Size-Exclusion Properties of Nanoporous Films Derived from Polystyrene−Poly(methylmethacrylate) Diblock Copolymers Assessed Using Direct Electrochemistry of Ferritin

This paper reports the size-exclusion properties of nanoporous films derived from polystyrene−poly(methylmethacrylate) diblock copolymers (PS-b-PMMA) for biomacromolecules. These properties were assessed by measuring cyclic voltammetry of ferritin (12 nm in diameter) adsorbed onto recessed nanodisk-array gold electrodes (RNEs) fabricated from the nanoporous films having different effective pore diameters and surface functionalities. RNEs having 20-nm-diameter nanopores modified with a poly(ethylene glycol) (PEG) layer showed the redox currents of ferritin after their immersion in a ferritin solution (5 mg/mL) for longer than 2 h. The currents originated from the direct electron transfer reaction of ferritin molecules immobilized on the underlying gold surface as a result of their penetration through the 20-nm-diameter nanopores. The PEG modification of the nanopore surface was required for the penetration of ferritin, probably because it reduced the nonspecific adsorption of ferritin to the nanopore surface. In contrast, no redox current of ferritin was observed for RNEs having PEG-modified 15-nm-diameter nanopores after their immersion in the ferritin solution for 12 h, indicating the size-exclusion of ferritin from the 15-nm nanopores. The distinct size-exclusion properties of the PS-b-PMMA-derived nanoporous films reflect their uniform diameters and shapes and will provide a means for fabricating separation membranes for biomolecules with high size-based selectivity

Complexation-Induced Control of Electron Propagation Based on Bounded Diffusion through Nanopore-Tethered Ferrocenes

This paper reports complexation-induced control of electron propagation based on bounded diffusion through ferrocene moieties that are covalently tethered onto nanopores (19 or 24 nm in diameter) derived from cylinder-forming polystyrene–poly­(methylmethacrylate) diblock copolymers. The nanopores are oriented vertically and attach to a gold surface, and thus allow a faradaic current originating from the bounded diffusion to be measured using cyclic voltammetry. Such faradaic current decreases with increasing concentration of β-cyclodextrin (β-CD) in an aqueous solution, and recovers upon addition of excess 1-adamantanol as a competitive guest to the solution. These observations indicate that electron propagation can be reversibly inhibited by the formation of an inclusion complex with the surface-tethered redox moieties. Interestingly, the decrease in faradaic current is observed at an unexpectedly low β-CD concentration (ca. 1 × 10–7 M) due to the enhanced partition of β-CD into the nanopores. These results will lead to designing highly sensitive molecular switches and electrochemical sensors based on the control of bounded diffusion by the host–guest chemistry of nanopore-tethered redox moieties

Surface Chemical Properties of Nanoscale Domains on UV-Treated Polystyrene−Poly(methyl methacrylate) Diblock Copolymer Films Studied Using Scanning Force Microscopy

This paper reports the surface chemical properties of ca. 20 nm wide domains on a UV-treated thin film of a polystyrene−poly(methyl methacrylate) diblock copolymer (PS-b-PMMA; 0.3 as the PMMA volume fraction). UV irradiation and subsequent acetic acid (AcOH) treatment were used for selectively etching horizontally aligned PMMA domains on a thin PS-b-PMMA film to obtain nanoscale trenches and ridges. The surface charge and hydrophilicity of the trenches (etched PMMA domains) and ridges (PS domains) were investigated using three approaches based on scanning force microscopy. Chemical force titration data with a COOH-terminated tip showed a prominent decrease in adhesion force from pH 3 to 4.5 due to electrostatic repulsion between negatively charged functional groups on the tip and film surface but could not clarify the difference in chemical properties between the two nanoscale domains. Friction force images in n-dodecane showed higher friction over etched PMMA and PS domains with an OH-terminated tip and a CH3-terminated tip, respectively, exhibiting higher hydrophilicity of the etched PMMA domains. In an atomic force microscopy image of a UV/AcOH-treated PS-b-PMMA film upon immersion in a ferritin solution, ∼80% of the ferritin deposited on the film was found on the PS domains. The preferential deposition of ferritin on the PS domains was probably due to the electrostatic repulsion between negatively charged ferritin and negatively charged etched PMMA surface in addition to the hydrophobic interaction between ferritin and the PS surface. These results indicated that the etched PMMA domains were more hydrophilic than the PS domains due to the presence of acidic functional groups (e.g., −COOH groups) at a higher density

