Charge, Diffusion, and Current Fluctuations of Single-Stranded DNA Trapped in an MspA Nanopore

Fleming, Stephen Jordan; Lu, Bo; Golovchenko, Jene Andrew

doi:10.1016/j.bpj.2016.12.007

Cited by 10 publications

(7 citation statements)

References 37 publications

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“…It should be noted that even a quantity as commonplace as a diffusion constant can be observed to change dramatically in the context of a periodic attractive potential [20, 61]. Indeed, the values observed here, while quite reasonable, are significantly smaller than those reported for ssDNA in the MspA channel in the context of a simplified energy landscape model [62].…”

Section: Discussionmentioning

confidence: 47%

Voltage‐activated complexation of α‐synuclein with three diverse β‐barrel channels: VDAC, MspA, and α‐hemolysin

et al. 2021

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Voltage-activated complexation is the process by which a transmembrane potential drives complex formation between a membrane-embedded channel and a soluble or membrane-peripheral target protein. Metabolite and calcium flux across the mitochondrial outer membrane was shown to be regulated by voltage-activated complexation of the voltage-dependent anion channel (VDAC) and either dimeric tubulin or αsynuclein (αSyn). However, the roles played by VDAC's characteristic attributes-its anion selectivity and voltage gating behavior-have remained unclear. Here, we compare in vitro measurements of voltage-activated complexation of αSyn with three wellcharacterized β-barrel channels-VDAC, MspA, and α-hemolysin-that differ widely in their organism of origin, structure, geometry, charge density distribution, and voltage gating behavior. The voltage dependences of the complexation dynamics for the different channels are observed to differ quantitatively but have similar qualitative features. In each case, energy landscape modeling describes the complexation dynamics in a manner consistent with the known properties of the individual channels, while voltage gating does not appear to play a role. The reaction free energy landscapes thus calculated reveal a non-trivial dependence of the αSyn/channel complex stability on the surface density of αSyn.

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Section: Discussionmentioning

confidence: 47%

Voltage‐activated complexation of α‐synuclein with three diverse β‐barrel channels: VDAC, MspA, and α‐hemolysin

et al. 2021

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“…Dividing eq by eq , we obtain where ε 0 is the permittivity of free space. The zeta potential ζ and relative permittivity of filter paper ε r are 20 mV and 80, respectively, and the effective charge of ssDNA133a is 1.936 –18 C (determined using the effective charge of single base of ssDNA Q eff = 0.55e – , base size r 0 = 0.34 nm, and the number of bases n = 22). By substituting the above-mentioned number into eq , it can be seen that v ep is around 12 times higher than v eof , indicating that v ep is the dominant behavior and ssDNA is thus continuously transported from the cathodic side to the anodic side.…”

Section: Resultsmentioning

confidence: 99%

Microfluidic Paper-Based Preconcentration and Retrieval for Rapid Ribonucleic Acid Biomarker Detection and Visualization

Fan

Smith

et al. 2022

Anal. Chem.

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Microfluidic paper-based analytical devices (μPADs) have attracted significant attention in the field of pointof-care (POC) diagnostics. However, the heterogeneous structure of the paper often impairs the limit of detection (LOD) for lowabundance targets when those targets are directly analyzed. One viable solution to bypass this limitation is to elevate the target concentration above the LOD on-site to reach a valid readout. Here, we developed a 3D μPADs preconcentrator (3D-μP 2 ) to increase sample concentration by electrokinetic trapping and demonstrated its application in increasing the LOD of a downstream colorimetric assay. The three-dimensional (3D) structure of this device was composed of a loading pad, a vertical fluid path formed by stacked absorbent pads, and an ion-selective membrane of PEDOT:PSS. This novel design facilitates fast preconcentration, high capacity in sample processing, and easy target retrieval. The concentration of an exemplary target, a single-stranded DNA sequence, was increased up to 170-fold within 80 s. The LOD of the colorimetric assay to verify the DNA target was increased 3 orders of magnitude with a preconcentrated sample compared to the control. The device and its analysis equipment used in this study were all cheap and portable. Thus, the 3D-μP 2 can be a powerful POC tool for sample pretreatment in resource-limited areas.

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“…The results have demonstrated that the engineered MspA has a single-base resolution and can distinguish four different bases comparable to α-HL . Subsequently, it has been widely used to investigate single-oligonucleotide analysis, methylcytosine detection, and even natural DNA sequencing. ,,− …”

Section: Biosensing Platforms Derived From Mdsmentioning

confidence: 99%

New Insights for Biosensing: Lessons from Microbial Defense Systems

Wan

Zong

et al. 2022

Chem. Rev.

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Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR−Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR−Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties.We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.

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Charge, Diffusion, and Current Fluctuations of Single-Stranded DNA Trapped in an MspA Nanopore

Cited by 10 publications

References 37 publications

Voltage‐activated complexation of α‐synuclein with three diverse β‐barrel channels: VDAC, MspA, and α‐hemolysin

Voltage‐activated complexation of α‐synuclein with three diverse β‐barrel channels: VDAC, MspA, and α‐hemolysin

Microfluidic Paper-Based Preconcentration and Retrieval for Rapid Ribonucleic Acid Biomarker Detection and Visualization

New Insights for Biosensing: Lessons from Microbial Defense Systems

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