Journal articles: '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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Huang, Jiaoqi, Yang Zhang, Zhongquan Lin, Wei Liu, Xueping Chen, Yu Liu, Huiyan Tian, et al. "Femtomolar detection of nucleic acid based on functionalized gold nanoparticles." Nanophotonics 8, no. 9 (May 23, 2019): 1495–503. http://dx.doi.org/10.1515/nanoph-2019-0050.

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AbstractDeoxyribonucleic acid (DNA) detection is essential for the accurate and early diagnosis of a disease. In this study, a femtomolar DNA detection method based on the exploitation of the localized surface plasmon (LSP) resonance of gold nanoparticles (AuNPs) was developed. We prepared Poly Ethylen Glycol (PEG) functionalized AuNPs with a specific DNA capture probe (CP) directly modified on the gold surface. Two strategies are proposed using different kinds of CP to detect the target DNA (tDNA). In the first strategy, CP is the complementary of the complete sequence of the DNA (CCP method). For the second strategy, we used two CPs, which were half complementary to tDNA, and these were hybridized with tDNA to form sandwich structures (MIX method). The results showed that our detection methods are highly sensitive and that the limits of detection of 124 am and 2.54 fm tDNA can be reached when using the CCP and MIX methods, respectively. In addition, the specificity of our two strategies is also demonstrated with mismatched DNAs. The proposed method provides a simple, fast, sensitive and specific DNA biosensor, which has the potential to be used for point-of-care tests (POCT).

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Christel, L. A., K. Petersen, W. McMillan, and M. A. Northrup. "Rapid, Automated Nucleic Acid Probe Assays Using Silicon Microstructures for Nucleic Acid Concentration." Journal of Biomechanical Engineering 121, no. 1 (February 1, 1999): 22–27. http://dx.doi.org/10.1115/1.2798037.

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A system for rapid point-of-use nucleic acid (NA) analysis based on PCR techniques is described. The extraction and concentration of DNA from test samples has been accomplished utilizing silicon fluidic microchips with high surface-area-to-volume ratios. Short (500 bp) and medium size (48,000 bp) DNA have been captured, washed, and eluted using the silicon dioxide surfaces of these chips. Chaotropic (GuHCl) salt solutions were used as binding agents. Wash and elution agents consisted of ethanol-based solutions and water, respectively. DNA quantities approaching 40 ng/cm2 of binding area were captured from input solutions in the 100–1000 ng/mL concentration range. For dilute samples of interest for pathogen detection, PCR and gel electrophoresis were used to demonstrate extraction efficiencies of about 50 percent, and concentration factors of about 10× using bacteriophage lambda DNA as the target. Rapid, multichannel PCR thermal cycling modules with integrated solid-state detection components have also been demonstrated. These results confirm the viability of utilizing these components as elements of a compact, disposable cartridge system for the detection of NA in applications such as clinical diagnostics, biowarfare agent detection, food quality control, and environmental monitoring.

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Prabhakar, Nirmal, Kavita Arora, Sunil K. Arya, Pratima R. Solanki, M. Iwamoto, Harpal Singh, and B. D. Malhotra. "Nucleic acid sensor for M. tuberculosis detection based on surface plasmon resonance." Analyst 133, no. 11 (2008): 1587. http://dx.doi.org/10.1039/b808225a.

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Gustafsdottir, Sigrun M., Ann Nordengrahn, Simon Fredriksson, Per Wallgren, Esteban Rivera, Edith Schallmeiner, Malik Merza, and Ulf Landegren. "Detection of Individual Microbial Pathogens by Proximity Ligation." Clinical Chemistry 52, no. 6 (June 1, 2006): 1152–60. http://dx.doi.org/10.1373/clinchem.2005.065847.

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Abstract Background: Nucleic acid amplification allows the detection of single infectious agents. Protein-based assays, although they provide information on ongoing infections, have substantially less detection sensitivity. Methods: We used proximity ligation reactions to detect proteins on bacteria and virus particles via nucleic acid amplification. Antibodies recognizing viral or bacterial surface proteins were equipped with DNA strands that could be joined by ligation when several antibodies were bound in proximity to surface proteins of individual infectious agents. Results: Detection sensitivities similar to those of nucleic acid-based detection reactions were achieved directly in infected samples for a parvovirus and an intracellular bacterium. Conclusions: This method enables detection of ligated DNA strands with good sensitivity by real-time PCR and could be of value for early diagnosis of infectious disease and in biodefense.

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Zezza, Paola, María Isabel Lucío, Estrella Fernández, Ángel Maquieira, and María-José Bañuls. "Surface Micro-Patterned Biofunctionalized Hydrogel for Direct Nucleic Acid Hybridization Detection." Biosensors 13, no. 3 (February 23, 2023): 312. http://dx.doi.org/10.3390/bios13030312.

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The present research is focused on the development of a biofunctionalized hydrogel with a surface diffractive micropattern as a label-free biosensing platform. The biosensors described in this paper were fabricated with a holographic recording of polyethylene terephthalate (PET) surface micro-structures, which were then transferred into a hydrogel material. Acrylamide-based hydrogels were obtained with free radical polymerization, and propargyl acrylate was added as a comonomer, which allowed for covalent immobilization of thiolated oligonucleotide probes into the hydrogel network, via thiol-yne photoclick chemistry. The comonomer was shown to significantly contribute to the immobilization of the probes based on fluorescence imaging. Two different immobilization approaches were demonstrated: during or after hydrogel synthesis. The second approach showed better loading capacity of the bioreceptor groups. Diffraction efficiency measurements of hydrogel gratings at 532 nm showed a selective response reaching a limit of detection in the complementary DNA strand of 2.47 µM. The label-free biosensor as designed could significantly contribute to direct and accurate analysis in medical diagnosis as it is cheap, easy to fabricate, and works without the need for further reagents.

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Wei, Shih-Chung, Chia-Chen Chang, Tsung-Liang Chuang, Kung-Bin Sung, and Chii-Wann Lin. "Rapid Detection of Virus Nucleic Acid via Isothermal Amplification on Plasmonic Enhanced Digitizing Biosensor." Biosensors 12, no. 2 (January 28, 2022): 75. http://dx.doi.org/10.3390/bios12020075.

