skip to main content


The NSF Public Access Repository (NSF-PAR) system and access will be unavailable from 10:00 PM ET on Friday, December 8 until 2:00 AM ET on Saturday, December 9 due to maintenance. We apologize for the inconvenience.

Title: Measuring interactions of DNA with nanoporous protein crystals by atomic force microscopy
Crosslinked porous protein crystals are a new biomaterial that can be engineered to encapsulate, stabilize, and organize guest molecules, nanoparticles, and biological moieties. In this study, for the first time, the combined interactions of DNA strands with porous protein crystals are quantitatively measured by high-resolution atomic force microscopy (AFM) and chemical force microscopy. The surface structure of protein crystals with unusually large pores was observed in liquid via high-resolution AFM. Force–distance ( F – D ) curves were also obtained using AFM tips modified to present or capture DNA. The modification of AFM tips allowed the tips to covalently bind DNA that was pre-loaded in the protein crystal nanopores. The modified tips enabled the interactions of DNA molecules with protein crystals to be quantitatively studied while revealing the morphology of the buffer-immersed protein crystal surface in detail, thereby preserving the structure and properties of protein crystals that could be disrupted or destroyed by drying. The hexagonal space group was manifest at the crystal surface, as were the strong interactions between DNA and the porous protein crystals in question. In sum, this study furthered our understanding of how a new protein-based biomaterial can be used to bind guest DNA assemblies.  more » « less
Award ID(s):
Author(s) / Creator(s):
; ; ; ;
Date Published:
Journal Name:
Page Range / eLocation ID:
10871 to 10881
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Recent developments such as multi-harmonic Atomic Force Microscopy (AFM) techniques have enabled fast, quantitative mapping of nanomechanical properties of living cells. Due to their high spatiotemporal resolution, these methods provide new insights into changes of mechanical properties of subcellular structures due to disease or drug response. Here, we propose three new improvements to significantly improve the resolution, identification, and mechanical property quantification of sub-cellular and sub-nuclear structures using multi-harmonic AFM on living cells. First, microcantilever tips are streamlined using long-carbon tips to minimize long-range hydrodynamic interactions with the cell surface, to enhance the spatial resolution of nanomechanical maps and minimize hydrodynamic artifacts. Second, simultaneous Spinning Disk Confocal Microscopy (SDC) with live-cell fluorescent markers enables the unambiguous correlation between observed heterogeneities in nanomechanical maps with subcellular structures. Third, computational approaches are then used to estimate the mechanical properties of sub-nuclear structures. Results are demonstrated on living NIH 3T3 fibroblasts and breast cancer MDA-MB-231 cells, where properties of nucleoli, a deep intracellular structure, were assessed. The integrated approach opens the door to study the mechanobiology of sub-cellular structures during disease or drug response.

    more » « less
  2. Atomic Force Microscopy (AFM) is widely used for topographic imaging of DNA and protein-DNA complexes in ambient conditions with nanometer resolution. In AFM studies of protein-DNA complexes, identifying the protein’s location on the DNA substrate is one of the major goals. Such studies require distinguishing between the DNA ends, which can be accomplished by end-specific labeling of the DNA substrate. We selected as labels three-way DNA junctions (3WJ) assembled from synthetic DNA oligonucleotides with two arms of 39–40 bp each. The third arm has a three-nucleotide overhang, GCT, which is paired with the sticky end of the DNA substrate generated by the SapI enzyme. Ligation of the 3WJ results in the formation of a Y-type structure at the end of the linear DNA mole cule, which is routinely identified in the AFM images. The yield of labeling is 69%. The relative orientation of arms in the Y-end varies, such dynamics were directly visualized with time-lapse AFM studies using high-speed AFM (HS-AFM). This labeling approach was applied to the characterization of the nucleosome arrays assembled on different DNA templates. HS-AFM experiments revealed a high dynamic of nucleosomes resulting in a spontaneous unraveling followed by disassembly of nucleosomes. 
    more » « less
  3. Abstract Bond breaking and forming are essential components of chemical reactions. Recently, the structure and formation of covalent bonds in single molecules have been studied by non-contact atomic force microscopy (AFM). Here, we report the details of a single dative bond breaking process using non-contact AFM. The dative bond between carbon monoxide and ferrous phthalocyanine was ruptured via mechanical forces applied by atomic force microscope tips; the process was quantitatively measured and characterized both experimentally and via quantum-based simulations. Our results show that the bond can be ruptured either by applying an attractive force of ~150 pN or by a repulsive force of ~220 pN with a significant contribution of shear forces, accompanied by changes of the spin state of the system. Our combined experimental and computational studies provide a deeper understanding of the chemical bond breaking process. 
    more » « less
  4. Abstract

