Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy

Suzuki, Yuki; Higuchi, Yuji; Hizume, Kohji; Yokokawa, Miwa; Yoshimura, Shige H.; Yoshikawa, Kenichi; Takeyasu, Kunio

doi:10.1016/j.ultramic.2010.02.032

Cited by 57 publications

(67 citation statements)

References 49 publications

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“…This behavior is more prominent with molecules imaged with Ni 2+ concentrations of 5 mM or lower. Although a direct correlation with surface distributions of Ni 2+ would be purely speculative without further in depth studies, the results together with previous findings on the distribution of Ni 2+ ions [30,40] suggest that positively charged Ni 2+ domains act as anchor points for the negatively charged DNA chains, with the interstitial regions governed by weak Mg 2+ associations, allowing for the desired mobility.…”

Section: Identification Of Discrete Surface Anchor Pointsmentioning

confidence: 64%

“…A previous study has attempted the direct superposition of sequential images aligned to immobile parts of the molecule [37] or to a reference elsewhere in the frame [38]. Deriving additional details by analysis of vectorized molecules has also been undertaken through hand-tracing methods [39] in order to examine quantities such as elastic bending energies [40] and the influence of the AFM probe [11]. However, such studies lack detail due to the crude alignment and vector derivation methodologies, which yield mobility analyses based on single point mapping of center-of-mass or chain termini only.…”

Section: Quantifying the Mobility Of Dna Moleculesmentioning

confidence: 99%

“…It is reasonable to assume that the density of surface-associated Ni 2+ ions increases with increasing Ni 2+ concentration during incubation. It has previously been demonstrated that the distribution of Ni 2+ on the surface is highly non-uniform [40] and lacks homogeneity [30]. However, it may be possible to gain further insight into the Ni 2+ /Mg 2+ -governed surface interactions by identifying regions of specific surface association by examining the motion of the DNA chains.…”

Section: Identification Of Discrete Surface Anchor Pointsmentioning

confidence: 99%

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Tuning the translational freedom of DNA for high speed AFM

et al. 2015

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Direct observation is arguably the preferred way to investigate the interactions between two molecular complexes. With the development of high speed atomic force microscopy (AFM), it is becoming possible to observe directly DNA-protein interactions with relevant spatial and temporal resolutions. These interactions are of central importance to biology, bionanotechnology, and functional biologically inspired materials. As in all microscopy studies, sample preparation plays a central role in AFM observation and minimal perturbation of the sample is desired. Here, we demonstrate the ability to tune the interactions between DNA molecules and the surface to create an association strong enough to enable high-resolution AFM imaging while also providing sufficient translational freedom to allow the relevant protein-DNA interactions to take place. Furthermore, we describe a quantitative method for measuring DNA mobility, while also determining the individual forces contributing to DNA movement. We found that for a weak surface association, a significant contribution to the movement arises from the interaction of the AFM tip with the DNA. In combination, these methods enable the tuning of the surface translational freedom of DNA molecules to allow the direct study of a wide range of nucleo-protein interactions by high speed atomic force microscopy.

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Section: Identification Of Discrete Surface Anchor Pointsmentioning

confidence: 64%

Section: Quantifying the Mobility Of Dna Moleculesmentioning

confidence: 99%

Section: Identification Of Discrete Surface Anchor Pointsmentioning

confidence: 99%

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Tuning the translational freedom of DNA for high speed AFM

et al. 2015

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“…Regarding DNA-protein interactions, there are a wide range of subjects to be studied by high-speed AFM imaging but only a few studies have thus far been performed; reaction by methyltransferase restriction enzymes [84,104], unwrapping of DAN-histone complex [108], and reaction by DNA base-excision repair enzyme [103]. Synthetic DNA nanodevices are also interesting targets of dynamic AFM imaging.…”

Section: Dna-binding Proteins and Synthetic Dna Devicesmentioning

confidence: 99%

High-speed atomic force microscopy coming of age

Ando¹

2012

Nanotechnology

322

246

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High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed.

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“…Recently developed fast-scanning AFM has the ability to investigate DNA and nucleosome dynamics in solution. Single-molecule fluorescence resonance energy transfer (FRET) techniques have detected a local dissociation of DNA from the histone core particle that occurs on the sub-second time scale [32]. Using a Brownian dynamics simulation, the interaction of DNA with histone was numerically studied [33].…”

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confidence: 99%

Study of the interaction of DNA and histones by spin-stretching and droplet evaporation

et al. 2011

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Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, DNA-histone complexes are stretched on a hydrophobic polymethyl methacrylate (PMMA) surface and observed directly. We have developed a new method to stretch single DNA-histone complexes, termed spin-stretching. The results show that the histones markedly enhance DNA binding to the PMMA surface. DNA winds around the histones and therefore decreases in length. The number of histones that bind to each DNA molecule is found to correlate with the histone concentration. The combed DNA-histone complexes are found to depend on two factors: the binding force on the surface and the centrifugal force at its local position. Na + ions should compete with histones for binding to DNA; however, the observed competitive binding effect of Na + ions at low concentrations was negligible. Molecular combing is a novel approach for stretching DNA molecules. In recent years, many combing methods have been developed for stretching DNA. Such methods include dynamic molecular combing (meniscus moving on a coverslip [14]), spin-stretching [8,9], the evaporation of small droplets of DNA solutions [15,16], the stretching of DNA with a cover slip [17], the mechanical movement of a *Corresponding author (email: 51888lyy@sina.com) meniscus [18], droplet motion driven by a nitrogen gas flow [19], the precise control of the meniscus motion [20], the ordered stretching of DNA between micro fabricated polystyrene lines [21], the moving droplet method [22] and aligning DNA molecules on a SiO 2 surface using a diamond-like carbon (DLC) thin film [23]. Combined with other techniques, the applications of the molecular combing method can be widened to include positioning genes on chromosomes [14], the genomic studies of DNA replication [24], the observation of transcription on a single combed DNA [25], the study of the interaction between DNA and enzymes [26,27] and the self-organized DNA network between two cover slips [28].Eukaryotic genes do not exist as naked DNA molecules in the nucleus of a cell. Instead, they combine with particular proteins, especially the basic proteins called histones, to form a substance known as chromatin [29]. Chromatin controls gene activity and the inheritance of traits. The fun-

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Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy

Cited by 57 publications

References 49 publications

Tuning the translational freedom of DNA for high speed AFM

Tuning the translational freedom of DNA for high speed AFM

High-speed atomic force microscopy coming of age

Study of the interaction of DNA and histones by spin-stretching and droplet evaporation

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