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Rapid detection for infectious diseases is highly demanded in diagnosis and infection prevention. In this work, we introduced a plasmonic enhanced digitizing biosensor for the rapid detection of nucleic acids. The sensor successfully achieved the detection of loop-mediated isothermal amplification for the hepatitis virus in this work. The sensor comprised a nanodisc array and Bst polymerases conjugated on the rough surface of a nanodisc. The rough surface of the nanodisc provided plasmonic hot spots to enhance the fluorescence signal. The virus DNA was detected by conducting a modified loop-mediated isothermal amplification with fluorescence resonance energy transfer reporter conjugated primers on the sensor. The modified isothermal amplification improved the signal contrast and detection time compared to the original assay. By integrating the modified amplification assay and plasmonic enhancement sensor, we achieved rapid detection of the hepatitis virus. Nucleic acid with a concentration of 10−3 to 10−4 mg/mL was detected within a few minutes by our design. Our digitizing plasmonic nanoarray biosensor also showed 20–30 min earlier detection compared to conventional loop-mediated isothermal amplification sensors.

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Ostroff, Rachel M., Deborah Hopkins, Ayla B. Haeberli, Wahab Baouchi, and Barry Polisky. "Thin Film Biosensor for Rapid Visual Detection of Nucleic Acid Targets." Clinical Chemistry 45, no. 9 (September 1, 1999): 1659–64. http://dx.doi.org/10.1093/clinchem/45.9.1659.

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Abstract Background: We have developed a silicon-based biosensor that generates a visual signal in response to nucleic acid targets. Methods: In this system, capture oligonucleotide probes are immobilized on the surface of the biosensor. Interaction of the capture probes with a complementary target and a biotinylated detector oligonucleotide allows initiation of formation of an organic thin film on the biosensor. Thin film formation is completed by enzymatic activity of peroxidase conjugated to an anti-biotin antibody. Peroxidase catalyzes deposition of an insoluble product onto the silicon surface, generating a uniform thin film. The increased thickness on the surface alters the perceived color of the biosensor through changes in the interference patterns of reflected light from the surface, causing a color change from gold to purple. Results: The biosensor results may be evaluated by direct visual inspection or quantified by ellipsometry. Results are obtained in 25 min with a detection limit of 5 pmol/L (150 amol/sample). Selectivity of the biosensor is demonstrated by discrimination of single nucleotide mismatches. Multitarget arrays are also analyzed with the thin film biosensor, and the system is capable of detecting targets from human serum and urine. Conclusions: The biosensor surface is inexpensive to produce, and the assay format is simple and rapid. The thin film biosensor is adaptable to a wide variety of nucleic acid detection applications, including rapid diagnostic testing for infectious disease panels, antibiotic resistance panels, or allelic discrimination of specific genetic markers.

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Prakash, Ravi, and Karan V. I. S. Kaler. "Liquid dielectrophoresis dispensing of vesicles for on-chip nucleic acid isolation and detection." Colloids and Surfaces A: Physicochemical and Engineering Aspects 432 (September 2013): 42–49. http://dx.doi.org/10.1016/j.colsurfa.2013.05.037.

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Liu, Qing Ye, Gui Qing Wen, Fang Gui Ye, and Ai Hui Liang. "Surface-Enhanced Resonance Raman Scattering Spectral Probe Based on Functional Nucleic Acid and Nanoparticle." Advanced Materials Research 680 (April 2013): 145–48. http://dx.doi.org/10.4028/www.scientific.net/amr.680.145.

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Highly sensitive and selective surface-enhanced resonance Raman scattering (SERRS) spectral detection technique are developed by combining the functional nucleic acid (FNA) including aptamer and DNAzyme, and nanoparticle such as gold/silver (NG/NS) aggregation. The recent progress of SERRS was reviewed in this paper.

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Lamture, Jagannath B., Kenneth LBeattie, Barry E. Burke, Mitchell D. Eggers, Dan J. Ehrlich, Rick Fowler, Mark A. Hollis, et al. "Direct detection of nucleic acid hybridization on the surface of a charge coupled device." Nucleic Acids Research 22, no. 11 (1994): 2121–25. http://dx.doi.org/10.1093/nar/22.11.2121.

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Dubrovin, E. V., G. V. Presnova, M. Yu Rubtsova, A. M. Egorov, V. G. Grigorenko, and I. V. Yaminsky. "The Use of Atomic Force Microscopy for 3D Analysis of Nucleic Acid Hybridization on Microarrays." Acta Naturae 7, no. 2 (June 15, 2015): 108–14. http://dx.doi.org/10.32607/20758251-2015-7-2-108-114.

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Oligonucleotide microarrays are considered today to be one of the most efficient methods of gene diagnostics. The capability of atomic force microscopy (AFM) to characterize the three-dimensional morphology of single molecules on a surface allows one to use it as an effective tool for the 3D analysis of a microarray for the detection of nucleic acids. The high resolution of AFM offers ways to decrease the detection threshold of target DNA and increase the signal-to-noise ratio. In this work, we suggest an approach to the evaluation of the results of hybridization of gold nanoparticle-labeled nucleic acids on silicon microarrays based on an AFM analysis of the surface both in air and in liquid which takes into account of their three-dimensional structure. We suggest a quantitative measure of the hybridization results which is based on the fraction of the surface area occupied by the nanoparticles.

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Wu, Weidong, Manish Biyani, Daisuke Hirose, and Yuzuru Takamura. "Rapid and Highly Sensitive Detection of Leishmania by Combining Recombinase Polymerase Amplification and Solution-Processed Oxide Thin-Film Transistor Technology." Biosensors 13, no. 8 (July 28, 2023): 765. http://dx.doi.org/10.3390/bios13080765.

