Programmed folding of DNA origami structures through single-molecule force control

Bae, Wooli; Kim, Kipom; Min, Duyoung; Ryu, Ji Won; Hyeon, Changbong; Yoon, Tae–Young

doi:10.1038/ncomms6654

Cited by 45 publications

(39 citation statements)

References 45 publications

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“…For the eight-tube DNA, we found two major transitions of ∼62 and ∼26 nm during the longitudinal stretching (Figure 4E) and one transition of ∼11 nm during the horizontal stretching (Figure 4F). These change-in-extension histograms show broad distributions, which is expected as the transition events are likely mediated by one or more intermediates presented in DNA origami structures with large sizes (40,41). It is also possible that some reversible disassembly or melting processes may contribute to this broad feature.…”

Section: Resultsmentioning

confidence: 78%

Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores

et al. 2016

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DNA nanoassemblies have demonstrated wide applications in various fields including nanomaterials, drug delivery and biosensing. In DNA origami, single-stranded DNA template is shaped into desired nanostructure by DNA staples that form Holliday junctions with the template. Limited by current methodologies, however, mechanical properties of DNA origami structures have not been adequately characterized, which hinders further applications of these materials. Using laser tweezers, here, we have described two mechanical properties of DNA nanoassemblies represented by DNA nanotubes, DNA nanopyramids and DNA nanotiles. First, mechanical stability of DNA origami structures is determined by the effective density of Holliday junctions along a particular stress direction. Second, mechanical isomerization observed between two conformations of DNA nanotubes at 10–35 pN has been ascribed to the collective actions of individual Holliday junctions, which are only possible in DNA origami with rotational symmetric arrangements of Holliday junctions, such as those in DNA nanotubes. Our results indicate that Holliday junctions control mechanical behaviors of DNA nanoassemblies. Therefore, they can be considered as ‘mechanophores’ that sustain mechanical properties of origami nanoassemblies. The mechanical properties observed here provide insights for designing better DNA nanostructures. In addition, the unprecedented mechanical isomerization process brings new strategies for the development of nano-sensors and actuators.

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Section: Resultsmentioning

confidence: 78%

Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores

et al. 2016

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“…High production yield is achieved by thermal annealing and slow cooling of the system. Such annealing has also been performed chemically, isothermally, and mechanically [10][11][12].The hybridization of double strand DNA (dsDNA) has been well studied, particularly under physiological conditions [13,14]. The formation of dsDNA from ssDNA is driven by base stacking interactions and is highly influenced by the GC content of the nucleobase sequence, the sequence length, and the salt concentration [13].…”

mentioning

confidence: 99%

“…High production yield is achieved by thermal annealing and slow cooling of the system. Such annealing has also been performed chemically, isothermally, and mechanically [10][11][12].…”

mentioning

confidence: 99%

Competitive annealing of multiple DNA origami: formation of chimeric origami

2016

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Scaffolded DNA origami are a robust tool for building discrete nanoscale objects at high yield. This strategy ensures, in the design process, that the desired nanostructure is the minimum free energy state for the designed set of DNA sequences. Despite aiming for the minimum free energy structure, the folding process which leads to that conformation is difficult to characterize, although it has been the subject of much research. In order to shed light on the molecular folding pathways, this study intentionally frustrates the folding process of these systems by simultaneously annealing the staple pools for multiple target or parent origami structures, forcing competition. A surprising result of these competitive, simultaneous anneals is the formation of chimeric DNA origami which inherit structural regions from both parent origami. By comparing the regions inherited from the parent origami, relative stability of substructures were compared. This allowed examination of the folding process with typical characterization techniques and materials. Anneal curves were then used as a means to rapidly generate a phase diagram of anticipated behavior as a function of staple excess and parent staple ratio. This initial study shows that competitive anneals provide an exciting way to create diverse new nanostructures and may be used to examine the relative stability of various structural motifs.The commercial development of inexpensive and quickly produced DNA of arbitrary nucleobase sequence has fueled the growth of DNA nanotechnology as a field [1]. DNA nanotechnology has made promising advances toward light harvesting [2], computation [3], cancer treatement [4,5], and assembly of nanoelectronics [6]. While many DNA self-assembly strategies exist [7,8], scaffolded DNA origami has received significant attention as a convenient way to design and create discrete nanoscale objects [9]. Scaffolded DNA origami consist of single strand DNA (ssDNA) of two types, synthetic oligomers and circular viral genomes; the viral scaffold is forced to route through the designed structure by the binding of complementary subsequences on the synthetic oligomers, or staples. Staples are added in excess, often 10× relative to the scaffold concentration, strongly driving the viral ssDNA scaffold to fold into the target structure. Although 10× is a common staple excess anneals have been successfully performed as low as 2.5× staple excess. As this study involves multiple staple pools, staple excess will always refer to the total staple concentration relative to the scaffold, while the parent staple ratio will refer to how much of that total corresponds to the staple pool for each target origami. High production yield is achieved by thermal annealing and slow cooling of the system. Such annealing has also been performed chemically, isothermally, and mechanically [10][11][12].The hybridization of double strand DNA (dsDNA) has been well studied, particularly under physiological conditions [13,14]. The formation of dsDNA from ssDNA is driven by base stack...

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“…These excitation wavelengths are different for the individual fluorescent molecules, and therefore the selected release or multiplexed release of ssDNA will be achievable when the BHQ is used as an acceptor. In addition, FRET is an excellent probing system for detection of the states of DNA nanostructures [22,23]. By combining a FRET-based DNA release system with a DNA nanostructure, ssDNA will be released, depending on its state.…”

Section: Exciatationmentioning

confidence: 99%

Optically controlled release of DNA based on nonradiative relaxation process of quenchers

Ogura

Onishi

Nishimura

et al. 2016

Biomed. Opt. Express

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Abstract:Optically controlled release of a DNA strand based on a nonradiative relaxation process of black hole quenchers (BHQs), which are a sort of dark quenchers, is presented. BHQs act as efficient energy sources because they relax completely via a nonradiative process, i.e., without fluorescent emission-based energy losses. A DNA strand is modified with BHQs and the release of its complementary strand is controlled by excitation of the BHQs. Experimental results showed that up to 50% of the target strands were released, and these strands were capable of inducing subsequent reactions. The controlled release was localized on a substrate within an area of no more than 5 micrometers in diameter.

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Programmed folding of DNA origami structures through single-molecule force control

Cited by 45 publications

References 45 publications

Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores

Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores

Competitive annealing of multiple DNA origami: formation of chimeric origami

Optically controlled release of DNA based on nonradiative relaxation process of quenchers

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