Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami

Kick, Benjamin; Praetorius, Florian; Dietz, Hendrik; Weuster‐Botz, Dirk

doi:10.1021/acs.nanolett.5b01461

Cited by 104 publications

(112 citation statements)

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“…We thank F. Praetorius for the scaffold DNA preparations ( 65 ), A. Flaus (National University of Ireland Galway) for advice on the design of nucleosomes with nicks and branches, C. Regnard and C. Albig [Biomedical Center (BMC), Ludwig-Maximilians-Universität München] for advice on histone acetylation assays, P. Becker (BMC, LMU Munich) for advice on histone acetylation via MOF histone acetyltransferase, and H. Scherman (Colorado State University) for the preparation of recombinant histones. Funding: This work was supported by the European Research Council Starting Grant (GA no.…”

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confidence: 99%

Uncovering the forces between nucleosomes using DNA origami

et al. 2016

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Section: Acknowledgmentsmentioning

confidence: 99%

Uncovering the forces between nucleosomes using DNA origami

et al. 2016

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“…However, since the entire research field is constantly growing and developing, it is likely that scaling up of the production and simultaneous knockdown of the price will take place rapidly [3,64]. Very recent examples [65][66][67][68] promisingly show that production quantities of pure DNA origami objects are currently about to upgrade from micro-/milligram scale to gram scale. Today, 1 gram of scaffolded megadalton-sized DNA origamis costs approximately 100,000 $.…”

Section: Concluding Remarks and Future Perspectivesmentioning

confidence: 99%

DNA Nanostructures as Smart Drug-Delivery Vehicles and Molecular Devices

Linko

Ora

Kostiainen

2015

Trends in Biotechnology

227

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Emerging DNA nanotechnologyThe field of structural DNA nanotechnology started around 30 years ago when Ned Seeman performed pioneering research with DNA junctions and lattices [1]. To date, a cornucopia of different DNA nanostructures and shapes based on WatsonCrick basepairing [2] have been designed and demonstrated, and the whole research area has enjoyed a rapid progress especially during the past decade [3]. The key player in the fast development of DNA nanotechnology has been the invention of DNA origami in 2006 [4]. The DNA origami method is based on folding a long single-stranded "DNA scaffold strand" into a customized shape with a set of short synthetic staple strands. The robustness of the technique has made it widely accessible.Since then, the method has been generalized to 3D-fabrication [5][6][7][8][9][10], and it enables shapes with custom curvatures, twists and bends [11,12]. Very recently, techniques for modular scaffold-free fabrication [13,14], 3D meshing and wireframe-based approaches [15][16][17], as well as shape-complementarity-based construction [18] of DNA objects have been introduced. In addition, powerful computational tools for designing and analyzing DNA nanostructures have been developed [19][20][21], which appreciably help researchers to create their own DNA nanoarchitectures for any conceivable application. Table 1 lists and 2 describes the novel design strategies that can be used for fabricating diverse DNA origami nanostructures and other complex DNA-based shapes for various nanotechnological purposes.The platonic DNA nanostructures and DNA origamis are by all means remarkably impressive examples of precise engineering and constructing at the nanoscale. However, the attractiveness of the origami method lies in the fact that one can add any desired functionality to the tailored DNA shapes by assembling other biomolecules and molecular components to them with nanometer precision. Importantly, DNA is inherently biocompatible, and its stability can be further tuned by the optional functionalization [20,[22][23][24]. Aforementioned superior features can be eventually exploited in designing artificial DNA-based biomachinery, such as nucleic acid devices [25] and protein-DNA hybrid structures [26] for nanomedicine and biosensing. In this focused review, we discuss the recent progress of the nanomedical applications of self-assembled DNA systems; especially the drug delivery vehicles and nanomachines based on the DNA origami technique. Towards DNA-based drug delivery vehicles and advanced therapeuticsThe tremendous self-assembly properties of DNA can be exploited in creating various programmable shapes and larger assemblies for cellular delivery for e.g. cancer and enzyme replacement therapy. The very first DNA origami nano-objects proposed to work as molecular containers for drug delivery applications were single-layer origamis, which were further assembled into 3D shapes -a tetrahedron [5] or hollow cubes [6,7] (Fig. 1A). Since then, cellular uptake for various DNA structures (based o...

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“…One of the most popular methods is the DNA origami technique, which utilizes hundreds of short DNA oligomers, called “staples” to fold a long DNA scaffold into a desired shape 1a,1c…”

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Orthogonal Protein Assembly on DNA Nanostructures Using Relaxases

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DNA‐binding proteins are promising reagents for the sequence‐specific modification of DNA‐based nanostructures. Here, we investigate the utility of a series of relaxase proteins—TrwC, TraI, and MobA—for nanofunctionalization. Relaxases are involved in the conjugative transfer of plasmids between bacteria, and bind to their DNA target sites via a covalent phosphotyrosine linkage. We study the binding of the relaxases to two standard DNA origami structures—rodlike six‐helix bundles and flat rectangular origami sheets. We find highly orthogonal binding of the proteins with binding yields of 40–50 % per binding site, which is comparable to other functionalization methods. The yields differ for the two origami structures and also depend on the position of the binding sites. Due to their specificity for a single‐stranded DNA target, their orthogonality, and their binding properties, relaxases are a uniquely useful addition to the toolbox available for the modification of DNA nanostructures with proteins.

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Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami

Cited by 104 publications

References 47 publications

Uncovering the forces between nucleosomes using DNA origami

Uncovering the forces between nucleosomes using DNA origami

DNA Nanostructures as Smart Drug-Delivery Vehicles and Molecular Devices

Orthogonal Protein Assembly on DNA Nanostructures Using Relaxases

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