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Nucleic acid detection is widely used to identify infectious diseases and ensure food safety. However, conventional PCR-based techniques are time consuming. Thus, this study aims to combine recombinase polymerase amplification (RPA), which enables the rapid amplification of even trace amounts of nucleic acid fragments within 10–40 min at 37–42 °C, and solution-processed oxide thin-film transistor (TFT) technology, which exhibits high detection sensitivity, to detect Leishmania. A single-stranded anti-probe was incorporated into the RPA primer to facilitate effective hybridization between the RPA product and the immobilized probe on the solution-processed oxide TFT. The RPA-amplified product carrying an anti-probe enabled specific binding to the chip surface. Changes in current were monitored before and after sample incubation to identify the target nucleic acids in the samples accurately. The proposed method achieved a remarkable limit of detection of 101 copies/μL of the Leishmania HSP70 fragment within 30 min. The design of the probes on the solution-processed oxide TFT surface and the anti-probe simplified the detection of other target nucleic acids, eliminating the need to denature DNA double-strands for specific binding during nucleic acid detection. Thus, the novel method offers the advantage of requiring minimal reagent resources and eliminates the need for complex procedures.

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Graham, Duncan, Karen Faulds, David Thompson, Fiona Mackenzie, Robert Stokes, and Alexandra Macaskill. "Functionalized nanoparticles for nucleic acid sequence analysis using optical spectroscopies." Biochemical Society Transactions 37, no. 2 (March 20, 2009): 441–44. http://dx.doi.org/10.1042/bst0370441.

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SERRS (surface-enhanced resonance Raman scattering) is a vibrational spectroscopy which allows extremely sensitive and selective detection of labelled DNA sequences with detection limits which rival, and in most cases surpass, that of fluorescence. SERRS relies on a visible chromophore adsorbing on to an enhancing surface. DNA itself is not SERRS-active, as it lacks a suitable visible chromophore and has poor adsorption properties on to the surfaces used for enhancement. The surface normally used for enhancement in these sorts of studies are metallic nanoparticles and, through modification of DNA probes by the addition of suitable SERRS labels, signals can be obtained that are highly sensitive and very selective. The aggregation state of the nanoparticles is critical to the sensitivity, and, in the present paper, we show how straightforward detection of labelled DNA probes can be achieved using SERRS in a quantitative manner and with a variety of different commercially available labels. In a second approach, we show how the properties of aggregation to turn on the SERRS effect can be exploited through DNA hybridization to give identification of a particular DNA sequence. This approach lends itself to closed-tube formats and is a promising way forward for molecular diagnostics using SERRS.

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Jenison, Robert, Helen La, Ayla Haeberli, Rachel Ostroff, and Barry Polisky. "Silicon-based Biosensors for Rapid Detection of Protein or Nucleic Acid Targets." Clinical Chemistry 47, no. 10 (October 1, 2001): 1894–900. http://dx.doi.org/10.1093/clinchem/47.10.1894.

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Abstract Background: We developed a silicon-based biosensor that generates visual, qualitative results or quantitative results for the detection of protein or nucleic acid targets in a multiplex format. Methods: Capture probes were immobilized either passively or covalently on the optically coated surface of the biosensor. Intermolecular interactions of the immobilized capture probe with specific target molecules were transduced into a molecular thin film. Thin films were generated by enzyme-catalyzed deposition in the vicinity of the surface-bound target. The increased thickness on the surface changed the apparent color of the biosensor by altering the interference pattern of reflected light. Results: Cytokine detection was achieved in a 40-min multiplex assay. Detection limits were 4 ng/L for interleukin (IL)-6, 31 ng/L for IL1-β, and 437 ng/L for interferon-γ. In multianalyte experiments, cytokines were specifically detected with signal-to-noise ratios ranging from 15 to 80. With a modified optical surface, specificity was also demonstrated in a nucleic acid array with unambiguous discrimination of single-base changes in a 15-min assay. For homozygous wild-type and homozygous mutant samples, signal-to-noise ratios of ∼100 were observed. Heterozygous samples yielded approximately equivalent signals for wild-type and mutant capture probes. Conclusions: The thin-film biosensor allows rapid, sensitive, and specific detection of protein or nucleic acid targets in an array format with results read visually or quantified with a charge-coupled device camera. This biosensor is suited for multianalyte detection in clinical diagnostic assays.

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Erdem, Arzum, and Ece Eksin. "Zip Nucleic Acid-Based Genomagnetic Assay for Electrochemical Detection of microRNA-34a." Biosensors 13, no. 1 (January 15, 2023): 144. http://dx.doi.org/10.3390/bios13010144.

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Zip nucleic acid (ZNA)-based genomagnetic assay was developed herein for the electrochemical detection of microRNA-34a (miR-34a), which is related to neurological disorders and cancer. The hybridization between the ZNA probe and miR-34a target was performed in the solution phase; then, the resultant hybrids were immobilized onto the surface of magnetic beads (MBs). After magnetic separation, the hybrids were separated from the surface of MBs and then immobilized on the surface of pencil graphite electrodes (PGEs). In the case of a full-match hybridization, the guanine oxidation signal was measured via the differential pulse voltammetry (DPV) technique. All the experimental parameters that influenced the hybridization efficiency (i.e., hybridization strategy, probe concentration, hybridization temperature, etc.) were optimized. The cross-selectivity of the genomagnetic assay was tested against two different miRNAs, miR-155 and miR-181b, individually as well as in mixture samples. To show the applicability of the ZNA-based genomagnetic assay for miR-34a detection in real samples, a batch of experiments was carried out in this study by using the total RNA samples isolated from the human hepatocellular carcinoma cell line (HUH-7).

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Zhang, Hao, Yu Liu, Jian Gao, and Junhui Zhen. "A sensitive SERS detection of miRNA using a label-free multifunctional probe." Chemical Communications 51, no. 94 (2015): 16836–39. http://dx.doi.org/10.1039/c5cc06225j.

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A novel surface enhanced Raman scattering (SERS) detection method is fabricated for miRNA based on a smart multifunctional probe for dual cyclical nucleic acid strand-displacement polymerization (CNDP).

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Lee, Kang-Ho, Dongkyu Lee, Jongsu Yoon, Ohwon Kwon, and Jaejong Lee. "A Sensitive Potentiometric Sensor for Isothermal Amplification-Coupled Detection of Nucleic Acids." Sensors 18, no. 7 (July 14, 2018): 2277. http://dx.doi.org/10.3390/s18072277.

