Conformation Dynamics of Single Polymer Strands in Solution

Abstract

structures. For example, intrinsically disordered proteins, which account for one-third of the proteins in the human proteome, do not adopt a standardized 3D structure, and their spontaneous interconversion between unfolded states is crucial in dynamic biological processes. [4] In addition, various synthetic polymers, which are highly regulated by complex molecular interactions and the resulting conformational changes, form a variety of highorder structures via the self-structuring of individual molecules. [5][6][7][8] Thus, it is important to understand the intrinsic structural diversity and dynamic behaviors of individual macromolecules at the single-chain level.Over the last few decades, the conformation and dynamics of a single chain have been widely studied both theoretically and experimentally. Theoretical and computational modeling of single-chain dynamics in ideal solutions are well established in the field of polymer physics. [9][10][11][12] Moreover, enhanced sampling simulation techniques can efficiently locate candidates for energetically stable structures and calculate the free energy differences between their distinct states. [13][14][15] Nonetheless, it is still challenging to understand realistic single-chain behaviors using computational methods, as it is not trivial to simulate ion-solute interactions, crowding, or confinement in polymer solutions. [16][17][18] Furthermore, it is not rare to find a Conformational changes in macromolecules significantly affect their functions and assembly into high-level structures. Despite advances in theoretical and experimental studies, investigations into the intrinsic conformational variations and dynamic motions of single macromolecules remain challenging. Here, liquid-phase transmission electron microscopy enables the real-time tracking of single-chain polymers. Imaging linear polymers, synthetically dendronized with conjugated aromatic groups, in organic solvent confined within graphene liquid cells, directly exhibits chain-resolved conformational dynamics of individual semiflexible polymers. These experimental and theoretical analyses reveal that the dynamic conformational transitions of the single-chain polymer originate from the degree of intrachain interactions. In situ observations also show that such dynamics of the single-chain polymer are significantly affected by environmental factors, including surfaces and interfaces.

Experimental Guidelines to Image Transient Single-Molecule Events Using Graphene Liquid Cell Electron Microscopy

“…(2) One graphene-covered EM grid is used to scoop the sample solution, on which a free graphene sheet is suspended . (3) The sample droplet is placed on a graphene-covered EM grid which is then flipped to touch down a free-floating graphene sheet. ,,, (4) A loop is used to transfer the sample solution on which a graphene sheet is suspended to a graphene-covered EM grid …”

“…After several rounds of collision, the polymer chain breaks at the point where it touches the surface of gold nanoparticles, indicating a reaction hot spot at the surface, likely due to catalysis or accumulations of charges and radicals . Likewise, on a bubble (Figure h), chain scission appears to have occurred in the middle, as the two broken pieces are similar in size, likely because the shear stress built up the center as the molecule interacted with the curved bubble surface, qualitatively similar to what was recently observed in ref for a more rigid polymer. In contrast to the isotropic degradation pattern of a polymer chain, quantification revealed the difference summarized in Figure j and captured the formation of two pieces from chain scission and their similar (g) and different sizes (h).…”

“…This criterion is important for samples, especially biological samples, of limited quantity and high cost. Others too have found this protocol to provide better contrast. , Using protocol 3, an ∼1 μL drop suffices to assemble a grid, while protocols 2 and 4 require transferring free-floating graphene onto the sample solution with the corresponding requirement of a significantly larger solution volume. We now describe the procedure in detail (Figure ).…”

Single Molecule Imaging with Liquid Phase Electron Microscopy

“…(c) Single chain surface hopping event. Time lapsed plot of the center‐of‐mass position (left) and the corresponding images of the polymer chain at 1 s and 31 s. (d—h) A rigid polymer, images adapted from reference 4 with permission. (d) Schematic depiction of a second‐generation dendronized polymer (PTD‐MUG2) sandwiched between graphene sheets.…”

Deep learning-assisted analysis of single molecule dynamics from liquid-phase electron microscopy

“…Electron microscopy has become a common single-molecule characterization tool. With breakthroughs in the fabrication of liquid cells that seal the liquid against a vacuum, electron microscopy is now compatible with liquid samples, enabling direct imaging of synthetic macromolecules, 1,2 DNA, 1,3 peptides, 4 lipid assembly, 5 and proteins, 6,7 resolving previously hidden transient processes, due to its unique combination of nanometer spatial resolution and temporal resolution at several frames per second.…”