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Results for “Nanopore and AFM”

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9 recordsLinked to original sources

PubMed2026

Seeing and Feeling DNA Methylation: Single-Molecule Biophysics Meets Machine Learning.

DNA methylation at 5-methylcytosine (5mC) is crucial for embryonic development and cellular function, while aberrant patterns strongly drive disease onset and progression. Its reversible nature offers substantial therapeutic potential, emphasizing the need for precise, context-specific genome wide 5mC mapping. Conventional techniques such as bisulfite sequencing and ensemble biosensor assays are hindered by DNA degradation, amplification bias, high cost, and inability to resolve single-molecule structural and mechanical effects of methylation. This review examines advances in single-molecule biophysical methods (nanopore sensing, smFRET, optical/magnetic tweezers, and AFM) that provide direct, label-free/minimally invasive 5mC detection, along with quantitative insights into DNA conformation, mechanics, and protein-DNA interactions. These techniques complement traditional methylome mapping by linking genomic localization to molecular mechanisms. Emerging machine-learning approaches are revolutionizing analysis, particularly in nanopore sensing, while promising applications in smFRET, tweezers, and AFM address throughput and reproducibility challenges. Their convergence promises scalable, high-resolution epigenetic profiling, advancing precision epigenomics toward clinical application.

DNA Methylation↗

PubMed2006

Deposition of DNA-functionalized gold nanospheres into nanoporous surfaces.

We report the deposition of DNA-conjugated gold nanospheres into arrays of surface nanopores obtained from hexagonally ordered thin polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) diblock copolymer films on silicon. The deposition occurs spontaneously from aqueous solution and is driven by either electrostatic interactions or specific DNA hybridization events between the DNA nanospheres and the surface nanopores. To mitigate this spontaneous deposition, we have chemically modified the nanopores with either positively charged aminosilanes or oligonucleotide probe sequences. The deposition of DNA nanospheres into the surface nanopores was characterized by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). We have observed preferential immobilization of individual DNA nanospheres within the nanopores, based on the size matching between the two entities. The inclusion density and selectivity of DNA nanosphere deposition into the surface nanopores was found to depend predominantly on the methods through which the nanoporous surfaces were prepared and chemically functionalized.

DNA↗

PubMed2002

Electrochemical imaging of diffusion through single nanoscale pores.

A combined scanning electrochemical-atomic force microscope (SECM-AFM) has been used to probe the diffusional transport of target electroactive solutes in isolated nanopores of a track-etched membrane. A polycarbonate membrane (100-nm-diam pore size) hydrated with an electrolyte solution, containing a redox-active probe molecule, such as IrCl6(3-) or Fe(phen)3(2+), functions as the model membrane system. The use of a mobile Pt-coated AFM probe enables individual solution-filled pores to be topographically identified. Analysis of the corresponding current images for the diffusion-limited oxidation of the redox mediator indicates that solution is largely confined to pores in the membrane. Moreover, the tip collector current response provides information on diffusion of the mediator through the pore. Force-distance tip approach and retract measurements allow the radius of contact between the electrochemical-AFM tip and solution confined within a pore at the point of pull-off to be estimated.

Journal Article↗

PubMed2006

Self-assembly and liquid-crystalline properties of 5-fluoroalkylporphyrins.

We report three crystal structures of a synthetic 5-fluoroalkylporphyrin molecule that was programmed for self-assembly. All the X-ray structures of zincated and free-base porphyrins Zn2 b, Zn5 a, and 2 b revealed rigorous pi-pi stacking and extremely hydrophobic interactions. Other the other hand, the strong aggregation of 5-fluoroalkylporphyrins in solution was also found. Interestingly, the regular nanopore formation of the 5-fluoroalkylporphyrin was visualized by atomic force microscopy (AFM). Importantly, the 5-fluoroalkylporphyrins possess liquid-crystalline properties that were confirmed by using a combination of differential scanning calorimetry (DSC) and polarizing optical microscopy (POM) techniques. By comparison, the self-assembly of non-fluorine-containing porphyrins with similar structure showed much lower aggregation ability, as investigated by NMR techniques. Additionally, no birefringent mesophase was observed for the non-fluorine-containing porphyrin.

Crystallography, X-Ray↗

PubMed2005

A novel atomic force microscope operating in liquid for in situ investigation of electrochemical preparation of porous alumina.