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A disposable potentiometric sensor was newly developed for the amplification-coupled detection of nucleic acids. The hydrogen-ion is generally released during isothermal amplification of nucleic acids. The surface potential on the oxide-functionalized electrode of the extended gate was directly measured using full electrical circuits with the commercial metal-oxide semiconductor field-effect transistors (MOSFETs) and ring oscillator components, which resulted in cost-effective, portable and scalable real-time nucleic acid analysis. The current-starved ring oscillator changes surface potential to its frequency depending on the square of the variation in pH with a high signal-to-noise ratio during isothermal amplification. The device achieves a conversion rate of 20.5 kHz/mV and a detection resolution of 200 µV for the surface potential. It is demonstrated that the sensor successfully monitors in real-time isothermal amplification of the extracted nucleic acids from Salmonella pathogenic bacteria. The in situ variations in the frequency of the pH-sensitive sensor were compared with the results of both a conventional optical device and pH-meter during isothermal amplification.

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Terracciano, Monica, Ilaria Rea, Nicola Borbone, Rosalba Moretta, Giorgia Oliviero, Gennaro Piccialli, and Luca De Stefano. "Porous Silicon-Based Aptasensors: The Next Generation of Label-Free Devices for Health Monitoring." Molecules 24, no. 12 (June 13, 2019): 2216. http://dx.doi.org/10.3390/molecules24122216.

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Aptamers are artificial nucleic acid ligands identified and obtained from combinatorial libraries of synthetic nucleic acids through the in vitro process SELEX (systematic evolution of ligands by exponential enrichment). Aptamers are able to bind an ample range of non-nucleic acid targets with great specificity and affinity. Devices based on aptamers as bio-recognition elements open up a new generation of biosensors called aptasensors. This review focuses on some recent achievements in the design of advanced label-free optical aptasensors using porous silicon (PSi) as a transducer surface for the detection of pathogenic microorganisms and diagnostic molecules with high sensitivity, reliability and low limit of detection (LoD).

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Park, Moo Eon, and Jeong Ho Chang. "Polyamine Group Assembled Silica Coated Ferrite Nanoparticle or Lambda DNA Detection." Materials Science Forum 534-536 (January 2007): 1357–60. http://dx.doi.org/10.4028/www.scientific.net/msf.534-536.1357.

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This study describes the development of a high throughput purification process of nucleic acid using amino-functionalized silica coated ferrite nanoparticles. The magnetic ferrite nanoparticles were synthesized and coated by a silica precursor in controlling the coating thicknesses and sizeses. The surface modification was performed with amino-functionalized organic silanes on silica coated magnetic nanoparticles. The spectroscopic measurements such as a FT-IR (ATR-method) and Vibrational Sample Magnetometer (VSM) were used to characterize the chemical structures and magnetic strengths. To elucidate the relationship between surface area, pore size distribution and reactivity of the materials, BET and Zeta potential were used. The use of functionalized self-assembled magnetic ferrite nanoparticles for a nucleic acid separation process provides a lot of advantages compared to the conventional silica based process.

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Huang, Yafeng, Lulu Zhang, Hao Zhang, Yichen Li, Luyao Liu, Yuanyuan Chen, Xianbo Qiu, and Duli Yu. "Development of a Portable SPR Sensor for Nucleic Acid Detection." Micromachines 11, no. 5 (May 21, 2020): 526. http://dx.doi.org/10.3390/mi11050526.

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Nucleic acid detection is of great significance in clinical diagnosis, environmental monitoring and food safety. Compared with the traditional nucleic acid amplification detection method, surface plasmon resonance (SPR) sensing technology has the advantages of being label-free, having simple operation, and providing real-time detection. However, the angle scanning system in many SPR angle modulation detection applications usually requires a high-resolution stepper motor and complex mechanical structure to adjust the angle. In this paper, a portable multi-angle scanning SPR sensor was designed. The sensor only uses one stepping motor to rotate a belt, and the belt pulls the mechanical linkages of incident light and reflected light to move in opposite directions for achieving the SPR angle scanning mode that keeps the incident angle and reflected angle equal. The sensor has an angle scanning accuracy of 0.002°, response sensitivity of 3.72 × 10−6 RIU (refractive index unit), and an angle scanning range of 30°–74°. The overall size of the system is only 480 mm × 150 mm × 180 mm. The portable SPR sensor was used to detect nucleic acid hybridization on a gold film chip modified with bovine serum albumin (BSA). The result revealed that the sensor had high sensitivity and fast response, and could successfully accomplish the hybridization detection of target DNA solution of 0.01 μmol/mL.

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Solanki, Pratima R., Nirmal Prabhakar, M. K. Pandey, and B. D. Malhotra. "Self-assembled monolayer for toxicant detection using nucleic acid sensor based on surface plasmon resonance technique." Biomedical Microdevices 10, no. 5 (June 24, 2008): 757–67. http://dx.doi.org/10.1007/s10544-008-9188-1.

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Ivanov, Yuri D., Vadim Yu Tatur, Alexander V. Glukhov, and Vadim S. Ziborov. "Concentration Sensitivity of Nucleic Acid and Protein Molecule Detection Using Nanowire Biosensors." Biophysica 1, no. 3 (August 14, 2021): 328–33. http://dx.doi.org/10.3390/biophysica1030024.

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The concentration detection limit (DL) of biomacromolecules attainable using a nanowire detector has become a topical issue. A DL of 10−15 M is required to reveal oncological and infectious diseases at an early stage. This study discusses the DL experimentally attainable in the subfemtomolar concentration range, and possible mechanisms explaining such a low-concentration DL through the cooperative effect of biomacromolecular complexes formed on the surface of the nanowire (NW) chip near the nanowire.

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Eksin, Ece, and Arzum Erdem. "Recent Progress on Optical Biosensors Developed for Nucleic Acid Detection Related to Infectious Viral Diseases." Micromachines 14, no. 2 (January 23, 2023): 295. http://dx.doi.org/10.3390/mi14020295.

