Amorphous Red Phosphorus: Host-Guest Assembly with Cyclodextrin.

Single-molecule mechanics of synthetic aromatic amide helices: Ultrafast and robust non-dissipative winding

Probing Single Individual Proteins Unfold and Refold with 1-μs Resolution: Improved AFM-Based Single Molecule Force Spectroscopy

Lattice dynamics of Hittorf's phosphorus and identification of structural groups and defects in amorphous red phosphorus

Amorphous red phosphorous embedded in carbon nanotubes scaffold as promising anode materials for lithium-ion batteries

The investigations on macromolecular interactions at the single-molecule level using atomic force microscopy(AFM) imaging and AFM-based single-molecule force spectroscopy(SMFS),with an emphasis on the combination of these two methods,have been discussed on the base of the author's recent work in related fields.First,AFM imaging(including static air phase and in situ liquid phase AFM imaging) is used to detect the effect of protein-binding on the topology of double stranded DNA(dsDNA) based on the characteristic(spaghetti-like) AFM image of dsDNA.Then,SMFS study on the nature of force-induced conformation transition of dsDNA is demonstrated.The force-fingerprint of dsDNA can then be used to study protein-DNA interactions revealing the effects of protein-binding on the dynamic conformation of dsDNA.In addition,the application of AFM-based SMFS in the investigation of RNA-protein coat interactions in an intact plant virus,tobacco mosaic virus(TMV),has been demonstrated.To realize this,a TMV particle is immobilized perpendicularly on a gold-coated substrate.The genetic RNA can then be pulled step-by-step out of the TMV particle through its 5′ opening.This study extends the force spectroscopy technique to the investigation of nucleic acid-protein interactions in more complicated biological systems(i.e.,in the virus particle).Finally,the attempt in the quantitative study of polymer interactions in a polyethylene oxide(PEO) single crystal is successfully accomplished by pulling a single PEO chain via its thiol-labelled end out of its single crystal by a good in situ combination of AFM imaging and SMFS.The generality of the established method in the investigation of crystallization of other polymers is discussed.This quantitative information on inter-and intramolecular interactions of macromolecules is useful in revealing the mechanism of many important biological processes(such as DNA replication) as well as in the design of high-performance polymer materials.

Atomic force microscopy (AFM)-based single molecule force spectroscopy (SMFS) is one of the most useful methods in the investigation of intra- or intermolecular interactions. To simplify the sample system and the data analysis, real biological and material systems have usually been simplified, and the target molecule of interest is normally extracted and bridged between the AFM tip and substrate for study, which is an effective way of understanding the real systems. With the development of technology (including the improvement of sample immobilization method), it is possible now to directly investigate molecular interactions in living system and real materials. The information obtained will be more useful for the better control of relevant biological processes and the design of high performance polymer materials. In this paper, recent progresses in AFM-SMFS study of molecular interactions in living cells and polymer materials are reviewed.

Single-stranded DNA binding proteins (SSB) interact with single-stranded DNA (ssDNA) specifically. Taking advantage of this character, we have employed Bacillus subtilis SSB protein to investigate the nature of force-induced conformation transition of double-stranded DNA (dsDNA) by using AFM-based single molecule force spectroscopy (SMFS) technique. Our results show that, when a dsDNA is stretched beyond its contour length, the dsDNA is partially melted, producing some ssDNA segments which can be captured by SSB proteins. We have also systematically investigated the effects of stretching length, waiting time, and salt concentration on the conformation transition of dsDNA and SSB-ssDNA interactions, respectively. Furthermore, the effect of proflavine, a DNA intercalator, on the SSB-DNA interactions has been investigated, and the results indicate that the proflavine-saturated dsDNA can be stabilized to the extent that the dsDNA will no longer melt into ssDNA under the mechanical force even up to 150 pN, and no SSB-DNA interactions are detectable.

Pulling Geometry-Induced Errors in Single Molecule Force Spectroscopy Measurements

The study on the nanoparticle-polymer interactions is very important for the design/preparation of high performance polymer nanocomposite. Here we present a method to quantify the polymer-particle interaction at single molecule level by using AFM-based single molecule force spectroscopy (SMFS). As a proof-of-concept study, we choose poly-l-lysine (PLL) as the polymer and several different types of polyoxometalates (POM) as the model particles to construct several different polymer nanocomposites and to reveal the binding mode and quantify the binding strength in these systems. Our results reveal that the shape of the nanoparticle and the binding geometry in the composite have significantly influenced the binding strength of the PLL/POM complexes. Our dynamic force spectroscopy studies indicate that the disk-like geometry facilitate the unbinding of PLL/AlMo6 complexes in shearing mode, while the unzipping mode becomes dominate in spherical PLL-P8W48 system. We have also systematically investigated the effects of charge numbers, particle size, and ionic strength on the binding strength and binding mode of PLL/POM, respectively. Our results show that electrostatic interactions dominate the stability of PLL/POM complexes. These findings provide a way for tuning the mechanical properties of polyelectrolyte-nanoparticle composites.

Atomic force microscopy (AFM) enables the pick up of a single protein molecule to apply a mechanical force. This technique, called “force spectroscopy,” provides unique information about the intermediates and free energy landscape of the mechanical unfolding of proteins. In this review, we introduce the AFM-based single molecule force spectroscopy of proteins and describe recent studies that answer some fundamental questions such as “is the mechanical resistance of proteins isotropic?”, “what is the structure of the transition state in mechanical unfolding?”, and “is mechanical unfolding related to biological functions?”