Additional file 3 of Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA

Additional file 3: Table S4. – The colocalization of short cfDNA peaks with transcription factor binding sites as defined via ENCODE

Additional file 1 of Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA

Additional file 1: Figures S1-S18, Tables S1-2, S6-11, Supplementary methods, Supplementary Information. Figure S1. – Short single-stranded DNA in cell-free blood fractions. Figure S2. – The membranous fraction of the plasma does not contain cfDNA. Figure S3. – TACS-T4 scheme for the library preparation from ssDNA. Figure S4. – The size distributions of cfDNA fragments in the libraries prepared with different pretreatments reflect different forms of DNA. Figure S5. – Two major clusters of cfDNA were consistently detected with the three ssDNA-adapted library preparation methods. Figure S6. – Locations of the C3D peaks are well conserved among individuals. Figure S7. – C3D is enriched in the regulatory regions of genes. Figure S8. – The short single-stranded cfDNA detected by other studies is enriched in the open chromatin regions and TFBS. Figure S9. – The colocalization of C3D peaks with TFBS. Figure S10. – The colocalization of short single-stranded cfDNA with TFBS based on the literature. Figure S11. – The colocalization of C3Don and C3Doff reads and short single-stranded cfDNA with the open chromatin regions and TFBS based on the literature. Figure S12. – The base composition of C3D peaks was highly biased. Figure S13. – The antisense strand of G4-Seq reads well localize on the C3D peaks. Figure S14. – Colocalization analysis of the G4 structure with short single-stranded cfDNA in the literature as well as C3Don and C3Doff reads. Figure S15. – Enriched C3D reads on the G4 structure with different library preparation methods. Figure S16. – C3D peaks without antisense G4 structures are less enriched in the regulatory regions. Figure S17. – Colocalization of C3D peaks and repetitive sequences. Figure S18. – The antisense strands of G4 motifs are enriched at the 5′-end of C3D peaks. Table S1. – Summary of the library preparations and sequencing methods Table S2. – The number of reads and peaks calculated from two publicly available single-stranded cfDNA datasets Table S6. – Numbers of uniquely mapped reads and multiply mapped reads TableS7. – Blood samples used in the current study Table S8. – Oligonucleotides used in the current study Table S9. – Indexing sequences Table S10. – Sources of publicly available data used in the current study Table S11. – Files of the ENCODE datasets downloaded from the UCSC Table Browser Information S1. – Nucleotide sequence of a gene encoding codon-optimized TS2126 RNA ligase with a Strep-Tag. Information S2. – Nucleotide sequence of a gene encoding codon-optimized human aprataxin. Information S3. – Flowcharts for bioinformatic analyses

Additional file 2 of Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA

Additional file 2: Table S3. – The colocalization of C3D peaks with transcription factor binding sites as defined via ENCODE

Additional file 4 of Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA

Additional file 4: Table S5. – The colocalization of C3D peaks with transcription factor binding sites as defined using ChIP-Atlas

Nanoconfinement and Mass Transport in Silica Mesopores: the Role of Charge at the Single Molecule and Single Pore Levels

