Nanotemplate-directed DNA segmental thermal motion

Dubrovin, Evgeniy V.; Schächtele, Marc; Schäffer, Tilman E.

doi:10.1039/c6ra14383k

Cited by 10 publications

(20 citation statements)

References 44 publications

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“…1 ) is in fact a two-layer system with an in-plane orientation of GA molecules, comprising a lower highly ordered close-packed epitaxial lamellar sublayer (L) and an upper granular adlayer (AL). DNA adsorbed directly on the lamellar layer adopts the “template-directed” conformation with long segments electrostatically stretched along lamellae [ 29 ]. A sketch on the right of the panel in Fig.…”

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 – 27 , 29 ]. With the exclusion of the AFM imaging of the freely equilibrated DNA on the weakly charged mica surface [ 17 – 20 ], all the reported DNA images were obtained on these films and they show that the DNA adopts kinetically trapped conformations.…”

Section: Resultsmentioning

confidence: 99%

“…2a and the analysis of hexaglycylamide epitaxial structures on HOPG [31]. One-dimensional lamellae with the side-by-side molecular arrangement parallel to the crystal substrates are typical surface-grown structures formed at the first stage of adsorption of many short rod-like oligomer molecules and long (bio)polymers on various crystalline substrates such as graphite [26,29,31,36,37], mica [37][38][39][40] and silica [41]. The GA lamellar self-assembly thus renders the charge distribution in the L-sublayer one-dimensionally periodically charged.…”

Section: Highly Anisotropic Orientational Impact Of the Periodically Charged Epitaxial Lamellar Sublayermentioning

confidence: 99%

“…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%

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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: Resultsmentioning

confidence: 99%

Section: Highly Anisotropic Orientational Impact Of the Periodically Charged Epitaxial Lamellar Sublayermentioning

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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“…С и с п о л ь з о в а н и е м о б о р у д о в а н и я Ц К П "Бионаноскопия" подготовлено более 120 статей, 20 из которых ( [2][3][4][5][6][7][8][9][10][11][12] и другие) опубликованы за последние три года в журналах, входящих в рейтинговые системы Web of Science и Scopus.…”

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