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Optical biosensors have many advantages over traditional analytical methods. They enable the identification of several biological and chemical compounds directly, instantly, and without the need of labels. Their benefits include excellent specificity, sensitivity, compact size, and low cost. In this review, the main focus is placed on the nucleic acid-based optical biosensor technologies, including colorimetric, fluorescence, surface plasmon resonance (SPR), Evanescent-Wave Optical, Fiber optic and bioluminescent optical fibre. The fundamentals of each type of biosensor are briefly explained, and particular emphasis has been placed on the achievements which have been gained in the last decade on the field of diagnosis of infectious viral diseases. Concluding remarks concerning the perspectives of further developments are discussed.

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Jauset-Rubio, Miriam, Mayreli Ortiz, and Ciara K. O’Sullivan. "Exploiting the Nucleic Acid Nature of Aptamers for Signal Amplification." Biosensors 12, no. 11 (November 4, 2022): 972. http://dx.doi.org/10.3390/bios12110972.

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Aptamer-based assays and sensors are garnering increasing interest as alternatives to antibodies, particularly due to their increased flexibility for implementation in alternative assay formats, as they can be employed in assays designed for nucleic acids, such as molecular aptamer beacons or aptamer detection combined with amplification. In this work, we took advantage of the inherent nucleic acid nature of aptamers to enhance sensitivity in a rapid and facile assay format. An aptamer selected against the anaphylactic allergen β-conglutin was used to demonstrate the proof of concept. The aptamer was generated by using biotinylated dUTPs, and the affinity of the modified aptamer as compared to the unmodified aptamer was determined by using surface plasmon resonance to calculate the dissociation constant (KD), and no significant improvement in affinity due to the incorporation of the hydrophobic biotin was observed. The modified aptamer was then applied in a colorimetric competitive enzyme-linked oligonucleotide assay, where β-conglutin was immobilized on the wells of a microtiter plate, competing with β-conglutin free in solution for the binding to the aptamer. The limit of detection achieved was 68 pM, demonstrating an improvement in detection limit of three orders of magnitude as compared with the aptamer simply modified with a terminal biotin label. The concept was then exploited by using electrochemical detection and screen-printed electrodes where detection limits of 326 fM and 7.89 fM were obtained with carbon and gold electrodes, respectively. The assay format is generic in nature and can be applied to all aptamers, facilitating an easy and cost-effective means to achieve lower detection limits.

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Bhatt, Geeta, and Shantanu Bhattacharya. "Biosensors on chip: A critical review from an aspect of micro/nanoscales." Journal of Micromanufacturing 2, no. 2 (June 17, 2019): 198–219. http://dx.doi.org/10.1177/2516598419847913.

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Biosensors are a very well cherished research topic and have found an inseparable status from clinical diagnostics in specific and society at large. As the name suggests, biosensors or biological sensors are devices which detect the presence of biological entities or their constituents and derivatives. The field started decades ago and has matured quite well since its inception. The most important performance factors that are associated with biosensors are sensitivity, specificity, and limit of detection. The remaining efforts of the biosensor research domain focus on miniaturization aspects of the sensors. The growing advancements in this field have evolved the technology of biosensors to cater to full-scale diagnosis on microchips, bedside diagnostics, reduced cost, and increased speed of diagnostics. Biosensors are characterized through many different aspects; for example, one way is to classify them on the basis of the type of bio-recognition step that they would utilize or another way can be based on the type of detection scheme that they may integrate, etc. Depending on the bio-recognition layer’s properties, biosensors can be cell based, nucleic acid probe based, antibody/antigen based, or aptamer based, while depending on the type of detection scheme, biosensors can be viewed as colorimetric sensors, optical sensors, electrochemical sensors, mechanical sensors, etc. There are some other parallel areas of research like microfluidics and microelectromechanical systems where one of the main applications lies in the biosensor domain. This review article discusses the various aspects of biosensors, from their design, realization, to testing, along with various detection strategies. The assembly includes fabrication strategies particularly for microchip technology-based biosensing solutions, microchannels, integration to microfluidics, etc., while categorization deals with various kinds and applications of different biosensors.

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Choi, Hye Kyu, and Jinho Yoon. "Nanotechnology-Assisted Biosensors for the Detection of Viral Nucleic Acids: An Overview." Biosensors 13, no. 2 (January 30, 2023): 208. http://dx.doi.org/10.3390/bios13020208.

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The accurate and rapid diagnosis of viral diseases has garnered increasing attention in the field of biosensors. The development of highly sensitive, selective, and accessible biosensors is crucial for early disease detection and preventing mortality. However, developing biosensors optimized for viral disease diagnosis has several limitations, including the accurate detection of mutations. For decades, nanotechnology has been applied in numerous biological fields such as biosensors, bioelectronics, and regenerative medicine. Nanotechnology offers a promising strategy to address the current limitations of conventional viral nucleic acid-based biosensors. The implementation of nanotechnologies, such as functional nanomaterials, nanoplatform-fabrication techniques, and surface nanoengineering, to biosensors has not only improved the performance of biosensors but has also expanded the range of sensing targets. Therefore, a deep understanding of the combination of nanotechnologies and biosensors is required to prepare for sanitary emergencies such as the recent COVID-19 pandemic. In this review, we provide interdisciplinary information on nanotechnology-assisted biosensors. First, representative nanotechnologies for biosensors are discussed, after which this review summarizes various nanotechnology-assisted viral nucleic acid biosensors. Therefore, we expect that this review will provide a valuable basis for the development of novel viral nucleic acid biosensors.

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Kim, Ki Tae, Simona Angerani, and Nicolas Winssinger. "A minimal hybridization chain reaction (HCR) system using peptide nucleic acids." Chemical Science 12, no. 23 (2021): 8218–23. http://dx.doi.org/10.1039/d1sc01269j.

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A minimal peptide nucleic acid (PNA) HCR system based on a 5-mer stem and 5-mer loop/toehold hairpins was developed. The system was applied to the detection of a cancer biomarker on the surface of living cells.

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Zimmers, Zackary A., Alexander D. Boyd, Hannah E. Stepp, Nicholas M. Adams, and Frederick R. Haselton. "Development of an Automated, Non-Enzymatic Nucleic Acid Amplification Test." Micromachines 12, no. 10 (September 30, 2021): 1204. http://dx.doi.org/10.3390/mi12101204.

