Detection of unique Ebola virus oligonucleotides using fluorescently-labeled phosphorodiamidate morpholino oligonucleotide probe pairs

Xiong, Yijia; McQuistan, Tammie; Stanek, James W.; Summerton, James; Mata, John E.; Squier, Thomas C.

doi:10.1016/j.ab.2018.07.006

Cited by 9 publications

(5 citation statements)

References 48 publications

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“…Hence, RNA and DNA probes require high ionic strength conditions to shield their intermolecular repulsive force for hybridisations [ 136 ]. However, PMO probes have no net charge and they are insensitive to the ionic strength of the buffer, so they can retain their excellent binding affinity to target nucleic acid under the condition of low or high ionic strength [ 137 ].…”

Section: Strategies To Enhance the Biosensor Performancementioning

confidence: 99%

Emerging Biosensors to Detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Review

2021

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Coronavirus disease (COVID-19) is a global health crisis caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) is the gold standard test for diagnosing COVID-19. Although it is highly accurate, this lab test requires highly-trained personnel and the turn-around time is long. Rapid and inexpensive immuno-diagnostic tests (antigen or antibody test) are available, but these point of care (POC) tests are not as accurate as the RT-PCR test. Biosensors are promising alternatives to these rapid POC tests. Here we review three types of recently developed biosensors for SARS-CoV-2 detection: surface plasmon resonance (SPR)-based, electrochemical and field-effect transistor (FET)-based biosensors. We explain the sensing principles and discuss the advantages and limitations of these sensors. The accuracies of these sensors need to be improved before they could be translated into POC devices for commercial use. We suggest potential biorecognition elements with highly selective target-analyte binding that could be explored to increase the true negative detection rate. To increase the true positive detection rate, we suggest two-dimensional materials and nanomaterials that could be used to modify the sensor surface to increase the sensitivity of the sensor.

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Section: Strategies To Enhance the Biosensor Performancementioning

confidence: 99%

Emerging Biosensors to Detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Review

2021

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“…Furthermore, the LOD of 238 UO 2 + was estimated. The normalized intensities of the m/z + 270 peak of multiple data points acquired from all samples were used in the linear regression fitting to derive the LOD 23,24 . The LOD of 238 UO 2 + in liquid ToF‐SIMS was calculated based on LOD = 3 * std.…”

Section: Resultsmentioning

confidence: 99%

In situ liquid SIMS analysis of uranium oxide

Yao

Buck

et al. 2020

Surface & Interface Analysis

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Trace analysis of nuclear materials in solid particles collected in the environment or particles in liquid slurry generated in nuclear material manufacturing processes can pinpoint elemental, organic, and isotopic signatures of nuclear fuel cycle activities and processes. Such information can support nuclear safeguards programs by increasing our ability to detect undeclared nuclear materials, routine activities for safeguarding at declared facilities, and illicit activities. However, trace radioactive material analysis in liquids and slurries is challenging using bulk approaches. For example, one drawback of sensitive analysis such as inductively coupled plasma mass spectrometry (ICP-MS) is that sample is consumed or destroyed as a result of the technical approach. We developed a vacuum compatible microfluidic interface to enable surface analysis of liquids and solid-liquid interactions using time-of-flight secondary ion mass spectrometry (ToF-SIMS). In this work, we illustrate the initial results from the analysis of liquid uranium oxide standard solutions using in situ liquid SIMS. Because the liquid SIMS analysis is almost nondestructive, the same sample can then be analyzed by other analytical techniques or saved for future reference.Consequently, multimodal analysis is possible. Our results demonstrate that in situ liquid SIMS can be used as a new approach to analyze radioactive materials in liquid and slurry forms of relevance to diverse applications. K E Y W O R D Sin situ liquid ToF-SIMS, limit of detection, nuclear material, principal component analysis, uranium

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“…Usually, the observations regarding mismatched targets are interpreted as the ability of the sensor to distinguish one- or two-mismatch oligos from the target. Under circumstances, when the analyte is extremely pure, and its concentration is known, such ability can be indeed used to discriminate a ‘mutant’ nucleic acid sequence from the ‘wild-type’ [ 13 , 41 ]. However, when it comes to specifically detecting a target biomarker species from an entire community of bacteria, this ‘ability’ can prove to be less advantageous.…”

Section: Resultsmentioning

confidence: 99%

“…It is also worth noticing that while in the sequential scenario, a biotin–streptavidin binding takes place, which is a fast and extremely high-affinity process (K d on the order of ≈10 −14 mol/L), in the case of the capture approach, a morpholino–DNA hybridization must occur in order for the bead to become bound. While morpholino–DNA hybridization is still a high affinity binding process, the dissociation constants (K d ) of this reaction were found to be over 3 orders of magnitude higher, on the order of 10 −10 mol/L (0.18 ± 0.02 nM for a 25-nucleotide tetramethyl rhodamine labeled morpholino probe and 0.31 ± 0.04 nM for a 25-nucleotide Alexa488 labeled morpholino probe) in a solution containing 10 mM Tris (pH 7.5) and 1 mM EDTA [ 41 ]. The same authors also determined hybridization rates of the morpholino probes to the target DNA in high salt (150 mM NaCl, similar to the DPBS-T buffer used in this study) and in low salt (5 mM NaCl) buffers and found that the rate was three times higher in the low salt ((15 ± 2) × 10 5 M −1 ·s −1 ) in comparison to the high salt ((4.8 ± 0.5) × 10 5 M −1 ·s −1 ).…”

Section: Resultsmentioning

confidence: 99%

Implementing Morpholino-Based Nucleic Acid Sensing on a Portable Surface Plasmon Resonance Instrument for Future Application in Environmental Monitoring

Bagi

Soelberg

Furlong

et al. 2018

Sensors

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A portable surface plasmon resonance (SPR) instrument was tested for the first time for the detection of oligonucleotide sequences derived from the 16S rRNA gene of Oleispira antarctica RB-8, a bioindicator species of marine oil contamination, using morpholino-functionalized sensor surfaces. We evaluated the stability and specificity of morpholino coated sensor surfaces and tested two signal amplification regimes: (1) sequential injection of sample followed by magnetic bead amplifier and (2) a single injection of magnetic bead captured oligo. We found that the sensor surfaces could be regenerated for at least 85 consecutive sample injections without significant loss of signal intensity. Regarding specificity, the assay clearly differentiated analytes with only one or two mismatches. Signal intensities of mismatch oligos were lower than the exact match target at identical concentrations down to 200 nM, in standard phosphate buffered saline with 0.1 % Tween-20 added. Signal amplification was achieved with both strategies; however, significantly higher response was observed with the sequential approach (up to 16-fold), where first the binding of biotin-probe-labeled target oligo took place on the sensor surface, followed by the binding of the streptavidin magnetic beads onto the immobilized targets. Our experiments so far indicate that a simple coating procedure in combination with a relatively cost-efficient magnetic-bead-based signal amplification will provide robust SPR based nucleic acid sensing down to 0.5 nM of a 45-nucleotide long oligo target (7.2 ng/mL).

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Detection of unique Ebola virus oligonucleotides using fluorescently-labeled phosphorodiamidate morpholino oligonucleotide probe pairs

Cited by 9 publications

References 48 publications

Emerging Biosensors to Detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Review

Emerging Biosensors to Detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Review

In situ liquid SIMS analysis of uranium oxide

Implementing Morpholino-Based Nucleic Acid Sensing on a Portable Surface Plasmon Resonance Instrument for Future Application in Environmental Monitoring

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