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Journal articles on the topic 'Nucleic acid based detection'

Author: Grafiati

Published: 4 June 2021

Last updated: 2 February 2022

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1

Wolcott, M. J. "Advances in nucleic acid-based detection methods." Clinical Microbiology Reviews 5, no. 4 (1992): 370–86. http://dx.doi.org/10.1128/cmr.5.4.370.

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Laboratory techniques based on nucleic acid methods have increased in popularity over the last decade with clinical microbiologists and other laboratory scientists who are concerned with the diagnosis of infectious agents. This increase in popularity is a result primarily of advances made in nucleic acid amplification and detection techniques. Polymerase chain reaction, the original nucleic acid amplification technique, changed the way many people viewed and used nucleic acid techniques in clinical settings. After the potential of polymerase chain reaction became apparent, other methods of nucleic acid amplification and detection were developed. These alternative nucleic acid amplification methods may become serious contenders for application to routine laboratory analyses. This review presents some background information on nucleic acid analyses that might be used in clinical and anatomical laboratories and describes some recent advances in the amplification and detection of nucleic acids.

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2

Gorgannezhad, Lena, Helen Stratton, and Nam-Trung Nguyen. "Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology." Micromachines 10, no. 6 (2019): 408. http://dx.doi.org/10.3390/mi10060408.

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Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.

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3

Epstein, Jason R., Israel Biran, and David R. Walt. "Fluorescence-based nucleic acid detection and microarrays." Analytica Chimica Acta 469, no. 1 (2002): 3–36. http://dx.doi.org/10.1016/s0003-2670(02)00030-2.

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4

Wolcott, M. J. "Advances in nucleic acid-based detection methods." Clinical Microbiology Reviews 5, no. 4 (1992): 370–86. http://dx.doi.org/10.1128/cmr.5.4.370-386.1992.

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5

Sulianto, Ivana Agnes, Ida Parwati, Nina Tristina, and Agnes Rengga I. "HYBRIDIZATION-BASED NUCLEIC ACID AMPLIFICATION TEST TERHADAP CARTRIDGE-BASED NUCLEIC ACID AMPLIFICATION TEST TERKAIT MULTIDRUG-RESISTANT TUBERCULOSIS (Hybridization-Based Nucleic Acid Amplification Test towards Catridge-Based Nucleic Acid Amplification Test in Multidrug-Resistant Tuberculosis)." INDONESIAN JOURNAL OF CLINICAL PATHOLOGY AND MEDICAL LABORATORY 21, no. 3 (2018): 237. http://dx.doi.org/10.24293/ijcpml.v21i3.1274.

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Indonesia has high burden of multidrug-resistant tuberculosis (MDR-TB). Cartridge-based nucleic acid amplification test (CB-NAAT),which is recommended as a diagnostic method of MDR-TB by World Health Organization, is faster in achieving the result. This methoddetermines MDR-TB only from the rifampisin resistance, by detecting mutations that occur on the 81 bp hot-spot region of the rpoBgene. The isoniazid resistance is not included in the determination of MDR-TB by this method. Hybridization-based NAAT (HB-NAAT)detects MDR-TB not only from the rifampisin resistance (codon 526 and 531 rpoB gene), but also from the isoniazid resistance (codon315 katG gene). The aim of this study was to know the validity of the HB-NAAT in detecting MDR-TB using sputum with CB-NAATas the gold standard in a diagnostic study. All of 51 sputums were collected during June 2013 from patients suspected pulmonaryMDR-TB at Dr. Hasan Sadikin General Hospital. The result of CB-NAAT were 16 MDR-TB, 12 TB non MDR, and 23 non TB. HB-NAATexamination results were 3 MDR-TB, 25 TB non MDR (3 RMR, 6 IMR, 16 susceptible) and 23 non TB. The sensitivity of HB-NAAT was18.75% and specificity 100%. Low sensitivity values may due to the high mutation variations in the samples. So it could not be detectedonly by codons 526 and 531 for rifampisin resistance. For the detection of isoniazid resistance, HB-NAAT have optimal primer at lowconcentrations and it also need more than katG genes to detect isoniazid resistance. Based on this study, it can be conclued, that HBNAAThas low sensitivity but high specificity in the detecting MDR-TB.

