery of Nucleic Acids Involving Selected Well-Known and Rising Star Functional Nanomaterials." Nanomaterials 9, no. 11 (November 14, 2019): 1614. http://dx.doi.org/10.3390/nano9111614.

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In the last fifteen years, the nucleic acid biosensors and delivery area has seen a breakthrough due to the interrelation between the recognition of nucleic acid’s high specificity, the great sensitivity of electrochemical and optical transduction and the unprecedented opportunities imparted by nanotechnology. Advances in this area have demonstrated that the assembly of nanoscaled materials allows the performance enhancement, particularly in terms of sensitivity and response time, of functional nucleic acids’ biosensing and delivery to a level suitable for the construction of point-of-care diagnostic tools. Consequently, this has propelled detection methods using nanomaterials to the vanguard of the biosensing and delivery research fields. This review overviews the striking advancement in functional nanomaterials’ assisted biosensing and delivery of nucleic acids. We highlight the advantages demonstrated by selected well-known and rising star functional nanomaterials (metallic, magnetic and Janus nanomaterials) focusing on the literature produced in the past five years.
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Conference papers on the topic "Nanoscale ‘On-Surface’ Nucleic Acid Detection"

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Erickson, David. "Nanomedical Applications of Optofluidics." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13381.

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In this talk I will discuss some of the nanomedical applications of optofluidic systems. As will be demonstrated such devices hold significant promise for improving on the state of the art in detection sensitivity as well as enable entirely new modalities for molecular analysis. Two example platforms will be discussed. The first of these will be our Nanoscale Optofluidic Sensor Arrays which comprise of a series of 1D evanescently coupled linear optical resonators. In addition to demonstrating both nucleic acid (Dengue virus) and immunological detection (Interleukins), I will show how optical forces can be used to increase the functionality of these devices including single molecule analysis. The second platform described is a method for performing surface enhanced raman spectroscopy (SERS) on a chip. A unique ligase detection reaction based assay will be demonstrated to show the unique advantages of the approach.
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Yin Gu, Chunyan Wang, Yingjun Tan, and Yinghui Li. "Detection of microorganism nucleic acid based on surface plasmon resonance sensor." In 2011 International Conference on Remote Sensing, Environment and Transportation Engineering (RSETE). IEEE, 2011. http://dx.doi.org/10.1109/rsete.2011.5966099.

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Hu, Xiaomeng, Lin Wang, Qiaomei Guo, Jiatao Lou, Lin Huang, Ru Zhang, and Kun Qian. "Nanoparticles as Co-matrix for Sensitive Detection of Nucleic Acids by Mass Spectrometry." In 2018 IEEE International Conference on Manipulation, Manufacturing and Measurement on the Nanoscale (3M-NANO). IEEE, 2018. http://dx.doi.org/10.1109/3m-nano.2018.8552208.

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Martins, Diogo, Xi Wei, Rastislav Levicky, and Yong-Ak Song. "Accelerating the Mass Transport of DNA Biomolecules Onto DNA Microarray for Enhanced Detection by Electrokinetic Concentration in a Microfluidic Chip." In ASME 2016 5th International Conference on Micro/Nanoscale Heat and Mass Transfer. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/mnhmt2016-6562.

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Morpholinos (MOs) are synthetic nucleic acids analogues with a non-charged backbone of morpholine rings. To enhance the MO-DNA hybridization assay speed, we propose the integration of a MO microarray with an ion concentration polarization (ICP) based microfluidic concentrator. The ICP concentrator collects target biomolecules from a ∼μL fluidic DNA sample and concentrates them electrokinetically into a ∼nL plug located in the vicinity of the MO probes. ICP preconcentration not only reduces the analyte diffusion length but also increases the binding reaction rate, and as a result, ICP-enhanced MO microarrays allow much faster hybridization than standard diffusion-limited MO microarrays.
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Mijočević, H., H. Karimzadeh, J. Seebach, Z. Usman, M. Al-Mahtab, M. Bazinet, A. Vaillant, and M. Roggendorf. "Mutations in hepatitis B virus surface antigen during therapy with nucleic acid polymer REP 2139-Ca have no influence on treatment outcome or its detection by diagnostic assays." In 35. Jahrestagung der Deutschen Arbeitsgemeinschaft zum Studium der Leber. Georg Thieme Verlag KG, 2019. http://dx.doi.org/10.1055/s-0038-1677272.

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Wulfman, David R., Tracey L. Baas, and Ronald C. McGlennen. "Planar Waveguide Genetic Assay Readout Device." In ASME 2003 International Mechanical Engineering Congress and Exposition. ASMEDC, 2003. http://dx.doi.org/10.1115/imece2003-43442.

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A planar waveguide (PWG) device has been developed for the detection of fluorescently labeled nucleic acid sequences immobilized or hybridized to the surface of a planar waveguide. Unlike current technologies requiring image gathering and reading capabilities or specially textured waveguide surfaces, this instrument uses simple glass slide based arrays, providing a numerical output in proportion to the fluorescent intensity recorded. The system consists of an optical waveguide (a glass microscope slide), an excitation light source, a photo detector, filters for select fluorescent emissions and the positioning array cassette. A data analysis algorithm is presented for interpretation of two dimensionally organized arrays. Based on our experimental evaluations we conclude that this sensing system shows promise as a simple and effective means to read fluorescent microarrays.
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Erickson, David, Xuezhu Liu, Roberto Venditti, Ulrich Krull, and Dongqing Li. "A DNA Hybridization Chip With Electrokinetically-Based Single Nucleotide Polymorphism (SNP) Discrimination." In ASME 2004 International Mechanical Engineering Congress and Exposition. ASMEDC, 2004. http://dx.doi.org/10.1115/imece2004-59320.

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Biosensors and more specifically biochips exploit the interactions between a target analyte and an immobilized biological recognition element to produce a measurable signal. Systems based on surface phase nucleic acid hybridization, such as modern microarrays, are particularly attractive due to the high degree of selectivity in the binding interactions. In this work an electrokinetically controlled poly(dimethylsiloxane) based DNA hybridization microfluidic chip is presented. The electrokinetic delivery technique provides the ability to dispense controlled sample sizes to the hybridization array for quantitative analysis while serving to increase the mass transfer rate and therefore reduce the overall analysis time. An automatic, electrokinetically based, single-nucleotide polymorphism (SNP) discrimination technique (that takes advantage of the combined effects of joule heating, applied potential field and the shear gradients within the double layer field on the thermodynamic stability of the target: probe complex) will also be described for the first time. The clinical utility of the technique will be demonstrated through the detection of genetic markers associated with spinal muscular atrophy, specifically the common C←T mutation in the SMN1 gene.
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