Biomimetic Nanopores: A New Age of DNA Sequencing?

Abstract

The discoveries about the central role of ion channels in the dynamics of neuronal excitability (resting membrane potential, depolarization, action potential, repolarization, and hyperpolarization) have been regarded as one of the greatest neuroscience breakthroughs of the 20th century. The English physiologists Hodgkin and Huxley from the University of Cambridge (8) were awarded the Nobel Prize in Physiology and Medicine in 1963 for their pioneering studies on the basic biophysical principles of cell membranes, which established a solid theoretical framework for the next generation of experimental studies on the nature of neuronal conduction. Defective ion channels have been implicated in the pathophysiology of various neurologic diseases. Abnormal sodium channels have been identified in patients with epilepsy (14), multiple sclerosis (3), and neuropathic pain (12). Water channels (so-called aquaporins) have been shown to be involved in the etiology of some demyelinating diseases (e.g., neuromyelitis optica) (15) as well as in the induction of brain edema in several different scenarios (e.g., after traumatic brain injury, stroke, and subarachnoid hemorrhage) (6). Pathologic calcium channels have been regarded as playing a central role in the pathophysiology of different genetic hereditary neurological diseases, such as spinocerebellar ataxia, familial hemiplegic migraine (16), and possibly Alzheimer’s disease (24). In recent decades, the exponential progress in the technology of biocompatible nanomaterials has enabled the emergence of new perspectives for artificial manipulation of channels that regulate neural excitability by modulating the gradient of ions on both sides of the cellular membrane. Based on computational analysis and computational modeling of the basic biomolecular structure of such passageways, it has been possible to design both purely synthetic and synthetically modified biomolecules (the so-called biomimetic nanopores), which are able to closely reproduce the biochemical functions of their original counterparts (10). The first strategies to design artificial ion-selective membrane channels were quite primitive and consisted in ion (or electron)beam sculpting of tiny holes with a diameter of a few nanometers in freestanding silicon nitride or silicon dioxide films (11). Nevertheless, further technical refinements, such as the possibility of coating these rude synthetic membranes with a lipid bilayer, enabled researchers to build laminar structures with properties much more similar to those of natural cellular membranes. Finally, more recent studies have demonstrated that by grafting additional bioactive molecules to these artificial nanopores (from polymers to enzymes or single-stranded pieces of DNA), it is possible to modify them so that they become able to perform very selective functions. Using such a paradigm, several different types of “solid-state” nanopores (in opposition to “biological nanopores”), which closely mimic the biochemical properties of natural ion channels, have already been developed, including a zincactivated (20), a potassium-responsive (9), and a proton-reactive channel (25). By employing emerging frontline technologies in material engineering (such as graphene, a new atomic-scale carbon honeycomb lattice with unique electronic, optical, and quantum properties) (13), some groups have also explored the use of such membranes as ionic insulators which are capable of displaying different degrees of electronic conductivity depending on the transmembrane solution potentials (5). More recently, other researchers have shown that graphene sheets can be used to design biomimetic nanopores that display preferential selectivity to Naþ or Kþ depending on the functional groups that are attached to their walls (4 negatively charged carboxylate groups for a Naþselective biomimetic nanopore or 4 carbonyl groups for a Kþ-selective biomimetic nanopore) (7). By employing new emerging fluorescence imaging techniques, such as those developed by optogenetics, other groups have developed newmethods for single-molecule, super-resolutionmicroscopy that enable the study of the three-dimensional morphological features of nanopores (e.g., their width dimensions, degree of interchannel heterogeneity, and overall in situ porosity of nanochannel arrays) with an advanced imaging resolution up to 40 nm (4). A different strategy for the creation of biomimetic nanopores involves the design of cyclic peptide nanotubes that form artificial transmembrane channels capable of ion transport. It has already been shown that, depending on the size of such nanotubes, different ions (e.g., Liþ, Naþ, Rbþ, Cl ) or ion-water clusters may be inserted in such gateways, generating channels with very specific transportational properties (18). In addition, it has been demonstrated that the transport of ions through nanopores can be controlled by the addition of certain polymers to their walls, which, by exhibiting a temperature-dependent conformational transition, allows the creation of a gating effect (Figure 1) (26). A wide variety of artificial nanopores have already been designed, including nanotube-based biochannels (built either with