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6

Chen, Hui-Ling, Meng-Meng Guo, Hao Tang, et al. "Nucleic acid amplification-based methods for microRNA detection." Analytical Methods 7, no. 6 (2015): 2258–63. http://dx.doi.org/10.1039/c4ay02938k.

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7

Rajendran, L., R. Akila, G. Karthikeyan, T. Raguchander, D. Saravanakumar, and R. Samiyappan. "Nucleic acid based detection technique forGanoderma lucidumin coconut." Archives Of Phytopathology And Plant Protection 47, no. 6 (2013): 690–702. http://dx.doi.org/10.1080/03235408.2013.819160.

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8

Dolati, Somayeh, Mohammad Ramezani, Khalil Abnous, and Seyed Mohammad Taghdisi. "Recent nucleic acid based biosensors for Pb2+ detection." Sensors and Actuators B: Chemical 246 (July 2017): 864–78. http://dx.doi.org/10.1016/j.snb.2017.02.118.

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9

Zhang, Zhikun, Xiaojie Ye, Qingqing Liu, et al. "Colorimetric Nucleic Acid Detection Based on Gold Nanoparticles with Branched DNA." Nano 15, no. 08 (2020): 2050110. http://dx.doi.org/10.1142/s1793292020501106.

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Nucleic acid detection is becoming increasingly important in the diagnostics of genetic diseases for biological analysis. We herein propose gold nanoparticles as probe for colorimetric detection of nucleic acids with branched DNA nanostructures, which enables a novel and simple colorimetric biosensor. In our system, the target DNA specifically triggered two short-chain ssDNA probes to generate branched DNA nanostructures (Y-shape DNA), which prevent AuNPs from aggregation in aqueous NaCl solution. On the contrary, when the target DNA did not exist, gold nanoparticles were unstable and aggregated easily because there is no anti-aggregation function from Y-shape DNA. Sensor response was found to be proportional to the target DNA concentration from 5 to 100[Formula: see text]nM, with detection limits determined as 5[Formula: see text]nM. The developed platform is for colorimetric nucleic acid detection without enzymes, label and modification holds great promise for practical applications.

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10

Sulianto, Ivana Agnes, Ida Parwati, Nina Tristina, and Agnes Rengga I. "HYBRIDIZATION-BASED NUCLEIC ACID AMPLIFICATION TEST TERHADAP CARTRIDGE-BASED NUCLEIC ACID AMPLIFICATION TEST TERKAIT MULTIDRUG-RESISTANT TUBERCULOSIS." INDONESIAN JOURNAL OF CLINICAL PATHOLOGY AND MEDICAL LABORATORY 21, no. 3 (2016): 237. http://dx.doi.org/10.24293/ijcpml.v21i3.734.

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Indonesia has high burden of multidrug-resistant tuberculosis (MDR-TB). Cartridge-based nucleic acid amplification test (CB-NAAT), which is recommended as a diagnostic method of MDR-TB by World Health Organization, is faster in achieving the result. This method determines MDR-TB only from the rifampisin resistance, by detecting mutations that occur on the 81 bp hot-spot region of the rpoB gene. The isoniazid resistance is not included in the determination of MDR-TB by this method. Hybridization-based NAAT (HB-NAAT) detects MDR-TB not only from the rifampisin resistance (codon 526 and 531 rpoB gene), but also from the isoniazid resistance (codon 315 katG gene). The aim of this study was to know the validity of the HB-NAAT in detecting MDR-TB using sputum with CB-NAAT as the gold standard in a diagnostic study. All of 51 sputums were collected during June 2013 from patients suspected pulmonary MDR-TB at Dr. Hasan Sadikin General Hospital. The result of CB-NAAT were 16 MDR-TB, 12 TB non MDR, and 23 non TB. HB-NAAT examination results were 3 MDR-TB, 25 TB non MDR (3 RMR, 6 IMR, 16 susceptible) and 23 non TB. The sensitivity of HB-NAAT was 18.75% and specificity 100%. Low sensitivity values may due to the high mutation variations in the samples. So it could not be detected only by codons 526 and 531 for rifampisin resistance. For the detection of isoniazid resistance, HB-NAAT have optimal primer at low concentrations and it also need more than katG genes to detect isoniazid resistance. Based on this study, it can be conclued, that HBNAAT has low sensitivity but high specificity in the detecting MDR-TB.

