Charge evolution during the unfolding of a single DNA i-motif

Switchable Double Inversion of Chirality in a Helical Polyelectrolyte

Switchable inversion of chirality between opposite handedness by varying pH is discovered for a histidine pendant polymer, polymethyl (4-vinylbenzoyl) histidinate (PBHis), as demonstrated by the circular dichroism as well as the changes of hydrodynamic radius measured by fluorescence correlation spectroscopy at the single molecular level. The polyelectrolyte is found to take an M-helicity below pH 8.0 and change into P-helicity above pH 8.0. Such helicity further inverses into M-chirality above pH 10.6. All these helical structures with opposite handedness can be switched using pH variations. The mechanism of such a unique phenomenon is attributed to the protonation and deprotonation of the imidazole group and the hydroxide-ion-mediated hydrogen bonding, which determine the mutual orientation between the adjacent side groups under the hydrogen bonds and π-π stacking and therefore the handedness of the helical structure.

Poly(ethylene oxide) Is Positively Charged in Aqueous Solutions

There have been controversies about the binding of cations to poly(ethylene oxide) (PEO) chains in aqueous solutions. In the current study, single molecular evidence of charging PEO chains by cation binding in aqueous solutions is provided. From the adoption of the photon-counting histogram method, it is discovered that the local pH value at the vicinity of the PEO chain is higher than the bulk solution, showing that the PEO chain is positively charged. Such a situation exists with and without the presence of salt (NaCl) in the solution, presumably due to the binding of cations, such as hydronium and sodium ions. Single molecular electrophoresis experiments using fluorescence correlation spectroscopy demonstrate that the PEO chains are weakly charged with a charging extent of ~5%. In comparison to the salt-free condition, the addition of external salt (NaCl) at moderate concentrations further charges the chain. The charging causes the PEO chains to expand and a further increase in the salt concentration causes the chain to shrink, exhibiting a polyelectrolyte-like behavior, demonstrated by the hydrodynamic radii of a single PEO chain. The effect of ion identity is discovered with alkali cations, with the order of the charging capacity of Li+ < Na+ < Cs+ < K+.

Studying the physics of charged macromolecules by single molecule fluorescence spectroscopy

It is well documented that conventional methods such as dynamic light scattering have encountered difficulties in characterizing charged macromolecules and, therefore, it is desirable that new methods and techniques are introduced. With the ultra-high sensitivity, single molecule fluorescence spectroscopy has successfully lowered the detection limit considerably and enabled measurement under extreme dilution conditions-around the concentration of 10^-9M-at which the effect of inter-chain electrostatic repulsion is suppressed. Furthermore, the excellent spatial and temporal resolution as well as the capacity of molecular recognition of these methods help in obtaining rich information of charged macromolecules. This paper summarizes the applications of single molecule fluorescence spectroscopy, especially fluorescence correlation spectroscopy and photon counting histogram, in the studies on charged macromolecules in aqueous solutions and plenty of new information has been revealed on the molecular conformation, counterion distribution, and a few important governing factors. The powerfulness and effectiveness of single molecule fluorescence spectroscopy make it promising in the investigations of charged macromolecules.

Anomalous Diffusion Inside Soft Colloidal Suspensions Investigated by Variable Length Scale Fluorescence Correlation Spectroscopy

The diffusion of molecules and particles inside the aqueous suspension of soft colloids (polymer microgels) is investigated using variable length scale fluorescence correlation spectroscopy (VLS-FCS). Carbopol 940 is chosen as the model matrix system, and two factors affecting diffusion are investigated: the spatial hindrance and the diffusant-matrix interaction. By studying diffusion of molecules and particles with different sizes inside the suspension, VLS-FCS reveals the restricted motion at a short length scale, that is, in the gaps between the microgels, and normal diffusion at a larger length scale. The information on the gap's length scale is also accessed. On the other hand, by tuning the pH value, the diffusant-matrix electrostatic attraction is adjusted and the results expose a short-time fast diffusion of probe molecules inside the gaps and a long-time restricted diffusion because of trapping inside the microgels. It is proved that VLS-FCS is a powerful method, investigating anomalous diffusion at different length scales and it is a promising approach to investigate diffusion in complex soft matter systems.

Native Ion Mobility Mass Spectrometry: When Gas-Phase Ion Structures Depend on the Electrospray Charging Process

Ion mobility spectrometry (IMS) has become popular to characterize biomolecule folding. Numerous studies have shown that proteins that are folded in solution remain folded in the gas phase, whereas proteins that are unfolded in solution adopt more extended conformations in the gas phase. Here, we discuss how general this tenet is. We studied single-stranded DNAs (human telomeric cytosine-rich sequences with CCCTAA repeats), which fold into an intercalated motif (i-motif) structure in a pH-dependent manner, thanks to the formation of C-H⁺-C base pairs. As i-motif formation is favored at low ionic strength, we could investigate the ESI-IMS-MS behavior of i-motif structures at pH ~ 5.5 over a wide range of ammonium acetate concentrations (15 to 100 mM). The control experiments consisted of either the same sequence at pH ~ 7.5, wherein the sequence is unfolded, or sequence variants that cannot form i-motifs (CTCTAA repeats). The surprising results came from the control experiments. We found that the ionic strength of the solution had a greater effect on the compactness of the gas-phase structures than the solution folding state. This means that electrosprayed ions keep a memory of the charging process, which is influenced by the electrolyte concentration. We discuss these results in light of the analyte partitioning between the droplet interior and the droplet surface, which in turn influences the probability of being ionized via a charged residue-type pathway or a chain extrusion-type pathway.

Electrochemical Monitoring of the Reversible Folding of Surface-Immobilized DNA i-Motifs

Two cytosine (C) rich DNA sequences folding in i-motif upon protonation of C at low pH have been immobilized at gold electrodes to study the impact of the electrode|electrolyte interface on the stability of the noncanonical DNA secondary structure. The effects of the molecular composition and environment on the melting and folding of the structures immobilized at the gold surface have been compared to the properties of the DNA strands in solution. The DNA folding into i-motif upon protonation, both at the surface and in solution, results in a significant variation of the charge density which is monitored electrochemically through the electrostatic interactions between the DNA strand and the electroactive hexaammineruthenium(III). This method is shown to be sufficiently sensitive to distinguish hemiprotonated folded state and single strand unfolded state of i-motif. The pH of melting has been determined for both sequences in the bulk and at the gold|electrolyte interface. The results evidence a stabilizing effect of the interface on i-motif structure, whereby the pH of melting is higher for the sequences immobilized at the surface. The reversibility and precision of the electrochemical model described here allows a clear and simple characterization of DNA structures and does not require any labeling of the sequence.