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Among nucleic acid diagnostic strategies, non-enzymatic tests are the most promising for application at the point of care in low-resource settings. They remain relatively under-utilized, however, due to inadequate sensitivity. Inspired by a recent demonstration of a highly-sensitive dumbbell DNA amplification strategy, we developed an automated, self-contained assay for detection of target DNA. In this new diagnostic platform, called the automated Pi-powered looping oligonucleotide transporter, magnetic beads capture the target DNA and are then loaded into a microfluidic reaction cassette along with the other reaction solutions. A stepper motor controls the motion of the cassette relative to an external magnetic field, which moves the magnetic beads through the reaction solutions automatically. Real-time fluorescence is used to measure the accumulation of dumbbells on the magnetic bead surface. Left-handed DNA dumbbells produce a distinct signal which reflects the level of non-specific amplification, acting as an internal control. The autoPiLOT assay detected as little as 5 fM target DNA, and was also successfully applied to the detection of S. mansoni DNA. The autoPiLOT design is a novel step forward in the development of a sensitive, user-friendly, low-resource, non-enzymatic diagnostic test.

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WU, Lei, Hai-Chao LI, Hai-Feng ZHAO, Yu SUN, Hao-Ran XU, Ming LU, Chun-Hua YANG, Wen-Zhao LI, and Zheng-Qiang LI. "Detection of Nucleic Acid Bases by Surface Enhanced Raman Scattering Based on In Situ Photo-Reduced Silver Colloids." Chinese Journal of Analytical Chemistry 39, no. 8 (August 2011): 1159–64. http://dx.doi.org/10.1016/s1872-2040(10)60465-3.

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Yuan, Bi-feng, Yu-hua Hao, and Zheng Tan. "Universal Sensing Strategy for the Detection of Nucleic Acid Targets by Optical Biosensor Based on Surface Plasmon Resonance." Clinical Chemistry 50, no. 6 (June 1, 2004): 1057–60. http://dx.doi.org/10.1373/clinchem.2003.030783.

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Nakano, Michihiko, Masafumi Inaba, and Junya Suehiro. "Rapid and low-cost amplicon visualization for nucleic acid amplification tests using magnetic microbeads." Analyst 146, no. 9 (2021): 2818–24. http://dx.doi.org/10.1039/d0an02349c.

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A rapid and low-cost visible amplicon detection method has been proposed. The amplicons are attached to magnetic microbeads, suspended in deionized water, and subjected to a magnetic field on a hydrophilic surface resulting in visible agglomeration.

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Yoon, Jinho, Minkyu Shin, Taek Lee, and Jeong-Woo Choi. "Highly Sensitive Biosensors Based on Biomolecules and Functional Nanomaterials Depending on the Types of Nanomaterials: A Perspective Review." Materials 13, no. 2 (January 9, 2020): 299. http://dx.doi.org/10.3390/ma13020299.

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Biosensors are very important for detecting target molecules with high accuracy, selectivity, and signal-to-noise ratio. Biosensors developed using biomolecules such as enzymes or nucleic acids which were used as the probes for detecting the target molecules were studied widely due to their advantages. For example, enzymes can react with certain molecules rapidly and selectively, and nucleic acids can bind to their complementary sequences delicately in nanoscale. In addition, biomolecules can be immobilized and conjugated with other materials by surface modification through the recombination or introduction of chemical linkers. However, these biosensors have some essential limitations because of instability and low signal strength derived from the detector biomolecules. Functional nanomaterials offer a solution to overcome these limitations of biomolecules by hybridization with or replacing the biomolecules. Functional nanomaterials can give advantages for developing biosensors including the increment of electrochemical signals, retention of activity of biomolecules for a long-term period, and extension of investigating tools by using its unique plasmonic and optical properties. Up to now, various nanomaterials were synthesized and reported, from widely used gold nanoparticles to novel nanomaterials that are either carbon-based or transition-metal dichalcogenide (TMD)-based. These nanomaterials were utilized either by themselves or by hybridization with other nanomaterials to develop highly sensitive biosensors. In this review, highly sensitive biosensors developed from excellent novel nanomaterials are discussed through a selective overview of recently reported researches. We also suggest creative breakthroughs for the development of next-generation biosensors using the novel nanomaterials for detecting harmful target molecules with high sensitivity.

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Sanders, Joshua C., and Erik D. Holmstrom. "Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins." Essays in Biochemistry 65, no. 1 (April 2021): 37–49. http://dx.doi.org/10.1042/ebc20200022.

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Abstract The conformations of biological macromolecules are intimately related to their cellular functions. Conveniently, the well-characterized dipole–dipole distance-dependence of Förster resonance energy transfer (FRET) makes it possible to measure and monitor the nanoscale spatial dimensions of these conformations using fluorescence spectroscopy. For this reason, FRET is often used in conjunction with single-molecule detection to study a wide range of conformationally dynamic biochemical processes. Written for those not yet familiar with the subject, this review aims to introduce biochemists to the methodology associated with single-molecule FRET, with a particular emphasis on how it can be combined with biomolecular simulations to study diverse interactions between nucleic acids and proteins. In the first section, we highlight several conceptual and practical considerations related to this integrative approach. In the second section, we review a few recent research efforts wherein various combinations of single-molecule FRET and biomolecular simulations were used to study the structural and dynamic properties of biochemical systems involving different types of nucleic acids (e.g., DNA and RNA) and proteins (e.g., folded and disordered).

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Almadidy, Amer, James Watterson, Paul AE Piunno, Inge V. Foulds, Paul A. Horgen, and Ulrich Krull. "A fibre-optic biosensor for detection of microbial contamination." Canadian Journal of Chemistry 81, no. 5 (May 1, 2003): 339–49. http://dx.doi.org/10.1139/v03-070.