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11

Su, Xiaodi, Huey Fang Teh, Xiaohui Lieu, and Zhiqiang Gao. "Enzyme-Based Colorimetric Detection of Nucleic Acids Using Peptide Nucleic Acid-Immobilized Microwell Plates." Analytical Chemistry 79, no. 18 (2007): 7192–97. http://dx.doi.org/10.1021/ac0709403.

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12

Minunni, M. "Biosensors based on nucleic acid interaction." Spectroscopy 17, no. 2-3 (2003): 613–25. http://dx.doi.org/10.1155/2003/896705.

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DNA sensing is an emerging technology based on hybridisation reaction between an immobilised DNA probe and a molecular target, consisting of a probe complementary sequence in solution. Many application have been developed in the field of environmental, food and clinical analysis.Surface plasmon resonance and piezoelectric sensing are reported as transduction principles for DNA-based devices. These techniques are able to monitor in real-time and without the use of any label the hybridisation reaction between nucleic acids. Particular attention is given to Genetically Modified Organism detection.

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13

Vincelli, Paul, and Ned Tisserat. "Nucleic Acid–Based Pathogen Detection in Applied Plant Pathology." Plant Disease 92, no. 5 (2008): 660–69. http://dx.doi.org/10.1094/pdis-92-5-0660.

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Nucleic acid–based (NA-based) detection techniques are becoming fundamental for the applied plant pathologist. Their speed, sensitivity, specificity, versatility have resulted in the use of these tools to address an increasing number of applied questions and hypotheses. In order to use based detection techniques to best advantage, it is important to recognize only their advantages but also their limitations, such as the possibility particular NA-based tests may not have complete specificity for the of interest and only for that organism. The distinction between detection and disease diagnosis must also be recognized, and we believe NA-based tools are techniques for the former and not the latter. Several pathogen detection technologies are also discussed.

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14

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 (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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15

Rotbart, H. A. "Nucleic acid detection systems for enteroviruses." Clinical Microbiology Reviews 4, no. 2 (1991): 156–68. http://dx.doi.org/10.1128/cmr.4.2.156.

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The enteroviruses comprise nearly 70 human pathogens responsible for a wide array of diseases including poliomyelitis, meningitis, myocarditis, and neonatal sepsis. Current diagnostic tests for the enteroviruses are limited in their use by the slow growth, or failure to grow, of certain serotypes in culture, the antigenic diversity among the serotypes, and the low titer of virus in certain clinical specimens. Within the past 6 years, applications of molecular cloning techniques, in vitro transcription vectors, automated nucleic acid synthesis, and the polymerase chain reaction have resulted in significant progress toward nucleic acid-based detection systems for the enteroviruses that take advantage of conserved genomic sequences across many, if not all, serotypes. Similar approaches to the study of enteroviral pathogenesis have already produced dramatic advances in our understanding of how these important viruses cause their diverse clinical spectra.

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16

Bonvicini, Francesca, Claudia Filippone, Elisabetta Manaresi, et al. "Peptide Nucleic Acid–Based In Situ Hybridization Assay for Detection of Parvovirus B19 Nucleic Acids." Clinical Chemistry 52, no. 6 (2006): 973–78. http://dx.doi.org/10.1373/clinchem.2005.064741.

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Abstract Background: Peptide nucleic acid (PNA) molecules are known to bind complementary nucleic acid sequences with a much stronger affinity and with more stable binding than DNA or RNA molecules. We chose parvovirus B19, which is diagnosed by detection of nucleic acids by in situ hybridization assay (ISH) and/or PCR, as an experimental model to develop an ISH assay that uses biotinylated PNA probes to detect viral genome in clinical specimens. Methods: We first optimized the PNA-ISH assay on B19-infected and mock-infected UT-7/EpoS1 cells and then tested the assay on archival B19 specimens and on consecutive specimens. All data were compared with data obtained with a standardized DNA-based ISH assay and confirmed by a PCR-ELISA. Results: PNA-ISH detected B19 genome in a higher number of B19-infected UT-7/EpoS1 cells and with a more defined localization of viral nucleic acids than the standardized DNA-ISH assay. Moreover, PNA-ISH was able to detect B19 genome in all positive archival samples, whereas DNA-ISH failed in 5 samples. PNA-ISH detected more positive samples than DNA-ISH when consecutive specimens were analyzed, and a close agreement was found with PCR-ELISA results. Conclusions: The PNA-ISH assay had sensitivity and specificity comparable to a PCR assay and was more practical and quicker to perform than standard hybridization assays. The assay may be a suitable diagnostic test for the detection of viral nucleic acids in clinical specimens.

