PEGylated surfaces for the study of DNA–protein interactions by atomic force microscopy

Akpinar, Bernice; Haynes, Philip J.; Bell, Nicholas A. W.; Brunner, Katharina; Pyne, Alice L. B.; Hoogenboom, Bart W.

doi:10.1039/c9nr07104k

Cited by 18 publications

(21 citation statements)

References 46 publications

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“…[ 22 ]. Direct information on the (different) structure of the poly-L-lysine functionalized mica surface is provided by the recent high-resolution AFM measurements, which resolve the individual poly-L-lysine chains loosely packed in monolayer in a non-lamellar way [ 25 ].…”

Section: Resultsmentioning

confidence: 99%

“…The same issues are addressed to other seemingly uniform highly positively charged monomolecular films used to facilitate the DNA adsorption on the atomically flat mica and HOPG [21][22][23][24][25][26][27]29]. With the exclusion of the AFM imaging of the freely equilibrated DNA on the weakly charged mica surface [17][18][19][20], all the reported DNA images were obtained on these films and they show that the DNA adopts kinetically trapped conformations.…”

Section: Lateral Perturbative Impact In the General Case Of The Coarse-grained Surface Charge Distributionmentioning

confidence: 98%

“…Surprisingly, the validity of this assumption has never been discussed. In the microscopic analysis of surface DNA conformations observed by atomic force microscopy (AFM) for the last two decades, mainly large-scale behavior insensitive to structural peculiarities at the nanometer scale has been actively studied for DNA adsorbed on different surfaces such as mica [17][18][19][20][21], positively charged films on mica [21][22][23][24][25] and on highly oriented pyrolytic graphite (HOPG) [26][27][28][29]. Using end-to-end distance measurements, the DNA surface conformations were classified as the freely equilibrated (they are smooth at a nanometer scale and well described by the WLC model [30]) and much lesser smooth more compact kinetically trapped so-called projected DNA conformations [17].…”

Section: Introductionmentioning

confidence: 99%

“…Using end-to-end distance measurements, the DNA surface conformations were classified as the freely equilibrated (they are smooth at a nanometer scale and well described by the WLC model [30]) and much lesser smooth more compact kinetically trapped so-called projected DNA conformations [17]. The "projected" conformations were believed (in fact without any justification other than the large DNA bending stiffness) to follow the same WLC model as freely equilibrated conformations (corrected to fit the lower (2D) dimensionality) although many highly bent sites were observed in AFM images [22][23][24][25][26][27][28]. This striking contradiction with the expected WLC low-scale behavior was not recognized.…”

Section: Introductionmentioning

confidence: 99%

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Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

et al. 2021

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Highlights DNA kinking is inevitable for the highly anisotropic 1D–1D electrostatic interaction with the one-dimensionally periodically charged surface. The double helical structure of the DNA kinetically trapped on positively charged monomolecular films comprising the lamellar templates is strongly laterally stressed and extremely perturbed at the nanometer scale. The DNA kinetic trapping is not a smooth 3D—> 2D conformational flattening but is a complex nonlinear in-plane mechanical response (bending, tensile and unzipping) driven by the physics beyond the scope of the applicability of the linear worm-like chain approximation. Abstract Up to now, the DNA molecule adsorbed on a surface was believed to always preserve its native structure. This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been elucidated. High-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and supercoiled. We argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress (> 30 pNnm) inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface charges. In addition, the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of helicity. The previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale bending. The sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force mechanics. The results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially nonlinear. The underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.

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Section: Resultsmentioning

confidence: 99%

Section: Lateral Perturbative Impact In the General Case Of The Coarse-grained Surface Charge Distributionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

et al. 2021

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“…Me thods: Mica and DNA are both negatively charged at a neutral pH in aqueous solution. There are a number of methods used to facilitate the adsorption of DNA to the mica surface [9,24,[29][30][31]. The following sections describe three methods to facilitate DNA and DNA-protein adsorption on mica, which are appropriate for imaging DNA in liquid (see Note Note 5).…”

Section: Me Thodsmentioning

confidence: 99%

Atomic Force Microscopy of DNA and DNA-Protein Interactions v1

Haynes¹

2020

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Atomic force microscopy (AFM) is a microscopy technique that uses a sharp probe to trace a sample surface at nanometre resolution. For biological applications, one of its key advantages is its ability to visualize substructure of single molecules and molecular complexes in an aqueous environment. Here, we describe the application of AFM to determine the secondary and tertiary structure of surface-bound DNA, and it's interactions with proteins. Me thods:Me thods: Mica and DNA are both negatively charged at a neutral pH in aqueous solution. There are a number of methods used to facilitate the adsorption of DNA to the mica surface [9,24,[29][30][31]. The following sections describe three methods to facilitate DNA and DNA-protein adsorption on mica, which are appropriate for imaging DNA in liquid (see Note Note 5).Mica substrates can be attached to a steel disc to be mounted on magnetic sample holders as common in AFM instruments (see Note Note 6).

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Envision and Appraisal of Biomolecules and Their Interactions through Scanning Probe Microscopy

et al. 2023

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Scanning probe microscopy (SPM) has gifted a novel eye to envision nanotechnology and nanoscience. The SPM technique involves a sharp probe that moves over the sample surface and leads to produce signals, which facilitates a deep understanding of the structural, electronic, vibrational, optical, magnetic, (bio) chemical, and mechanical properties of the material. Scanning tunneling microscopy (STM) and atomic force microscopy (AFM) measure various kinds of physical properties such as electric current, force, and capacitance. Moreover, AFM shows a prominent feature over STM that it accepts insulating surfaces and can work under physiological conditions, making it feasible to study biological molecules. Herein, the SPM approach toward biomolecule imaging and appraising different physiological processes with molecular resolution is highlighted. The review raises awareness regarding current obstacles in biological sample preparation and possible ways to conquer these difficulties. Subsequently, the recent applications of STM and AFM on various biomolecules with representative examples like DNA, protein, and carbohydrates are discussed. The conductance measurement studies of the biological samples emphasize applications like drug delivery, biosensors, molecular electronics, and spintronics fields. This is followed by an outlook of future perspectives making a pavement toward the basic science and applied field of biomolecules using SPM technology.

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PEGylated surfaces for the study of DNA–protein interactions by atomic force microscopy

Abstract: Co-block polymer surfaces provide a platform on which to visualize DNA–protein interactions by atomic force microscopy at nanometre resolution.

Cited by 18 publications

References 46 publications

Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

Atomic Force Microscopy of DNA and DNA-Protein Interactions v1

Envision and Appraisal of Biomolecules and Their Interactions through Scanning Probe Microscopy

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