In this article, interactions between Bacillus subtilis single-stranded DNA binding proteins (BsSSB) and single-stranded DNA (ssDNA) were systematically studied. The effect of different molar ratios between BsSSB and ssDNA on their binding modes was first investigated by electrophoretic mobility shift assays (EMSAs). It is found that a high molar ratio of BsSSB to ssDNA can produce BsSSB-ssDNA complexes formed in the mode of two proteins binding one 65-nt (nucleotide) ssDNA whereas a low molar ratio facilitates the formation of BsSSB-ssDNA complexes in the mode of one protein binding one 65-nt ssDNA. Furthermore, two binding modes are in dynamic equilibrium. The unbinding force of BsSSB-ssDNA complexes was measured quantitatively in solutions with different salt concentrations by using AFM-based single-molecule force spectroscopy (SMFS). Our results show that the unbinding force is about 10 pN higher at high salt concentration (0.5 M NaCl) than at low salt concentration (0.1 M NaCl) and the lifetime of BsSSB-ssDNA complexes at high salt concentration is twice as long as that at low salt concentration. These results indicate that more tightly packed BsSSB-ssDNA complexes can form at high salt (0.5 M NaCl) concentration. In addition, the results of EMSA show that ssDNA, which is bound to BsSSB, can dissociate from BsSSB in the presence of the cDNA strand, indicating the dynamic nature of BsSSB-ssDNA interactions.

AFM-based single-molecule force spectroscopy (SMFS) is a powerful tool for the investigation of the elastic properties of a single polymer. Two typical organometallic polymers bearing ferrocene (Fc) groups in the backbone, poly(ferrocenyldimethylsilane) and poly(ferrocenylmethylphenylsilane), were investigated by SMFS to reveal their single-chain mechanical properties in normal and oxidized forms. We have found that the two polymers show similar elasticity in normal forms, though bearing different side groups. However, they exhibit different enthalpic elasticity after oxidation probably because of steric effects. Moreover, all experiments confirm that the single-chain elongation of poly(ferrocenyldimethylsilane) or poly(ferrocenylmethylphenylsilane) is reversible.

We report here a systematic investigation of the interactions between two heteropolymer DNA single-strands (ssDNA) and graphite surfaces using AFM-based single-molecule force spectroscopy (SMFS). For this purpose, force-displacement (FD) curves are recorded by peeling single-molecule ssDNA from graphite. We find that the unbinding forces are affected both by the DNA sequences and the ionic strength of the liquid environment. In particular, the unbinding force decreases with the increase of ionic strength. Dynamic force measurements indicate that the unbinding force increases nonlinearly with the logarithm of the applied loading rate. The force data at different loading rates can be fitted with a recently developed single-barrier adsorption model, which is used here as a mean of quantifying the differences in the adsorption between different sequences. In addition, we investigate the effect of DNA hybridization and the presence of mismatch pairing defects and find that flawless hybridization to a complementary oligomer significantly decreases the unbinding force but mismatched hybridization has no obvious effect on it. These results can help optimize a recently envisaged SMFS-based biosensing technology for label-free DNA detection.

Violet phosphorus is the most stable phosphorus allotrope with a layered structure. The corresponding violet phosphorene, a more stable two-dimensional semiconducting structure than black phosphorene, is a promising two-dimensional material for electronic and optoelectronic devices. The synthesis of violet phosphorus is the key factor to its experimental research. However, no clear evidence has been reported for the synthesis of violet phosphorus since its first proposal in 1865. The violet phosphorus was even debated to be a metastable intermediate phase. Until recently, the violet phosphorus crystals have just been successfully produced and exfoliated to give violet phosphorene. High yield synthesis of highly crystalline and pure violet phosphorus is crucial for the further exploration of violet phosphorus and phosphorene. In this work, highly crystalline and pure violet phosphorus crystals have been produced with a yield as high as 80%. The vapor transport, nucleation, crystal growth conditions, and synthesis mechanism have been studied to obtain violet phosphorus instead of black phosphorus. The mixture of transport agents and amorphous red phosphorus was heated to 600 °C to form P–Sn–I vapor and transported to the cooler zone (580 °C). The phosphorus was separated out from the P–Sn–I composites after cooling down to 530 °C to form violet phosphorus nuclei. The nucleation time and further cooling time correspond to the amount and crystallinity of violet phosphorus crystals. The precipitation has been demonstrated to be SnI2 crystals with a space group of C2/m (12) after the growth of violet phosphorus crystals. The synthesis of highly crystalline and pure violet phosphorus with high yield provides the application possibility of violet phosphorus and phosphorene in mechanic, electronic, optoelectronic, catalysts, and medical fields.

Alloying anodes are promising high‐capacity electrode materials for K‐ion batteries (KIBs). However, KIBs based on alloying anodes suffer from rapid capacity decay due to the instability of K metal and large volume expansion of alloying anodes. Herein, the effects of salts and solvents on the cycling stability of KIBs based on a typical alloying anode such as amorphous red phosphorus (RP) are investigated, and the potassium bis(fluorosulfonyl)imide (KFSI) salt‐based carbonate electrolyte is versatile to achieve simultaneous stabilization of K metal and RP electrodes for highly stable KIBs. This salt‐solvent complex with a moderate solvation energy can alleviate side reactions between K metal and the electrolyte and facilitate K+ ion diffusion/desolvation. Moreover, robust SEI layers that form on K metal and RP electrodes can suppress K dendrite growth and resist RP volume change. This strategy of electrolyte regulation can be applicable to other alloying anodes for high‐performance KIBs.