Applications for atomic force microscopy of DNA

Hansma, Helen G.; Laney, Daniel E.; Bezanilla, Magdalena; Sinsheimer, Robert L.; Hansma, Paul K.

doi:10.1016/s0006-3495(95)80343-7

Cited by 250 publications

(174 citation statements)

References 29 publications

(34 reference statements)

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“…Actin filaments and microtubules have been imaged after adsorption to mica, but in this case tapping mode AFM was used to prevent displacement of the sample (Fritz et al, 1995a,b). Tapping mode imaging has also been key to imaging DNA physisorbed to mica (Hansma et al, 1992(Hansma et al, & 1995. These examples document that the preparation technique described here is of general use for all biological scanning probe microscopes.…”

Section: Resultsmentioning

confidence: 73%

Adsorption of Biological Molecules to a Solid Support for Scanning Probe Microscopy

Müller

Amrein

Engel

1997

Journal of Structural Biology

286

206

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Section: Resultsmentioning

confidence: 73%

Adsorption of Biological Molecules to a Solid Support for Scanning Probe Microscopy

Müller

Amrein

Engel

1997

Journal of Structural Biology

286

206

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“…NGF can induce cell death through the p75 neurotrophin receptor (p75NTR), a member of the tumor necrosis factor receptor superfamily [29]. A previous report supports this concept, demonstrating that A␤-derived diffusible ligands (ADDLs) potently alter NGF-mediated signaling in cultured cells [30].…”

Section: Receptor-mediated A␤ Oligomer Neurotoxicitymentioning

confidence: 95%

Molecular Mechanisms of Amyloid Oligomers Toxicity

Kayed

Lasagna‐Reeves

2012

JAD

322

283

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Abstract. Amyloid oligomers have emerged as the most toxic species of amyloid-␤ (A␤). This hypothesis might explain the lack of correlation between amyloid plaques and memory impairment or cellular dysfunction. However, despite the numerous published research articles supporting the critical role A␤ oligomers in synaptic dysfunction and cell death, the exact definition and mechanism of amyloid oligomers formation and toxicity still elusive. Here we review the evidence supporting the many molecular mechanisms proposed for amyloid oligomers toxicity and suggest that the complexity and dynamic nature of amyloid oligomers may be responsible for the discrepancy among these mechanisms and the proposed cellular targets for amyloid oligomers.

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“…AFM imaging was performed in air with a Nanoscope III (Digital Instruments, Santa Barbara, CA) operating in tapping mode with silicon tapping mode tips (Olympus, Tokyo). Bungee cords were used for vibration isolation (24). Images were processed by flattening to remove the background slope with the Digital Instruments Nanoscope software package.…”

mentioning

confidence: 99%

Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy

Henn

Medalia

Shi

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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The Escherichia coli protein DbpA is unique in its subclass of DEAD box RNA helicases, because it possesses ATPase-specific activity toward the peptidyl transferase center in 23S rRNA. Although its remarkable ATPase activity had been well defined toward various substrates, its RNA helicase activity remained to be characterized. Herein, we show by using biochemical assays and atomic force microscopy that DbpA exhibits ATP-stimulated unwinding activity of RNA duplex regardless of its primary sequence. This work presents an attempt to investigate the action of DEAD box proteins by a single-molecule visualization methodology. Our atomic force microscopy images enabled us to observe directly the unwinding reaction of a DEAD box helicase on long stretches of double-stranded RNA. Specifically, we could differentiate between the binding of DbpA to RNA in the absence of ATP and the formation of a Y-shaped intermediate after its progression through double-stranded RNA in the presence of ATP. Recent studies have questioned the designation of DbpA, in particular, and DEAD box proteins in general as RNA helicases. However, accumulated evidence and the results reported herein suggest that these proteins are indeed helicases that resemble in many aspects the DNA helicases.M any putative RNA helicases are members of the DEAD box protein family, which catalyzes the hydrolysis of ATP in the presence of RNA presumably unwinding the duplex regions of RNA and RNA-DNA hybrids. They are characterized by the ''DEAD'' motif (Asp-Glu-Ala-Asp) as well as by seven other conserved amino acid motifs including two ATP binding domains A and B (1-3). These proteins are found in a wide range of organisms ranging from viruses to higher eukaryotes. Importantly, RNA helicases participate in many essential cellular processes such as transcription, translation, ribosome assembly, cell differentiation, cell development, RNA processing, and mRNA splicing (4-6). Furthermore, the unwinding of the RNA secondary structure is the rate-limiting step in obtaining the functional conformation of RNA, required in these biological processes (2). Therefore, helicases may play a key role in regulating these biological processes by controlling RNA structures. Although the unwinding activity has been demonstrated in vitro for a few RNA helicases (7-11), it has not been shown for many other members of the DEAD box family. It was suggested that, unlike DNA helicases (12), RNA helicases may not be required to unwind long stretches of double-stranded RNA (dsRNA; ref.2). The mode of action of a DEAD box helicase was recently analyzed in detail in the vaccinia nucleoside-triphosphate phosphohydrolase-II (NPH-II) protein (11). NPH-II exhibited highly processive 3Ј to 5Ј helicase activity, in an ATP-dependent manner. These results raised the possibility that the mode of action of RNA and DNA helicases is similar and that the differences between them may be the result of their particular substrates and their interactions with other proteins (10).DbpA was identified by its hom...

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Applications for atomic force microscopy of DNA

Cited by 250 publications

References 29 publications

Adsorption of Biological Molecules to a Solid Support for Scanning Probe Microscopy

Adsorption of Biological Molecules to a Solid Support for Scanning Probe Microscopy

Molecular Mechanisms of Amyloid Oligomers Toxicity

Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy

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