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17

Singh, SarveshPal. "Nucleic acid-based methods for early detection of sepsis." Annals of Cardiac Anaesthesia 20, no. 1 (2017): 112. http://dx.doi.org/10.4103/0971-9784.197850.

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18

Ludwig, Wolfgang, Elke Brockmann, Claudia Beimfohr, Christian Hertel, Bodil Jacobsen, and Karl Heinz Schleifer. "Nucleic Acid Based Detection Systems for Genetically Modified Bacteria." Systematic and Applied Microbiology 18, no. 4 (1995): 477–85. http://dx.doi.org/10.1016/s0723-2020(11)80407-8.

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19

Das, Maumita, Gajjala Sumana, R. Nagarajan, and B. D. Malhotra. "Zirconia based nucleic acid sensor for Mycobacterium tuberculosis detection." Applied Physics Letters 96, no. 13 (2010): 133703. http://dx.doi.org/10.1063/1.3293447.

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20

Wang, Hsin-Neng, Andrew M. Fales, and Tuan Vo-Dinh. "Plasmonics-based SERS nanobiosensor for homogeneous nucleic acid detection." Nanomedicine: Nanotechnology, Biology and Medicine 11, no. 4 (2015): 811–14. http://dx.doi.org/10.1016/j.nano.2014.12.012.

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21

Sidransky, D. "Nucleic Acid-Based Methods for the Detection of Cancer." Science 278, no. 5340 (1997): 1054–58. http://dx.doi.org/10.1126/science.278.5340.1054.

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22

Johnson, John, Robert Okyere, Adam Taylor, Anupama Joseph, Karin Musier-Forsyth, and Besik Kankia. "Quadruplex-Based Technology for Nucleic Acid Amplification and Detection." Biophysical Journal 102, no. 3 (2012): 15a. http://dx.doi.org/10.1016/j.bpj.2011.11.105.

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23

Picard, François J., and Michel G. Bergeron. "Rapid Diagnosis of Bacterial Infections Using Technologies Based on Nucleic Acid Detection." Canadian Journal of Infectious Diseases 10, suppl c (1999): 16C—24C. http://dx.doi.org/10.1155/1999/872430.

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Bacterial identification and antibiotic susceptibility testing methods used in clinical microbiology laboratories generally require at least two days. This long delay often forces physicians to treat patients presumptively with broad-spectrum antibiotics. Novel diagnostic tests based on the detection of nucleic acids (DNA or RNA) offer a great potential for the rapid (approximately 1 h) diagnosis of bacterial infections. The present article reviews various aspects of the development and validation of nucleic acid-based assays suitable for the detection and identification of bacteria as well as for the detection of associated antibiotic resistance genes. The potential of these assays for routine use in clinical microbiology laboratories is also discussed.

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24

Li, Hanying, Thomas H. LaBean, and Kam W. Leong. "Nucleic acid-based nanoengineering: novel structures for biomedical applications." Interface Focus 1, no. 5 (2011): 702–24. http://dx.doi.org/10.1098/rsfs.2011.0040.

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Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.

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25

Terracciano, Monica, Ilaria Rea, Nicola Borbone, et al. "Porous Silicon-Based Aptasensors: The Next Generation of Label-Free Devices for Health Monitoring." Molecules 24, no. 12 (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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26

Huang, Jiaoqi, Yang Zhang, Zhongquan Lin, et al. "Femtomolar detection of nucleic acid based on functionalized gold nanoparticles." Nanophotonics 8, no. 9 (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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27

Elskens, Joke, and Annemieke Madder. "Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection." RSC Chemical Biology 2, no. 2 (2021): 410–22. http://dx.doi.org/10.1039/d0cb00236d.