    Variations in cell wall composition and biomechanical properties can contribute to the cellular plasticity required during complex processes such as polarized growth and elongation in microbial cells. This study utilizes atomic force microscopy (AFM) to map the cell surface topography of fission yeast,Schizosaccharomyces pombe, at the pole regions and to characterize the biophysical properties within these regions under physiological, hydrated conditions. High‐resolution images acquired from AFM topographic scanning reveal decreased surface roughness at the cell poles. Force extension curves acquired by nanoindentation probing with AFM cantilever tips under low applied force revealed increased cell wall deformation and decreased cellular stiffness (cellular spring constant) at cell poles (17 ± 4 mN/m) relative to the main body of the cell that is not undergoing growth and expansion (44 ± 10 mN/m). These findings suggest that the increased deformation and decreased stiffness at regions of polarized growth at fission yeast cell poles provide the plasticity necessary for cellular extension. This study provides a direct biophysical characterization of theS. pombecell surface by AFM, and it provides a foundation for future investigation of how the surface topography and local nanomechanical properties vary during different cellular processes.

    more » « less
  5. Membrane separations are simple to operate, scalable, versatile, and energy efficient, but their broader use is curtailed by fouling or performance decline due to feed component depositing on the membrane surface. Surface functionalization with groups such as zwitterions can mitigate the adsorption of organic compounds, thus limiting fouling. This can be achieved by using surface-segregating copolymer additives during membrane manufacture, but there is a need for better understanding of how the polymer structure and architecture affect the effectiveness of these additives in improving membrane performance. In this study, we aim to explore the impact of the architecture of zwitterionic copolymer additives for polyvinylidene fluoride (PVDF)-based membranes in fouling mitigation and ionic strength response. We prepared membranes from blends of PVDF with zwitterionic (ZI) copolymers with two different architectures, random and comb-shaped. As the random copolymer, we used poly(methyl methacrylate- random- sulfobetaine-2-vinyl pyridine) (PMMA- r -SB2VP) synthesized by free radical polymerization. The comb-shaped copolymer was synthesized by grafting SB2VP side-chains from a PVDF backbone by controlled radical polymerization. Membranes were fabricated from PVDF-copolymer blends containing up to 5 wt% ZI copolymer. Compared to the additive-free PVDF membrane, water permeance increased five-fold with 5 wt% addition of either copolymer. The comb copolymer additive led to better resistance to fouling by a saline oil-in-water emulsion and to simulated protein adsorption in Atomic Force Microscopy (AFM) force measurements. The additive architecture had a significant influence on how membranes respond to changes in feed salinity, which is known to affect intra- and inter-molecular interactions in zwitterionic polymers. The random copolymer containing membrane showed a small and mostly reversible decrease in its permeance with salinity. In contrast, the comb copolymer-containing membrane underwent a conformational reorganization in saline solutions that leads to an irreversible permeance decrease, increased zwitterionic group content on the membrane surface, and smoother surface topography. The higher mobility of the zwitterionic groups in the comb-shaped architecture facilitates reorganization of the zwitterionic side-chains in response to ionic strength. Overall, this study establishes a new approach for developing highly fouling resistant membranes and defines how the architecture of a zwitterionic copolymer additive impacts the ionic strength response and fouling resistance of the membrane. 
    more » « less