Quantitative Analysis of the Transcription Factor AP2 Binding to DNA by Atomic Force Microscopy

Nettikadan, Saju; Tokumasu, Fuyuki

doi:10.1006/bbrc.1996.1409

Cited by 36 publications

(36 citation statements)

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“…The scanning rate was set at 2-3 Hz, and images were captured in 512 512 pixel format. To measure the width and length of the structures in AFM images, the tip effect was removed by using the apparent size of nucleosomes as a reference (Nettikadan et al, 1996). In this study, DNA, which has the width of 2 nm, was imaged and used as a standard.…”

Section: Afm Imaging Of α Actinin-4 On the Mica Surfacementioning

confidence: 99%

“…The imaging mode has been used to visualize various biological structures and processes (reviewed in Hirano et al, 2008). Nano-scale structures and the dynamics of cells, cytoskeletons (Henderson et al, 1992;Hofmann et al, 1997;Haga et al, 2000;de Jager et al, 2001;Yoshimura et al, 2003;Mucke et al, 2004), DNA-protein interactions (Nettikadan et al, 1996;de Jager et al, 2001;Schnitzler et al, 2001;Yoshimura et al, 2002;Rivetti …”

Section: Introductionmentioning

confidence: 99%

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Single-molecule anatomy by atomic force microscopy and recognition imaging

Takahashi

Hizume

Kumeta

et al. 2009

Archives of Histology and Cytology

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vinculin-actinin adaptor-interaction, we investigated their structural properties using the recognition mode of AFM. For this purpose, we attached an anti-Actinin-4 monoclonal antibody to the AFM cantilever and performed recognition imaging against Actinin-4. We finally succeeded in mapping the epitopic region within the Actinin-4 molecule. Thus, recognition imaging using an antibody coupled AFM cantilever will be useful for singlemolecule anatomy of biological macromolecules and structures. IntroductionAtomic force microscopy (AFM) can be operated in two different modes; imaging and force modes. The imaging mode has been used to visualize various biological structures and processes (reviewed in Hirano et al., 2008). Nano-scale structures and the dynamics of cells, cytoskeletons (Henderson et al., 1992; Hofmann et al., 1997; Haga et al., 2000; de Jager et al., 2001;Yoshimura et al., 2003;Mucke et al., 2004), DNA-protein interactions (Nettikadan et al., 1996; de Jager et al., 2001;Schnitzler et al., 2001;Yoshimura et al., 2002;Rivetti

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Section: Afm Imaging Of α Actinin-4 On the Mica Surfacementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Single-molecule anatomy by atomic force microscopy and recognition imaging

Takahashi

Hizume

Kumeta

et al. 2009

Archives of Histology and Cytology

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“…An AFM procedure to determine the degree of multimerization of DNA-binding proteins was described previously (Nettikadan et al 1996). In brief, the relationship between the experimental width of the sample in the image, W, the radius of the curvature of the tip, Rc, and the radius of the curvature of the sample, Rm, is given by the equation W 4(Rc´Rm) 1/2 (eqn 1).…”

Section: Estimation Of Protein Sizesmentioning

confidence: 99%

Long range interaction of cis‐DNA elements mediated by architectural transcription factor Bach1

et al. 1999

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Background: A central question in vertebrate transcriptional regulation is how cis-regulatory modules, including enhancers, silencers and promoters, communicate with each other over long distances to mandate proper gene expression. In order to address this question we analysed protein/DNA interactions in the human b-globin locus control region (LCR). One of the many proteins that are potentially implicated in LCR function is Bach1. Bach1 possesses a basic leucine zipper (bZip) domain, as well as a BTB/POZ domain that has been shown to be involved in the regulation of chromatin structure. Bach1 forms heterodimers with small Maf proteins through its leucine zipper and binds to Maf recognition elements (MARE).

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“…However, the EM photographs do not show directly three-dimensional structures of the pitch (8,9), and the three-dimensional structures presented are simply a model based on a reconstruction analysis (10,11). In contrast, atomic force microscopy (AFM) is a powerful tool for visualizing biomaterials as it can be employed not only in vacuo but also in air and in aqueous solutions (12)(13)(14)(15)(16)(17). Molecular resolution is obtainable without special fixation or labeling, although AFM is a still developing methodology.…”

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confidence: 93%