A novel atomic force microscope (AFM) operating in liquid is described in this article. The specially designed AFM probe involves a tip attached to a cantilever, a tip holder, and a circular Plexiglas window. When the probe dives into the fluid, a circular meniscus is established around the Plexiglas window, preventing the tip from being affected or destroyed by surface tension of the liquid. In this setup, the whole scanning probe and the sample can completely dive into fluid. Meanwhile, the probe tip scans over the sample surface when the instrument works. These advantages enable the instrument to scan comparatively large or heavy samples with a high speed. The highest scan rate is about 30 lines/s or 14 s for a 400 x 400-pixel, 3 x 3 microm image. Using the new AFM, we carry out in-situ investigation of the formation processes of porous alumina during electrochemical anodic oxidation. A lead ring and an aluminum foil serve as cathode and anode, respectively. They are entirely immersed in the bath electrolyte, which is oxalic acid solution. During anodic oxidation, the AFM images of the sample surface are successively acquired without elevating the sample out of the solution. Experiments reveal that electrochemical reactions take place soon after the power supply is switched on, and with the progression of anodization, nanostructures of porous alumina gradually occur on the aluminum substrate, finally yielding ordered arrays of nanopores. As a typical example of applications, the results of this work show that the new AFM is an ideal and powerful tool for in-situ observation and study of materials or samples in aqueous solutions.

Aluminum Oxide↗

PubMed2006

Atomic force microscopy study of different effects of natural and semisynthetic beta-lactam on the cell envelope of Escherichia coli.

The effects of native and semisynthetic beta-lactam on the surface of E. coli cells were investigated using tapping mode atomic force microscopy (AFM). These studies were done on both single cell and cell colonies. This allowed us to achieve a complete understanding of the effects, since previous related AFM analysis was only performed on single cells. Our results indicated that although amoxycillin and penicillin could both induce nanoporous damage to the envelope of E. coli, the distribution of the pores was different: those induced by penicillin were randomly distributed on the cell surface, while those induced by amoxycillin were far more numerous and mainly on the two ends of the cell. These findings could explain why the effect of amoxycillin is stronger than that of native penicillin. Ofloxacin was used as a control due to its inactive membrane, and no cell wall damages were observed. Our results demonstrate that AFM is a useful tool in discerning and verifying antibiotic mechanisms and can be helpful to explain the relationship between chemical structure and the function of antibiotics.

Anti-Bacterial Agents↗

PubMed2004

Nanopore formation by self-assembly of the model genetically engineered elastin-like polymer [(VPGVG)2(VPGEG)(VPGVG)2]15.

The self-assembly characteristics of the model genetically engineered elastin-like polymer [(VPGVG)2(VPGEG)(VPGVG)2]15 have been studied in this work. An AFM study of the topology of polymer films deposited from acid and basic solutions on a hydrophobic silicon substrate has been carried out. Under acidic conditions, polymer deposition results in a flat surface with no particular topological features. However, from basic solutions, polymer deposition clearly shows an aperiodic pattern of nanopores ( approximately 70 nm width and separated about 150 nm). This dramatic dependence of film topology on pH is explained in terms of the different polarity of the free gamma-carboxyl group of the glutamic acid. In the carboxylate form, this moiety shows a markedly higher polarity than the rest of the polymer domains and the substrate itself. Under these conditions, the charged carboxylates impede hydrophobic contact with their surroundings, which is the predominant assembly pathway for this type of polymer. The charged domains, along with their hydration sphere, are then segregated from the hydrophobic surroundings giving rise to nanopores.

Biomimetic Materials↗

PubMed2003

Nanoporous materials with spherical and gyroid cavities created by quantitative etching of polydimethylsiloxane in polystyrene-polydimethylsiloxane block copolymers.

A new method for quantitative etching of the poly(dimethylsiloxane) block in polystyrene-poly(dimethylsiloxane) (PS-PDMS) block copolymers is reported. Reacting the block copolymer with anhydrous hydrogen fluoride renders a nanoporous material (NPM) with the remaining glassy PS maintaining the original bulk morphology. 1H NMR, mass difference, size exclusion chromatography, and X-ray photoelectron spectroscopy were used to characterize the materials before and after etching. NPMs containing spherical and gyroid cavities were prepared, as ascertained by small-angle X-ray scattering. This is the first report on block copolymer-based NPM films of millimeter thickness containing secluded spherical holes. Surface images by AFM and SEM are consistent with the SAXS findings.

Journal Article↗

PubMed2005

Nanowell-array surfaces prepared by argon plasma etching through a nanopore alumina mask.

A method for preparing a glass surface containing an ordered array of nanowells is described. These nanowell arrays are prepared via a plasma-etch method using a nanopore alumina film as the etch mask. A replica of the pore structure of the alumina mask is etched into the glass. We demonstrate that chemical information in the form of negatively charged latex nanoparticles can be selectively stored within these nanowells and not indiscriminately deposited on the surface surrounding the nanowells. To accomplish this, the chemistry of the glass surfaces within these nanowells (walls and bottoms) must be different from the chemistry of the surface surrounding the nanowells. Two different procedures were developed to make the inside vs. surrounding surface chemistries different. Atomic force microscopy (AFM) was used to image the nanowells and, via friction-force measurements, to prove that the inner nanowell surfaces can be made chemically different from the surface surrounding the nanowells.

Aluminum Oxide↗