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Crosslinker-modified nucleic acid probes are promising substitutes for regular oligonucleotide probes in hybridization-based assays, as they allow a more selective and efficient detection of nucleic acid targets and nucleic acid biomarkers.

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28

Tong, CY William, and Harry Mallinson. "Moving to nucleic acid-based detection of genital Chlamydia trachomatis." Expert Review of Molecular Diagnostics 2, no. 3 (2002): 257–66. http://dx.doi.org/10.1586/14737159.2.3.257.

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29

Shubkin, Catherine D., Michael W. White, Mitchell S. Abrahamsen, Matthew C. Rognlie, and Stuart E. Knapp. "A Nucleic Acid-Based Test for Detection of Fasciola hepatica." Journal of Parasitology 78, no. 5 (1992): 817. http://dx.doi.org/10.2307/3283311.

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Pandey, Chandra Mouli, Gajjala Sumana, and Bansi D. Malhotra. "Microstructured Cystine Dendrites-Based Impedimetric Sensor for Nucleic Acid Detection." Biomacromolecules 12, no. 8 (2011): 2925–32. http://dx.doi.org/10.1021/bm200490b.

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31

Budiarto, Bugi Ratno, Pimpin Utama Pohan, and Desriani. "Nucleic acid amplification-based HER2 molecular detection for breast cancer." Journal of Oncological Sciences 5, no. 1 (2019): 31–41. http://dx.doi.org/10.1016/j.jons.2018.12.001.

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32

Monis, Paul T., and Steven Giglio. "Nucleic acid amplification-based techniques for pathogen detection and identification." Infection, Genetics and Evolution 6, no. 1 (2006): 2–12. http://dx.doi.org/10.1016/j.meegid.2005.08.004.

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33

Fu, Rongzhan, Taihua Li, and Hyun Gyu Park. "An ultrasensitive DNAzyme-based colorimetric strategy for nucleic acid detection." Chemical Communications, no. 39 (2009): 5838. http://dx.doi.org/10.1039/b907762f.

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Baeumner, Antje J., Michele C. Humiston, Richard A. Montagna, and Richard A. Durst. "Detection of Viable Oocysts ofCryptosporidiumparvumFollowing Nucleic Acid Sequence Based Amplification." Analytical Chemistry 73, no. 6 (2001): 1176–80. http://dx.doi.org/10.1021/ac001293h.

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Vora, Gary J., Carolyn E. Meador, David A. Stenger, and Joanne D. Andreadis. "Nucleic Acid Amplification Strategies for DNA Microarray-Based Pathogen Detection." Applied and Environmental Microbiology 70, no. 5 (2004): 3047–54. http://dx.doi.org/10.1128/aem.70.5.3047-3054.2004.

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ABSTRACT DNA microarray-based screening and diagnostic technologies have long promised comprehensive testing capabilities. However, the potential of these powerful tools has been limited by front-end target-specific nucleic acid amplification. Despite the sensitivity and specificity associated with PCR amplification, the inherent bias and limited throughput of this approach constrain the principal benefits of downstream microarray-based applications, especially for pathogen detection. To begin addressing alternative approaches, we investigated four front-end amplification strategies: random primed, isothermal Klenow fragment-based, φ29 DNA polymerase-based, and multiplex PCR. The utility of each amplification strategy was assessed by hybridizing amplicons to microarrays consisting of 70-mer oligonucleotide probes specific for enterohemorrhagic Escherichia coli O157:H7 and by quantitating their sensitivities for the detection of O157:H7 in laboratory and environmental samples. Although nearly identical levels of hybridization specificity were achieved for each method, multiplex PCR was at least 3 orders of magnitude more sensitive than any individual random amplification approach. However, the use of Klenow-plus-Klenow and φ29 polymerase-plus-Klenow tandem random amplification strategies provided better sensitivities than multiplex PCR. In addition, amplification biases among the five genetic loci tested were 2- to 20-fold for the random approaches, in contrast to >4 orders of magnitude for multiplex PCR. The same random amplification strategies were also able to detect all five diagnostic targets in a spiked environmental water sample that contained a 63-fold excess of contaminating DNA. The results presented here underscore the feasibility of using random amplification approaches and begin to systematically address the versatility of these approaches for unbiased pathogen detection from environmental sources.