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A fibre-optic biosensor is described for detection of genomic target sequences from Escherichia coli. A small portion of the LacZ DNA sequence is the basis for selection of DNA probe molecules that are produced by automated nucleic acid synthesis on the surface of optical fibres. Fluorescent intercalating agents are used to report the presence of hybridization events with target strands. This work reviews the fundamental design criteria for development of nucleic acid biosensors and reports a preliminary exploration of the use of the biosensor for detection of sequences that mark the presence of E. coli. The research work includes consideration of the length of the strands and non-selective binding interactions that can potentially block the selective chemistry or create background signals. The biosensors were able to detect genomic targets from E. coli at a picomole level in a time of a few minutes, and dozens of cycles of use have been demonstrated. In a step towards the preparation of a completely self-contained sensor technology, a new intercalating dye known as SYBR 101 (Molecular Probes, Inc.) has been end-labelled to the LacZ nucleic acid probe, to examine whether dye tethered onto an oligonucleotide terminus could fluorimetrically transduce the formation of hybrids. The results obtained from experiments in solution indicate that the use of tethered dye provides fluorescence signals that are due to hybridization, and that this process is functional even in the presence of a high concentration of non-selective background DNA obtained from sonicated salmon sperm. Key words: biosensor, DNA, fibre optic, hybridization, fluorescence, pathogen, E. coli.

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Pisamayarom, Kankanit, and Piyasak Chaumpluk. "RAPID LISTERIA MONOCYTOGENES ASSAY BASED ON HELICASE DEPENDENT AMPLIFICATION (HDA) AND NUCLEIC ACID HYBRIDIZATION IN BLUE SILVER NANOPLATES." International Journal of Research -GRANTHAALAYAH 5, no. 10 (October 31, 2017): 322–35. http://dx.doi.org/10.29121/granthaalayah.v5.i10.2017.2308.

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Listeria monocytogenes, a foodborne pathogen, is considered as one of the major problems in food safety. With strong safety regulations, a monitoring measure is essential for protecting the health and safety of consumers. Thus, a reliable monitoring method is required. In this study, a rapid assay based on a combination of helicase dependent amplification (HDA) and DNA signal detection via nucleic acid hybridization in blue silver nanoplates (AgNPls) was established. The assay started directly after short term enrichment in terrific broth using cotton ball swapping technique on seafood surface. A HDA amplification of hly gene of L. monocytogenes at 65 °C allowed DNA signals to be increased, whereas the rendered DNA products were detected via nucleic acid hybridization with an oligonucleotide probe in AgNPls solution. The positive specimens induced blue silver nanoplates’ aggregation resulting in pale gray change to colorless, while the negative specimens showed the blue color of non-aggregated nanoplates. The method had a detection limit at 100 copies of L. monocytogenes DNA per 50 g of sample. This method was rapid, simple, did not require laboratory facilities and was suitable for field food safety monitoring

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Ye, Wei Wei, and Mo Yang. "Optimal Surface Functionalization of Nanoporous Alumina Membrane for DNA Detection." Advanced Materials Research 631-632 (January 2013): 572–75. http://dx.doi.org/10.4028/www.scientific.net/amr.631-632.572.

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This study shows the study of optimal surface functionalization of nanoporous alumina membrane for "label-free" DNA detection. Single stranded DNA was first covalently immobilized on the nanopore walls via silane-PEG-NHS linker. The remained NHS group was hydrolyzed to form PEG layer to minimize the unspecific DNA binding during hybridization process. Optimal PEG-silane linker was achieved for better DNA immobilization efficiency. Using this optofluidic device, both ss-DNA immobilization and ds-DNA hybridization were successfully monitored via UV-Vis spectrum montoring. The nanopore size effect on DNA binding efficiency of membranes were also studied. With the increase of nanopore size, the DNA binding efficiency increased due to the increased reacted surface area. This portable optofluidic device integrated with nanoporos alumina membrane has the potential for nucleic acid in field detection in the application of food screening and environmental monitoring with high sensitivity

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Wang, Wei, Qijie Shang, and Haoyuan Lu. "Automatic COVID-19 Detection from Cough Sounds Using Multi-Headed Convolutional Neural Networks." Applied Sciences 13, no. 12 (June 9, 2023): 6976. http://dx.doi.org/10.3390/app13126976.

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Novel coronavirus disease 2019 (Corona Virus Disease 2019, COVID-19) is rampant all over the world, threatening human life and health. Currently, the detection of the presence of nucleic acid from SARS-CoV-2 is mainly based on the nucleic acid test as the standard. However, this method not only takes up a lot of medical resources but also takes a long time to achieve detection results. According to medical analysis, the surface protein of the novel coronavirus can invade the respiratory epithelial cells of patients and cause severe inflammation of the respiratory system, making the cough of COVID-19 patients different from that of healthy people. In this study, the cough sound is used as a large-scale pre-screening method before the nucleic acid test. Firstly, the Mel spectrum features, Mel Frequency Cepstral Coefficients, and VGG embeddings features of cough sound are extracted and oversampling technology is used to balance the dataset for classes with a small number of samples. In terms of the model, we designed multi-headed convolutional neural networks to predict audio samples, and adopted an early stop method to avoid the over-fitting problem of the model. The performance of the model is measured by the binary cross-entropy loss function. Our model performs well on the dataset of the AICovidVN 115M challenge that its accuracy rate is 98.1%, and on the dataset of the University of Cambridge that its accuracy rate is 91.36%.

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Tseng, Yen-Ta, Wan-Yun Li, Ya-Wen Yu, Chang-Yue Chiang, Su-Qin Liu, Lai-Kwan Chau, Ning-Sheng Lai, and Cheng-Chung Chou. "Fiber Optic Particle Plasmon Resonance Biosensor for Label-Free Detection of Nucleic Acids and Its Application to HLA-B27 mRNA Detection in Patients with Ankylosing Spondylitis." Sensors 20, no. 11 (June 1, 2020): 3137. http://dx.doi.org/10.3390/s20113137.

