Atomic Force Microscopy of Viruses: Stability, Disassembly, and Genome Release

In atomic force microscopy (AFM), the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study as a blind person manages a walking stick. In this way, AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables not only the manipulation of single protein cages but also the evaluation of each physicochemical property which is able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In this chapter, we start revising some recipes for adsorbing protein shells on surfaces and how the geometrical dilation of tips can affect to the AFM topographies. This work also deals with the abilities of AFM to monitor TGEV coronavirus under changing conditions of the liquid environment. Subsequently, we describe several AFM approaches to study cargo release, aging, and multilayered viruses with single indentation and fatigue assays. Finally, we comment on a combined AFM/fluorescence application to study the influence of crowding on GFP packed within individual P22 bacteriophage capsids.

Sensitive detection of heavy metal stress in aquatic plants by dissolved oxygen-quenched fluorescence/materials movement-induced beam deflection method

Sensitive detection of heavy metal (HM) stress in aquatic plants by dissolved oxygen (DO)-quenched fluorescence/materials movement-induced beam deflection method is demonstrated. Egeria densa Planchon and Cu2+ were used as a model aquatic plant and HM ion, respectively. Reproducibility and experimental errors of the method were first investigated in a control culture solution only containing 10-6 M Ru (II) complex (Tris (2,2'-bipyridyl) ruthenium (II) chloride) without addition of any fertilizer and Cu2+. Changes of DO concentration (∆DO) and deflection (∆DE) during the monitoring periods were used as parameters to quantitatively evaluate the experimental errors and detection limits. Averages or means ([Formula: see text], [Formula: see text]) and standard deviations (σ∆DO, σ∆DE) of ∆DO and ∆DE in seven control experiments with different aquatic plants sheets during both the respiration and photosynthesis processes were obtained. Next, DO and deflection at the middle vicinities of the aquatic plant were monitored during 2 h of both respiration and photosynthesis in presence of 10-10 ~ 10-6 M Cu2+. Experimental results showed that the aquatic plant began to suffer from the HM stress in some extent in presence of 10-9 M Cu2+. When the concentration of Cu2+ was higher than 10-8 M, changing trends of both DO and deflection with time were not reversed during the respiration and photosynthesis, implying that the materials movements in the physiological activities had been altered greatly. It is demonstrated that the method could sensitively detect the HM stress in the aquatic plants given by nM HM ions in culture solution without addition of a fertilizer. Furthermore, detection limits of the method were quantitatively discussed by considering [Formula: see text] σ∆DO and [Formula: see text] σ∆DE as the minimum detectable changes of DO and deflection caused by the HM stress, respectively.

Automatic Inverse Design of High-Performance Beam-Steering Metasurfaces via Genetic-type Tree Optimization

We introduce a genetic-type tree search (GTTS) algorithm combined with unsupervised clustering for the automatic inverse design of high-performance metasurfaces. With the proposed method, we realize highly directive beam-steering metasurfaces via the cooptimization of the amplitude and phase. In comparison with previous topology optimization approaches, the developed GTTS algorithm optimizes the organization of subwavelength nanoantennas and, thus, is applicable to the design of both passive and active metasurfaces. The optimized beam-steering metasurface specifically exhibits a nearly constant directivity when the steering angle varies from 5° to 30°. Furthermore, the optimized nonintuitive reflectance and phase profiles assist in achieving highly directive beam steering when the phase modulation range is <180°, which was previously challenging. Our approach can diminish the requirements of scattering light properties with substantially enhanced angular resolution of beam-steering metasurfaces, which enables the realization of high-performance metasurfaces that will be promising for a wide range of advanced nanophotonic applications.

Structural and Mechanical Characterization of Viruses with AFM

Microscopes are used to characterize small objects with the help of probes that interact with the specimen, such as photons and electrons in optical and electron microscopies, respectively. In atomic force microscopy (AFM) the probe is a nanometric tip located at the end of a micro cantilever which palpates the specimen under study as a blind person manages a walking stick. In this way AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables not only the manipulation of single protein cages, but also the characterization of every physicochemical property able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In this chapter we start revising some recipes for adsorbing protein shells on surfaces. Then we describe several AFM approaches to study individual protein cages, ranging from imaging to spectroscopic methodologies devoted for extracting physical information, such as mechanical and electrostatic properties. We also explain how a convenient combination of AFM and fluorescence methodologies entails monitoring genome release from individual viral shells during mechanical unpacking.

Atomic Force Microscopy of Protein Shells: Virus Capsids and Beyond

In Atomic Force Microscopy (AFM) the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study as a blind person uses a white cane. In this way AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables the manipulation of single protein cages, and the characterization a variety physicochemical properties able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In this chapter we start revising some recipes for adsorbing protein shells on surfaces. Then we describe several AFM approaches to study individual protein cages, ranging from imaging to spectroscopic methodologies devoted to extracting physical information, such as mechanical and electrostatic properties.

Atomic force microscopy of virus shells

Microscopes are used to characterize small specimens with the help of probes, such as photons and electrons in optical and electron microscopies, respectively. In atomic force microscopy (AFM) the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study as a blind person manages a white cane to explore the surrounding. In this way, AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables the manipulation of single protein cages, and the characterization of every physico-chemical property able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. Here we describe several AFM approaches to study individual protein cages, including imaging and spectroscopic methodologies for extracting mechanical and electrostatic properties. In addition, AFM allows discovering and testing the self-healing capabilities of protein cages because occasionally they may recover fractures induced by the AFM tip. Beyond the protein shells, AFM also is able of exploring the genome inside, obtaining, for instance, the condensation state of dsDNA and measuring its diffusion when the protein cage breaks.