Single Molecule Atomic Force Microscopy Studies of Photosensitized Singlet Oxygen Behavior on a DNA Origami Template

Helmig, Sarah; Rotaru, Alexandru; Arian, Dumitru; Kovbasyuk, Larisa; Arnbjerg, J.; Ogilby, Peter R.; Kjems, Jørgen; Mokhir, Andriy; Besenbacher, Flemming; Gothelf, Kurt V.

doi:10.1021/nn102701f

Cited by 57 publications

(66 citation statements)

References 30 publications

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“…[1,2] Designed nanomaterials have been developed by equipping DNA scaffolds [2,3] with chemical linkages to spatially arrange nanoparticles, [4] fluorophores, [5] or proteins.…”

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confidence: 99%

“…[1,2] Designed nanomaterials have been developed by equipping DNA scaffolds [2,3] with chemical linkages to spatially arrange nanoparticles, [4] fluorophores, [5] or proteins. [6] These DNA nanostructures have been mostly applied for cell-free applications but not for cell biology even though the latter field benefits from nanomaterials as demonstrated with canonical nucleic acids.…”

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confidence: 99%

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Back Cover: Membrane‐Spanning DNA Nanopores with Cytotoxic Effect (Angew. Chem. Int. Ed. 46/2014)

Burns¹,

Al‐Juffali²,

Janes³

et al. 2014

Angew Chem Int Ed

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Self-assembled DNA nanostructures with chemistry-enabled functionality are of great interest in nanobiotechnology. Herein, chemically modified DNA nanopores are designed to puncture cellular membranes and cause cytotoxicity. The nanopores are assembled from DNA oligonucleotides to form a 2 nm-high hydrophobic belt at one terminus. The belt is composed of charge-neutralized ethyl phosphorothioate (EP) groups which are required to decrease cell viability. The mode by which the pores achieve cell killing is elucidated with confocal microscopy. This study is the first to describe the interaction of DNA nanopores with cells. The work lays the foundation for the future development of cytotoxic agents with cancer type-specificity.Chemistry can play an important role in expanding the functional repertoire of DNA nanostructures. [1,2] Designed nanomaterials have been developed by equipping DNA scaffolds [2,3] with chemical linkages to spatially arrange nanoparticles, [4] fluorophores, [5] or proteins.[6] These DNA nanostructures have been mostly applied for cell-free applications but not for cell biology even though the latter field benefits from nanomaterials as demonstrated with canonical nucleic acids. [7,8] One class of chemically modified DNA nanostructures of potential in cell biology are membrane-spanning DNA nanopores. In general, engineered nanopores that facilitate transmembrane flux [9] can be used for cell permeabilization, drug delivery, [10] but also biosensing. [11][12][13] In the latter, label-free analytical strategy, individual molecules passing or binding inside a nanoscale pore are detected based on the associated changes in the ionic pore current. A wide range of analytes can be sensed, [11,14] and DNA can be sequenced by threading individual strands through the pore. [12,15] Nanopores have traditionally been constructed with re-engineered or de-novo protein scaffolds, or organic synthetic building blocks.[16]Nanopores composed of folded DNA are the most recent category. [17][18][19][20] Formed either by scaffold and staple strands [17] or short oligonucleotides, [18,19] the highly negatively charged DNA nanopores insert into hydrophobic bilayer membranes by chemical lipid anchors, whereby cholesterol, [17] porphyrin, [19] and a belt of EP tags [18] were successfully tested. In light of their established ability to span reconstituted membranes, we postulated that the pores could be adapted and exploited to puncture biological cell membranes. Our interest was spiked by the prospect of rationally designing DNA nanostructures for cell biological applications, such as gene transfection, drug permeabilization or targeted killing of diseased cells.Here we examine whether a membrane-spanning DNA nanopore can interact with cancer cells and potentially trigger cell death (Figure 1 a and b). Our nanopore was composed of a bundle of six DNA duplexes folded from six DNA strands (see Figure S1 in the Supporting Information). The hollow nanobarrel has a channel width of approximately 2 nm, an Figure 1. A membrane-...

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“…[1,2] Designed nanomaterials have been developed by equipping DNA scaffolds [2,3] with chemical linkages to spatially arrange nanoparticles, [4] fluorophores, [5] or proteins.…”

mentioning

confidence: 99%

mentioning

confidence: 99%

Back Cover: Membrane‐Spanning DNA Nanopores with Cytotoxic Effect (Angew. Chem. Int. Ed. 46/2014)

Burns¹,

Al‐Juffali²,

Janes³

et al. 2014

Angew Chem Int Ed

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“…This type of investigation was reported recently. [23] A single indium pyropheophorbide singlet-oxygen photosensitizer (IPS) was conjugated to a staple strand located in the middle of the origami tile. To monitor the behavior of singlet oxygen, biotinylated oligonucleotides containing a singlet-oxygen-cleavable linker were placed at both sides of the photosensitizer-conjugated strand (Figure 8 A).…”

Section: Photochemical Reactionsmentioning

confidence: 99%

“…[20] Although the origami method was used in DNA nanotechnology, single-molecule analysis was carried out first for the RNA hybridization assay [21] (if we exclude the nanopatterning of functional molecules [17][18][19] ). After this application, the method was used for various singlemolecule analyses, ranging from chemical, [22] photochemical, [23] and biochemical reactions [24] to determination of photophysical properties, [25] recognition of SNPs, [26] and conformational changes in DNA. [27] These types of analysis would not have been feasible using short DNA motifs.…”

Section: Introduction 875mentioning

confidence: 99%

Single‐Molecule Analysis Using DNA Origami

Rajendran¹,

Endo²,

Sugiyama³

2011

Angew Chem Int Ed

199

137

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During the last two decades, scientists have developed various methods that allow the detection and manipulation of single molecules, which have also been called "in singulo" approaches. Fundamental understanding of biochemical reactions, folding of biomolecules, and the screening of drugs were achieved by using these methods. Single-molecule analysis was also performed in the field of DNA nanotechnology, mainly by using atomic force microscopy. However, until recently, the approaches used commonly in nanotechnology adopted structures with a dimension of 10-20 nm, which is not suitable for many applications. The recent development of scaffolded DNA origami by Rothemund made it possible for the construction of larger defined assemblies. One of the most salient features of the origami method is the precise addressability of the structures formed: Each staple can serve as an attachment point for different kinds of nanoobjects. Thus, the method is suitable for the precise positioning of various functionalities and for the single-molecule analysis of many chemical and biochemical processes. Here we summarize recent progress in the area of single-molecule analysis using DNA origami and discuss the future directions of this research.

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“…Another field in great expansion is coupled to the advancement of single-molecule technologies, enabling for example the precise localization and counting of molecules in spatially distributed samples or the disclosure of anomalous kinetic events occurring on a time scale normally not accessible by standard methods [8,[35][36][37][38][39][40]. Recently, DNA nanostructures have also shown interesting properties in cells [41] and are currently explored as promising targeting and delivery systems [42,43].…”

Section: Introductionmentioning

confidence: 99%