Effect of Chain Conformation on the Single-Molecule Melting Force in Polymer Single Crystals: Steered Molecular Dynamics Simulations Study

Understanding the relationship between polymer chain conformation as well as the chain composition within the single crystal and the mechanical properties of the corresponding single polymer chain will facilitate the rational design of high performance polymer materials. Here three model systems of polymer single crystals, namely poly­(ethylene oxide) (PEO), polyethylene (PE), and nylon-66 (PA66) have been chosen to study the effects of chain conformation, helical (PEO) versus planar zigzag conformation (PE, PA66), and chain composition (PE versus PA66) on the mechanical properties of a single polymer chain. To do that, steered molecular dynamics simulations were performed on those polymer single crystals by pulling individual polymer chains out of the crystals. Our results show that the patterns of force–extension curve as well as the chain moving mode are closely related to the conformation of the polymer chain in the single crystal. In addition, hydrogen bonds can enhance greatly the force required to stretch the polymer chain out of the single crystal. The dynamic breaking and reformation of multivalent hydrogen bonds have been observed for the first time in PA66 at the single molecule level

Effect of Chain Conformation on the Single-Molecule Melting Force in Polymer Single Crystals: Steered Molecular Dynamics Simulations Study

Understanding the relationship between polymer chain conformation as well as the chain composition within the single crystal and the mechanical properties of the corresponding single polymer chain will facilitate the rational design of high performance polymer materials. Here three model systems of polymer single crystals, namely poly­(ethylene oxide) (PEO), polyethylene (PE), and nylon-66 (PA66) have been chosen to study the effects of chain conformation, helical (PEO) versus planar zigzag conformation (PE, PA66), and chain composition (PE versus PA66) on the mechanical properties of a single polymer chain. To do that, steered molecular dynamics simulations were performed on those polymer single crystals by pulling individual polymer chains out of the crystals. Our results show that the patterns of force–extension curve as well as the chain moving mode are closely related to the conformation of the polymer chain in the single crystal. In addition, hydrogen bonds can enhance greatly the force required to stretch the polymer chain out of the single crystal. The dynamic breaking and reformation of multivalent hydrogen bonds have been observed for the first time in PA66 at the single molecule level

Atomic Force Microscopy Imaging Study of Aligning DNA by Dumbbell-like Au–Fe₃O₄ Magnetic Nanoparticles

Studies on nucleic acid structure and interactions between nucleic acid and its binding molecules are of great importance for understanding and controlling many important biological processes. Atomic force microscopy (AFM) imaging is one of the most efficient methods to disclose the DNA structure and binding modes between DNA and DNA-binding molecules. Long-chain DNA tends to form a random coiled structure, which prevents direct AFM imaging observation of the subtle structure formed by DNA itself or protein binding. Aligning DNA from the random coiled state into the extended state is not only important for applications in DNA nanotechnology but also for elucidating the interaction mechanism between DNA and other molecules. Here, we developed an efficient method based on the magnetic field to align long-chain DNA on a silicon surface. We used AFM imaging to study the alignment of DNA at the single-molecule level, showing that DNA can be stretched and highly aligned by the manipulation of magnetic nanoparticles tethered to one end of DNA and that the aligned DNA can be imaged clearly by AFM. In the absence of the magnetic field, the aligned DNA can relax back to a random coiled state upon rinsing. Such alignment and relaxation can be repeated many times, which provides an efficient method for the manipulation of individual DNA molecules and the investigation of DNA and DNA-binding molecule interactions

EMSA and Single-Molecule Force Spectroscopy Study of Interactions between <i>Bacillus subtilis</i> Single-Stranded DNA-Binding Protein and Single-Stranded DNA

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

Direct Observation of Single-Molecule Stick–Slip Motion in Polyamide Single Crystals

Stick–slip is a ubiquitous motion in the hydrogen bonding network, which confers the corresponding materials with excellent toughness and strength. The experimental study of the stick–slip mechanism remains challenging because of the complexity of stress accumulation and release. An ideal system for study of this motion should comprise a defined molecular structure and chain arrangement and strong intermolecular interactions. In this study, we detected the stick–slip motion at the single-molecule level in the hydrogen bonding network of polyamide (PA) single crystals through atomic force microscopy (AFM)-based single-molecule force spectroscopy. Our results show that a stiffer force-loading device can enhance the stick capacity by increasing the fracture force and facilitating stress release. We confirm that the chain rotates while slipping and the slip distance is dependent on the unit structure of the hydrogen bonding network

Coil–Globule Transition of a Water-Soluble Polymer

The coil–globule transition is a fundamental issue in polymer science and key to the performance of many smart materials. However, an experimental study on the globule structure and real-time dynamics of transition remains a challenge. Using single-molecule magnetic tweezers (MT) and atomic force microscopy (AFM) imaging, the temperature- and solvent-dependent transition of poly(N-isopropylacrylamide) (PNIPAM) single chain, a water-soluble thermoresponsive polymer, is directly observed under an external force. Surprisingly, the globule structure is composed of quantized beads with a basic/minimum size of ∼31 repeat units. Our results indicate that upon heating or salt concentration change, the PNIPAM coil first forms a series of nuclei each consisting of ∼31 repeat units, rather than random sizes. The subsequent transition involves a mergence of adjacent beads. Finally, the beads gradually stack to form a loose spheroidal aggregate, rather than a uniform compact globule. The distinct collapsing rates and mechanical stabilities for different collapsed structures are identified for the first time

Exploring the Folding Pattern of a Polymer Chain in a Single Crystal by Combining Single-Molecule Force Spectroscopy and Steered Molecular Dynamics Simulations

Understanding the folding pattern of a single polymer chain within its single crystal will shed light on the mechanism of crystallization. Here, we use the combined techniques of atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations to study the folding pattern of a polyethylene oxide (PEO) chain in its single crystal. Our results show that the folding pattern of a PEO chain in the crystal formed in dilute solution follows the adjacent re-entry folding model. While in the crystal obtained from the melt, the nonadjacent folding with large and irregular loops contributes to big force fluctuations in the force–extension curves. The method established here can offer a novel strategy to directly unravel the chain-folding pattern of polymer single crystals at single-molecule level

Quantifying the Chain Folding in Polymer Single Crystals by Single-Molecule Force Spectroscopy

Chain folding is a motif of polymer crystallization, which is essential for determining the crystallization kinetics. However, the experimental quantification of the chain folding remains a challenge because of limited instrumental resolution. Here, we quantify chain folding in solution-grown single crystals by using atomic force microscopy (AFM)-based single-molecule force spectroscopy. The fingerprint spectrum of force-induced chain motion allows us to decipher the adjacent and nonadjacent re-entry folding with spatial resolution of subnanometers. The average fractions of adjacent re-entry folds ⟨f⟩ are in the range 91–95% for polycaprolactone, poly-l-lactic acid, and polyamide 66, which is higher than the values determined by other classical technologies. The established single-molecule method is applicable to a broad range of crystalline polymer systems with different chain conformations or compositions

Extracting a Single Polyethylene Oxide Chain from a Single Crystal by a Combination of Atomic Force Microscopy Imaging and Single-Molecule Force Spectroscopy: Toward the Investigation of Molecular Interactions in Their Condensed States

A thiol-labeled single polyethylene oxide chain has been pulled out of its single crystal and the corresponding extraction force obtained quantitatively by a good combination of atomic force microscopy (AFM) imaging and AFM-based single-molecule force spectroscopy (SMFS). Our study extends the AFM-based SMFS to the investigation of polymer interactions in their condensed states (e.g., in polymer single crystals)