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Li, Zihan, Wenchang Zhao, Shixin Ma, Zexu Li, Yingjia Yao, and Teng Fei. "A chemical-enhanced system for CRISPR-Based nucleic acid detection." Biosensors and Bioelectronics 192 (November 2021): 113493. http://dx.doi.org/10.1016/j.bios.2021.113493.

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37

Su, Wentao, Duo Liang, and Mingqian Tan. "Nucleic acid-based detection for foodborne virus utilizing microfluidic systems." Trends in Food Science & Technology 113 (July 2021): 97–109. http://dx.doi.org/10.1016/j.tifs.2021.04.053.

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38

Vincelli, Paul, and Bernadette Amsden. "Comparison of Tissue-Disruption Methods for PCR-Based Detection of Plant Pathogens." Plant Disease 97, no. 3 (2013): 363–68. http://dx.doi.org/10.1094/pdis-06-12-0536-re.

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Polymerase chain reaction-based detection of plant-associated microbes depends on physical disruption of tissues of the host and microorganism in order to liberate nucleic acids during extraction. Using six types of plant tissues as well as an oospore preparation of Phytophthora capsici, we evaluated the use of pressure-cycling technology (PCT) compared with several common techniques for physical tissue disruption. With all tissues tested, bead-beating provided excellent yields of amplifiable nucleic acid, with a few inconsistent exceptions. The use of PCT did not consistently improve nucleic acid yields or “amplifiability”. The use of a mortar and pestle to physically disrupt plant tissue also provided good results at low cost, though it was not consistently as effective as the bead-beater. Furthermore, handling of ground tissues in an open mortar may present more challenges in minimizing cross-contamination than working with tissues pulverized in a bead-beater tube.

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Zozulia, Oleksii, Tobias Bachmann, Nina S. Deussner-Helfmann, Frank Beierlein, Mike Heilemann, and Andriy Mokhir. "Red light-triggered nucleic acid-templated reaction based on cyclic oligonucleotide substrates." Chemical Communications 55, no. 72 (2019): 10713–16. http://dx.doi.org/10.1039/c9cc03587g.

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We developed a red light-triggered, fluorogenic chemical reaction based on cyclic oligonucleotide substrates that is accelerated over 30-fold by nucleic acid templates that allows quick and sequence specific detection of nucleic acid down to 1 nM.

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40

Fykse, Else M., Gunnar Skogan, William Davies, Jaran Strand Olsen, and Janet M. Blatny. "Detection of Vibrio cholerae by Real-Time Nucleic Acid Sequence-Based Amplification." Applied and Environmental Microbiology 73, no. 5 (2007): 1457–66. http://dx.doi.org/10.1128/aem.01635-06.

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ABSTRACT A multitarget molecular beacon-based real-time nucleic acid sequence-based amplification (NASBA) assay for the specific detection of Vibrio cholerae has been developed. The genes encoding the cholera toxin (ctxA), the toxin-coregulated pilus (tcpA; colonization factor), the ctxA toxin regulator (toxR), hemolysin (hlyA), and the 60-kDa chaperonin product (groEL) were selected as target sequences for detection. The beacons for the five different genetic targets were evaluated by serial dilution of RNA from V. cholerae cells. RNase treatment of the nucleic acids eliminated all NASBA, whereas DNase treatment had no effect, showing that RNA and not DNA was amplified. The specificity of the assay was investigated by testing several isolates of V. cholerae, other Vibrio species, and Bacillus cereus, Salmonella enterica, and Escherichia coli strains. The toxR, groEL, and hlyA beacons identified all V. cholerae isolates, whereas the ctxA and tcpA beacons identified the O1 toxigenic clinical isolates. The NASBA assay detected V. cholerae at 50 CFU/ml by using the general marker groEL and tcpA that specifically indicates toxigenic strains. A correlation between cell viability and NASBA was demonstrated for the ctxA, toxR, and hlyA targets. RNA isolated from different environmental water samples spiked with V. cholerae was specifically detected by NASBA. These results indicate that NASBA can be used in the rapid detection of V. cholerae from various environmental water samples. This method has a strong potential for detecting toxigenic strains by using the tcpA and ctxA markers. The entire assay including RNA extraction and NASBA was completed within 3 h.