Polarization-dependent single molecule tracking was employed to simultaneously probe the translational and orientational diffusion of four perylene diimide (PDI) dyes, having different lengths and charges, within the one-dimensional (1D) nanoscale pores of surfactant-templated mesoporous silica films. The wide-field fluorescence videos acquired reveal that a significant fraction of the molecules follow 1D pathways and exhibit highly polarized fluorescence, consistent with their orientational confinement. Single-frame step size distributions prepared from these data were fit to a new model that accurately describes the distribution for 1D Fickian diffusion in the presence of finite localization precision. Average diffusion coefficients obtained from mean square displacement (DMSD) data were 20–100% larger for the two uncharged PDIs compared to the charged PDIs, reflecting electrostatic interactions of the latter with oppositely charged sites on the cationic surfactant headgroups and deprotonated silanol sites on the pore walls. Polarization-dependent tracking data show that the longest uncharged PDI was most strongly confined, while the three shorter dyes were less confined. The cationic PDI produced a wobbling angle distribution that was broader than the others, suggesting it explores more of the pore diameter. The results provide new knowledge on the mechanisms by which the dye molecules interact with the pore-filling medium and the pore surfaces, helping to elucidate the factors controlling the rate of mass transport

Molecular Length Dependence of Single Molecule Wobbling within Surfactant- and Solvent-Filled Silica Mesopores

The confined orientational motions of fluorescent dye molecules diffusing along one dimension (1D) within individual silica mesopores are investigated by simultaneous single molecule tracking (SMT) and single molecule emission dichroism (SMED) methods. Four perylene diimide (PDI) dyes of different lengths are employed as the probe species. Wobbling angles exhibited by the individual molecules are measured within cetyltrimethylammonium bromide-filled mesopores. The results show a clear dependence on probe molecule length, attributable to confinement of the molecular motions to small cavities within the surfactant- and solvent-filled mesopores. These results are used to obtain quantitative estimates of the accessible cavity diameters. Histograms of these data reveal a broad distribution of cavity sizes. The average cavity diameters are shown to be largely independent of molecular length and yield a global mean value of 1.06 ± 0.03 nm, corresponding to ∼1/3 the physical diameter of the silica mesopores, as estimated from X-ray scattering data. The difference in physical and accessible pore diameters is attributed to confinement of PDI orientational motions by nanostructuring of the solvent/surfactant medium filling the pores. It is proposed that the PDI molecules are confined to the most hydrophobic regions of the surfactant micelles and that formation of a water-rich solvent layer at the silica/surfactant boundary may also contribute. These results will facilitate a deeper understanding of solute–solvent interactions in nanoconfined systems and are relevant to applications of mesoporous silica materials in solution-phase catalysis and chemical separations

Linker-Based Control of Electron Propagation through Ferrocene Moieties Covalently Anchored onto Insulator-Based Nanopores Derived from a Polystyrene–Poly(methylmethacrylate) Diblock Copolymer

This paper reports the effects of linker length on electron propagation through ferrocene moieties covalently anchored onto insulator-based cylindrical nanopores derived from a cylinder-forming polystyrene–poly­(methylmethacrylate) diblock copolymer. These nanopores (24 nm in diameter, 30 nm long) aligned perpendicular to an underlying gold electrode were modified via esterification of their surface COOH groups with OH-terminated ferrocene derivatives having different alkyl linkers (FcCO­(CH₂)_<i>n</i>OH; <i>n</i> = 2, 5, 15). Cyclic voltammograms were measured in 0.1 M NaBF₄ at different scan rates to assess the efficiency of electron propagation through the ferrocene moieties. The redox peaks of the anchored ferrocenes were observed at nanoporous films decorated with FcCO­(CH₂)₁₅OH and FcCO­(CH₂)₅OH, but not at those with FcCO­(CH₂)₂OH. Importantly, the higher electron propagation efficiency was observed in the use of the longer linker, as shown by the apparent diffusion coefficients (ca. 10^–12 cm²/s for <i>n</i> = 15; ca. 10^–13 cm²/s for <i>n</i> = 5; no electron propagation for <i>n</i> = 2). The observed electron propagation resulted from electron hopping across relatively large spacing that was controlled by the motion of anchored redox sites (bounded diffusion). The longer linker led to the larger physical displacement range of anchored ferrocene moieties, facilitating the approach of the adjacent ferrocene moieties within a distance required for electron self-exchange reaction. The linker-based control of redox-involved electron propagation on nanostructured, insulating surfaces will provide a means for designing novel molecular electronics and electrochemical sensors