Determining the Physical Properties of Molecules with Nanometer-Scale Pores

Wang, Haiyan; Ettedgui, Jessica; Forstater, Jacob H.; Robertson, Joseph W. F.; Reiner, Joseph E.; Zhang, Huisheng; Chen, Siping; Kasianowicz, John J.

doi:10.1021/acssensors.7b00680

Cited by 30 publications

(30 citation statements)

References 147 publications

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“…Single molecule electrical sensing with engineered protein nanopores has been developed over the recent years to characterize the size, chemical composition, and structural conformation of macromolecules . A wide range of molecules such as metal ions, organic molecules, and nucleic acids have been detected using this methodology .…”

Section: Introductionmentioning

confidence: 99%

Controlling Interactions of Cyclic Oligosaccharides with Hetero‐Oligomeric Nanopores: Kinetics of Binding and Release at the Single‐Molecule Level

Satheesan

Krishnan

Mahendran

2018

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Controlling the molecular interactions through protein nanopores is crucial for effectively detecting single molecules. Here, the development of a hetero-oligomeric nanopore derived from Nocardia farcinica porin AB (NfpAB) is discussed for single-molecule sensing of biopolymers. Using single-channel recording, the interaction of cyclic oligosaccharides such as cationic cyclodextrins (CDs) of different symmetries and charges with NfpAB is measured. Studies of the transport kinetics of CDs reveal asymmetric geometry and charge distribution of NfpAB. The applied potential promotes the attachment of the cationic CDs to the negatively charged pore surface due to electrostatic interaction. Further, the attached CDs are released from the pore by reversing the applied potential in time-resolved blockages. Release of CDs from the pore depends on its charge, size, and magnitude of the applied potential. The kinetics of CD attachment and release is controlled by fine-tuning the applied potential demonstrating the successful molecular transport across these nanopores. It is suggested that such controlled molecular interactions with protein nanopores using organic templates can be useful for several applications in nanopore technology and single-molecule chemistry.

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Section: Introductionmentioning

confidence: 99%

Controlling Interactions of Cyclic Oligosaccharides with Hetero‐Oligomeric Nanopores: Kinetics of Binding and Release at the Single‐Molecule Level

Satheesan

Krishnan

Mahendran

2018

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“…Compared with those solid‐state ones, single‐molecule biological nanopores (e.g., aerolysin protein nanopore) feature accurately controlled nanostructure and interfacial chemistry, which are highly reproducible with atomic precision . These characteristics are of great benefits to acquire insightful knowledge and understand of (nanoconfined) SMRs .…”

Section: Measurements Of Single Molecule Reactionmentioning

confidence: 99%

Toward Precision Measurement and Manipulation of Single‐Molecule Reactions by a Confined Space

Qiu

Fato

Yuan

et al. 2019

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All chemical reactions can be divided into a series of single molecule reactions (SMRs), the elementary steps that involve only isomerization of, dissociation from, and addition to an individual molecule. Analyzing SMRs is of paramount importance to identify the intrinsic molecular mechanism of a complex chemical reaction, which is otherwise implausible to reveal in an ensemble fashion, owing to the significant static and dynamic heterogeneity of real‐world chemical systems. The single‐molecule measurement and manipulation methods developed recently are playing an increasingly irreplaceable role to detect and recognize short‐lived intermediates, visualize their transient existence, and determinate the kinetics and dynamics of single bond breaking and formation. Notably, none of the above SMRs characterizations can be realized without the aid of a confined space. Therefore, this Review aims to highlight the recent progress in the development of confined space enabled single‐molecule sensing, imaging, and tuning methods to study chemical reactions. Future prospects of SMRs research are also included, including a push toward the physical limit on transduction of information to signals and vice versa, transmission and recording of signals, computational modeling and simulation, and rational design of a confined space for precise SMRs.

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“…With this partition sum, the free energy is easily calculated. The center of mass calculation for the planar geometry involves employing Equations (21) and (23) in Equations (16) and (17). This calculation is described in the Appendix and here we outline the main results.…”

Section: Theory For a Planar Geometrymentioning

confidence: 99%

“…Most prominently this has been employed for DNA sequencing, which has led to the formation of several companies selling next generation sequencing devices (13,(18)(19)(20). Furthermore, adaptations of these devices to study RNA and protein structures is currently being explored (15,17,21). These biotechnologies in genomics and proteomics are an important aspect to advance personalized medicine.…”

Section: Introductionmentioning

confidence: 99%

Macromolecule Translocation in a Nanopore: Center of Mass Drift–Diffusion over an Entropic Barrier

Dell¹,

Muthukumar²

2019

Preprint

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Many fundamental biological processes involve moving macromolecules across membranes, through nanopores, in a process called translocation. Such motion is necessary for gene expression and regulation, tissue formation, and viral infection. Furthermore, in recent years nanopore technologies have been developed for single molecule detection of biological and synthetic macromolecules, which have been most notably employed in next generation DNA sequencing devices. Many successful theories have been established, which calculate the entropic barrier required to elongate a chain during translocation. However, these theories are at the level of the translocation coordinate (number of forward steps) and thus lack a clear connection to experiments and simulations. Furthermore, the proper diffusion coefficient for such a coordinate is unclear. In order to address these issues, we propose a center of mass (CM) theory for translocation. We start with the entropic barrier approach and show that the translocation coordinate is equivalent to the center of mass of the chain, providing a direct interpretation of previous theoretical studies. We thus recognize that the appropriate dynamics is given by CM diffusion, and calculate the appropriate diffusion constant (Rouse or Zimm) as the chain translocates. We illustrate our theoretical approach with a planar nanopore geometry and calculate some characteristic dynamical predictions. Our main result is the connection between the translocation coordinate and the chain CM, however, we also find that the translocation time is sped up by 1-2 orders of magnitude if hydrodynamic interactions are present. Our approach can be extended to include the details included in previous translocation theories. Most importantly this work provides a direct connection between theoretical approaches and experiments or simulations. SIGNIFICANCE Macromolecule motion through nanopores is critical for many biological processes, and has been recently employed for nucleic acid sequencing. Despite this, direct theoretical understandings of translocation are difficult to evaluate due to the introduction of the translocation coordinate. In this manuscript, we propose a theory for translocation written at the center of mass level of the polymer chain. This theoretical approach is more easily compared to experimental and simulation results, and additionally allows one to accurately account for hydrodynamic interactions on the macromolecule dynamics.

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Determining the Physical Properties of Molecules with Nanometer-Scale Pores

Cited by 30 publications

References 147 publications

Controlling Interactions of Cyclic Oligosaccharides with Hetero‐Oligomeric Nanopores: Kinetics of Binding and Release at the Single‐Molecule Level

Controlling Interactions of Cyclic Oligosaccharides with Hetero‐Oligomeric Nanopores: Kinetics of Binding and Release at the Single‐Molecule Level

Toward Precision Measurement and Manipulation of Single‐Molecule Reactions by a Confined Space

Macromolecule Translocation in a Nanopore: Center of Mass Drift–Diffusion over an Entropic Barrier

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