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Tang, Ruihua, Hui Yang, Yan Gong, et al. "A fully disposable and integrated paper-based device for nucleic acid extraction, amplification and detection." Lab on a Chip 17, no. 7 (2017): 1270–79. http://dx.doi.org/10.1039/c6lc01586g.

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Kabza, Adam M., and Jonathan T. Sczepanski. "l-DNA-Based Catalytic Hairpin Assembly Circuit." Molecules 25, no. 4 (2020): 947. http://dx.doi.org/10.3390/molecules25040947.

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Isothermal, enzyme-free amplification methods based on DNA strand-displacement reactions show great promise for applications in biosensing and disease diagnostics but operating such systems within biological environments remains extremely challenging due to the susceptibility of DNA to nuclease degradation. Here, we report a catalytic hairpin assembly (CHA) circuit constructed from nuclease-resistant l-DNA that is capable of unimpeded signal amplification in the presence of 10% fetal bovine serum (FBS). The superior biostability of the l-DNA CHA circuit relative to its native d-DNA counterpart was clearly demonstrated through a direct comparison of the two systems (d versus l) under various conditions. Importantly, we show that the l-CHA circuit can be sequence-specifically interfaced with an endogenous d-nucleic acid biomarker via an achiral peptide nucleic acid (PNA) intermediary, enabling catalytic detection of the target in FBS. Overall, this work establishes a blueprint for the detection of low-abundance nucleic acids in harsh biological environments and provides further impetus for the construction of DNA nanotechnology using l-oligonucleotides.

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Becheru, Diana, George Vlăsceanu, Adela Banciu, Eugeniu Vasile, Mariana Ioniţă, and Jorge Burns. "Optical Graphene-Based Biosensor for Nucleic Acid Detection; Influence of Graphene Functionalization and Ionic Strength." International Journal of Molecular Sciences 19, no. 10 (2018): 3230. http://dx.doi.org/10.3390/ijms19103230.

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A main challenge for optical graphene-based biosensors detecting nucleic acid is the selection of key parameters e.g. graphenic chemical structure, nanomaterial dispersion, ionic strength, and appropriate molecular interaction mechanisms. Herein we study interactions between a fluorescein-labelled DNA (FAM-DNA) probe and target single-stranded complementary DNA (cDNA) on three graphenic species, aiming to determine the most suitable platform for nucleic acid detection. Graphene oxide (GO), carboxyl graphene (GO-COOH) and reduced graphene oxide functionalized with PEGylated amino groups (rGO-PEG-NH2, PEG (polyethylene glycol)) were dispersed and characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The influence of ionic strength on molecular interaction with DNA was examined by fluorescence resonance energy transfer (FRET) comparing fluorescence intensity and anisotropy. Results indicated an effect of graphene functionalization, dispersion and concentration-dependent quenching, with GO and GO-COOH having the highest quenching abilities for FAM-DNA. Furthermore, GO and GO-COOH quenching was accentuated by the addition of either MgCl2 or MgSO4 cations. At 10 mM MgCl2 or MgSO4, the cDNA induced a decrease in fluorescence signal that was 2.7-fold for GO, 3.4-fold for GO-COOH and 4.1-fold for rGO-PEG-NH2. Best results, allowing accurate target detection, were observed when selecting rGO-PEG-NH2, MgCl2 and fluorescence anisotropy as an advantageous combination suitable for nucleic acid detection and further rational design biosensor development.

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Fang, Yile, Haoran Liu, Yue Wang, et al. "Fast and Accurate Control Strategy for Portable Nucleic Acid Detection (PNAD) System Based on Magnetic Nanoparticles." Journal of Biomedical Nanotechnology 17, no. 3 (2021): 407–15. http://dx.doi.org/10.1166/jbn.2021.3028.

