Single-Chain Mechanical Property of Poly(N-vinyl-2-pyrrolidone) and Interaction with Small Molecules

Environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by atomic force microscopy-based single-molecule force spectroscopy and the implications for advanced polymer materials

"The Tao begets the One. One begets all things of the world." This quote from Tao Te Ching is still inspiring for scientists in chemistry and materials science: The "One" can refer to a single molecule. A macroscopic material is composed of numerous molecules. Although the relationship between the properties of the single molecule and macroscopic material is not well understood yet, it is expected that a deeper understanding of the single-chain mechanics of macromolecules will certainly facilitate the development of materials science. Atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) has been exploited extensively as a powerful tool to study the single-chain behaviors of macromolecules. In this review, we summarize the recent advances in the emerging field of environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by means of AFM-SMFS. First, the single-chain inherent elasticities of several typical linear macromolecules are introduced, which are also confirmed by one of three polymer models with theoretical elasticities of the corresponding macromolecules obtained from quantum mechanical (QM) calculations. Then, the effects of the external environments on the single-chain mechanics of synthetic polymers and biomacromolecules are reviewed. Finally, the impacts of single-chain mechanics of macromolecules on the development of polymer science especially polymer materials are illustrated.

Effects of Water on the Single-Chain Elasticity of Poly(U) RNA

Water, the dominant component under the physiological condition, is a complicated solvent which greatly affects the properties of solute molecules. Here, we utilize atomic force microscope-based single-molecule force spectroscopy to study the influence of water on the single-molecule elasticity of an unstructured single-stranded RNA (poly(U)). In nonpolar solvents, RNA presents its inherent elasticity, which is consistent with the theoretical single-chain elasticity calculated by quantum mechanics calculations. In aqueous buffers, however, an additional energy of 1.88 kJ/mol·base is needed for the stretching of the ssRNA chain. This energy is consumed by the bound water rearrangement (Ew) during chain elongation. Further experimental results indicate that the Ew value is uncorrelated to the salt concentrations and stretching velocity. The results obtained in an 8 M guanidine·HCl solution provide more evidence that the bound water molecules around RNA give rise to the observed deviation between aqueous and nonaqueous environments. Compared to synthetic water-soluble polymers, the value of Ew of RNA is much lower. The weak interference of water is supposed to be the precondition for the RNA secondary structure to exist in aqueous solution.

Single-chain mechanics of poly(N,N-diethylacrylamide) and poly(N-isopropylacrylamide): comparative study reveals the effect of hydrogen bond donors

The single-chain mechanics of two similar thermosensitive polymers, poly(N,N-diethylacrylamide) (PDEAM) and poly(N-isopropylacrylamide) (PNIPAM), have been studied by atomic force microscopy-based single-molecule force spectroscopy (SMFS). In a typical nonpolar organic solvent, octane, both of the polymers show the same inherent elasticity, although they have different substitutional groups. However, the mechanics of the two polymers presents large differences in water. The energies needed for the rearrangement of the bound water during elongation at room temperature are estimated by the SMFS method at the single-chain level, which is ~1.13 ± 0.10 and ~5.19 ± 0.10 kJ/mol for PDEAM and PNIPAM, respectively. In addition, PNIPAM shows a temperature-dependent single-chain mechanics when the temperature is increased across the lower critical solution temperature (LCST), while PDEAM does not. These differences observed in aqueous solution originate from the different structures of the two polymers. With a hydrogen bond donor in the amide group, PNIPAM will be more hydrated when T < LCST. When T > LCST, PNIPAM will have larger changes in both conformation and hydration. These findings also suggest that PNIPAM is a good candidate for a thermo-driven single-molecule motor, while PDEAM is not.

Inherent stretching elasticity of a single polymer chain with a carbon-carbon backbone

We study the single-chain elasticities of three kinds of neutral polymers with a carbon-carbon (C-C) backbone by atomic force microscopy-based single-molecule force spectroscopy in a nonpolar solvent (octane), aiming at measuring the inherent chain elasticity of this very important class of polymers. The finding that the single-chain elasticities of all three polymers in octane are virtually identical in the entire force region implies that the side chains of the polymers have no detectable effects on the single-chain elasticity. By utilizing the single-chain elasticity from quantum mechanics calculations, the freely rotating chain model can provide the best fitting curve when each C-C bond is set to be the rotating unit. Although there are some exceptions when the side chain is very huge, our work provides a general result for the inherent elasticity of single neutral flexible polymer chains with C-C backbones.

EMSA and single-molecule force spectroscopy study of interactions between Bacillus subtilis 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.

Interrogation of Single Synthetic Polymer Chains and Polysaccharides by AFM-Based Force Spectroscopy

This contribution reviews selected mechanical experiments on individual flexible macromolecules using single-molecule force spectroscopy (SMFS) based on atomic force microscopy. Focus is placed on the analysis of elasticity and conformational changes in single polymer chains upon variation of the external environment, as well as on conformational changes induced by the mechanical stress applied to individual macromolecular chains. Various experimental strategies regarding single-molecule manipulation and SMFS testing are discussed, as is theoretical analysis through single-chain elasticity models derived from statistical mechanics. Moreover, a complete record, reported to date, of the parameters obtained when applying the models to fit experimental results on synthetic polymers and polysaccharides is presented.

Weakly Bound Water Molecules Shorten Single-Stranded DNA

In this paper, we measure the single chain elasticity of an oligomer single-stranded DNA (ssDNA) in both aqueous and nonaqueous, apolar liquid environments by AFM-based single molecule force spectroscopy. We find a marked deviation between the force-extension relations recorded for the two conditions. This difference is attributed to the additional energy required to break the H-bond-directed water bridges around the ssDNA chain in aqueous solutions, which are nonexistent in organic solvents. The results obtained in 8 M guanidine-HCl solution provide more evidence that water bridges around ssDNA originate the observed deviation. On the basis of the results obtained by an ab initio quantum mechanics calculation, a parameter-free freely rotating chain model is proposed. We find that this model is in perfect agreement with the experimental force-extension curve obtained in organic solvents, which further corroborates our assumption. On the basis of the experimental results, it is suggested that the weak H-bonding between ssDNA and water molecules may be a precondition for stable double-stranded DNA to exist in water.