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We developed a label-free, real-time, and highly sensitive nucleic acid biosensor based on fiber optic particle plasmon resonance (FOPPR). The biosensor employs a single-strand deoxyoligonucleotides (ssDNA) probe, conjugated to immobilized gold nanoparticles on the core surface of an optical fiber. We explore the steric effects on hybridization affinity and limit of detection (LOD), by using different ssDNA probe designs and surface chemistries, including diluent molecules of different lengths in mixed self-assembled monolayers, ssDNA probes of different oligonucleotide lengths, ssDNA probes in different orientations to accommodate target oligonucleotides with a hybridization region located unevenly in the strand. Based on the optimized ssDNA probe design and surface chemistry, we achieved LOD at sub-nM level, which makes detection of target oligonucleotides as low as 1 fmol possible in the 10-μL sensor chip. Additionally, the FOPPR biosensor shows a good correlation in determining HLA-B27 mRNA, in extracted blood samples from patients with ankylosing spondylitis (AS), with the clinically accepted real-time reverse transcription-polymerase chain reaction (RT-PCR) method. The results from this fundamental study should guide the design of ssDNA probe for anti-sense sensing. Further results through application to HLA-B27 mRNA detection illustrate the feasibility in detecting various nucleic acids of chemical and biological relevance.

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Tadimety, Amogha, M. Nabuan Naufer, Alison Burklund, David Luna, Timothy J. Palinski, Brian Vyhnalek, and Gary W. Hunter. "(Invited, Digital Presentation) Rational Design of Nanoplasmonic Array Geometries for Biosensing." ECS Meeting Abstracts MA2022-02, no. 61 (October 9, 2022): 2235. http://dx.doi.org/10.1149/ma2022-02612235mtgabs.

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Background: Molecular diagnostics provide early and accurate diagnosis, which is essential for the prevention and treatment of infectious as well as chronic diseases. These tests are designed to detect disease-specific bioanalytes such as nucleic acid (DNA or RNA) or protein (antigens, antibodies) biomarkers. In the context of infectious disease diagnosis, nucleic acid-based detection methods are known to provide more specific and sensitive results. Here, the presence of a unique sequence belonging to the pathogenic genomic material is targeted to identify species, organism, genera and/or antimicrobial resistant gene markers. The majority of the common nucleic acid based diagnostic techniques require amplification (polymerase chain reaction, isothermal amplification etc.) of the pathogenic genetic material prior to detection impacting diagnostic speed, complexity, and cost thereby limiting ease of use. Thus, the development of simplified nucleic acid-based diagnostics that can be even used in resource-poor settings may hugely benefit patients across the globe. Nanopath is a molecular diagnostics company utilizing a solid-state nanosensor to enable sequence-specific detection of target nucleic acids without the need of amplification. These nanostructures enable ultra-sensitive biomarker detection using geometric, feature-dependent properties highly dependent on the local dielectric environment, allowing them to be sensitive to low concentration binding events. This paper describes an application of this approach to provide highly relevant clinical information within a single doctor’s office visit. Introduction: The Nanopath team is in collaboration with NASA (National Aeronautics and Space Administration) and NIST (National Institute of Standards and Technology) to push the bounds of the fundamental physics associated with their biosensing platform. The ability of metals to support electromagnetic surface waves gives rise to surface plasmons when optically illuminated. This property, and its strong sensitivity to changes in the local refractive index, allows for the use of metal nanoparticles as ultra-sensitive transducers. In prior work by members of this team, ensembles of randomly oriented nanoparticles (i.e., colloidal nanorods dispersed on chip) were employed for sequence-specific nucleic acid sensing (1-3). While these particle sensors have the advantage of rapid fabrication, they suffer from low sensitivity and quality factor due to the random particle dispersity. In contrast, in this study we employ ordered array nanoparticle ensembles which can be used to improve sensor sensitivity and figure-of-merit. Study Methods Overview: In this talk, we detail the results of sensing experiments and computational simulations to outline a rational design of the structure of these plasmonic nanoparticle arrays for biomolecular sensing. Through simulation and experiment, we iteratively tailor nanostructure dimension to provide high quality signal and large resonance shifts upon modeled nucleic acid binding. In particular, full-wave electromagnetic simulations were conducted using Lumerical photonic simulation software in which periodic boundary conditions were applied in the x- and y- dimensions for each of the nanoplasmonic sensor geometries. To simulate the resonance response to changes in the bulk solution in contact with the sensor surface, the refractive index of the surrounding media was changed appropriately. Nucleic acid hybridization events were modeled using either using spherical structures approximating the relevant radius of genomic material as estimated by polymer models, or as conformal layers with the known refractive indices for nucleic acids. On the basis of initial simulations, nanosensors were fabricated using traditional electron-beam lithography protocols at NIST. To evaluate consensus between simulations and experiments, bulk sensing experiments were carried out in which the resonance peaks were obtained by submerging the sensors in refractive index standards. Key nanosensor characteristics including resonance peak locations, resonance peak shifts as a function of refractive index, and figure of merit (FOM) of extinction curves were examined between the experimental and simulation results prior to proceeding with simulations on additional geometries and more complex solution conditions, and further device fabrication. This iterative process is repeated toward a rational design of nanoplasmonic array geometries for biosensing optimizing response for targeted disease detection. In summary, this study puts forth a methodology for rational design and characterization of regularly spaced nanoparticle arrays for optics-based biosensing. The results of this study will allow for more informed design of nanostructure geometries towards sequence-specific nucleic acid detection. These improved designs have the potential to improve clinical sensitivity and limit-of-detection across disease indication. References: A. Tadimety, Y. Zhang, K.M. Kready, T.J. Palinski, G.J. Tsongalis, X.J. Zhang, Biosens. Bioelectron. 130 (2019) 236–244. A. Tadimety, Y. Zhang, G.J. Tsongalis, X.J. Zhang, S, J. Mol. Diagnostics. (2017) 915. https://doi.org/10.1016/S1525-1578(15)00191-9. A. Tadimety, Z. Wu, J.H. Molinski, R. Beckerman, C. Jin, L. Zhang, T.J. Palinski, J.X.J. Zhang, in: Proc. IEEE Sensors, Institute of Electrical and Electronics Engineers Inc., 2020.

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Somasundaram, Subramaniam, and Christopher J. Easley. "A Nucleic Acid Nanostructure Built through On-Electrode Ligation for Electrochemical Detection of a Broad Range of Analytes." Journal of the American Chemical Society 141, no. 29 (June 30, 2019): 11721–26. http://dx.doi.org/10.1021/jacs.9b06229.

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

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