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Portable nucleic acid detection (PNAD) systems are performed for sample processing, amplification and detection automatically in an individual device realizing "sample in, answer out." For this goal, numerous function modules should be integrated in a diminutive device, in which temperature controller is one of the most important modules. In a nucleic acid detection process, both sample processing and polymerase chain reaction (PCR) require fast and accurate temperature control to increase concentration and purity of the extraction product and to improve amplification efficiency. In this paper, a dual-channel temperature controller for PNAD systems is developed, which contains a printed circuit board (PCB) and an integrated control program with a fast and accurate control strategy. According to the principle of nucleic acid detection based on magnetic nanoparticles, the controller can work in different modes such as high-precision heating control for nucleic acid extraction, rapid thermal cycle control for PCR, and rate adjustable constant heating/cooling control for melting curve. Evaluatively, the average heating/cooling rate of the module can exceed about 6 C/s, while the temperature fluctuation was less than ± 0.1°C, which can meet the demands of PNAD systems very well.

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Yoo, Hyebin, Hyesung Jo, and Seung Soo Oh. "Detection and beyond: challenges and advances in aptamer-based biosensors." Materials Advances 1, no. 8 (2020): 2663–87. http://dx.doi.org/10.1039/d0ma00639d.

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Ouyang, Wei, and Jongyoon Han. "Universal amplification-free molecular diagnostics by billion-fold hierarchical nanofluidic concentration." Proceedings of the National Academy of Sciences 116, no. 33 (2019): 16240–49. http://dx.doi.org/10.1073/pnas.1904513116.

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Rapid and reliable detection of ultralow-abundance nucleic acids and proteins in complex biological media may greatly advance clinical diagnostics and biotechnology development. Currently, nucleic acid tests rely on enzymatic processes for target amplification (e.g., PCR), which have many inherent issues restricting their implementation in diagnostics. On the other hand, there exist no protein amplification techniques, greatly limiting the development of protein-based diagnosis. We report a universal biomolecule enrichment technique termed hierarchical nanofluidic molecular enrichment system (HOLMES) for amplification-free molecular diagnostics using massively paralleled and hierarchically cascaded nanofluidic concentrators. HOLMES achieves billion-fold enrichment of both nucleic acids and proteins within 30 min, which not only overcomes many inherent issues of nucleic acid amplification but also provides unprecedented enrichment performance for protein analysis. HOLMES features the ability to selectively enrich target biomolecules and simultaneously deplete nontargets directly in complex crude samples, thereby enormously enhancing the signal-to-noise ratio of detection. We demonstrate the direct detection of attomolar nucleic acids in urine and serum within 35 min and HIV p24 protein in serum within 60 min. The performance of HOLMES is comparable to that of nucleic acid amplification tests and near million-fold improvement over standard enzyme-linked immunosorbent assay (ELISA) for protein detection, being much simpler and faster in both applications. We additionally measured human cardiac troponin I protein in 9 human plasma samples, and showed excellent agreement with ELISA and detection below the limit of ELISA. HOLMES is in an unparalleled position to unleash the potential of protein-based diagnosis.

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Jun, Sun Hee, Kee Hyung Sung, Sang Hoon Song, et al. "Detection of Enterovirus using Real-Time Nucleic Acid Sequence-based Amplification." Korean Journal of Clinical Microbiology 13, no. 2 (2010): 53. http://dx.doi.org/10.5145/kjcm.2010.13.2.53.

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Li, Mei-Xing, Qiu-Mei Feng, Zhen Zhou, Wei Zhao, Jing-Juan Xu, and Hong-Yuan Chen. "Plasmon-Enhanced Electrochemiluminescence for Nucleic Acid Detection Based on Gold Nanodendrites." Analytical Chemistry 90, no. 2 (2017): 1340–47. http://dx.doi.org/10.1021/acs.analchem.7b04307.

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Xu, Ye, Yinghua Liu, Yan Wu, Xiaohu Xia, Yiqun Liao, and Qingge Li. "Fluorescent Probe-Based Lateral Flow Assay for Multiplex Nucleic Acid Detection." Analytical Chemistry 86, no. 12 (2014): 5611–14. http://dx.doi.org/10.1021/ac5010458.

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Moon, W. C., T. H. Kim, M. R. Oh, T. H. Uhm, and C. H. Noh. "PRELIMINARY STUDY ON PLASMA NUCLEIC ACID BASED DETECTION OF PROSTATE CANCER." European Urology Supplements 5, no. 2 (2006): 274. http://dx.doi.org/10.1016/s1569-9056(06)61010-5.

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