Multi-micron crisscross structures grown from DNA-origami slats

Wintersinger, Christopher M.; Minev, Dionis; Ershova, Anastasia; Sasaki, Hiroshi; Gowri, Gokul; Berengut, Jonathan F.; Corea-Dilbert, Flanklin E.; Yin, Peng; Shih, William M.

doi:10.1038/s41565-022-01283-1

Cited by 60 publications

(69 citation statements)

References 51 publications

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“…Here, we fold dsDNA scaffolds of up to 18000 nt (9 kbp). While other DNA-based methodologies have yielded even larger non-periodic structures 20,35,36,54,55,56 , triplex origami is the first to require fewer unique starting materials and thus substantially decreases the cost-of-entry to this assembly size. The work presented here ensures that each staple recognition domain is sequentially unique by a margin of at least two mismatches, in addition to a number of other assumed restrictions on sequence design.…”

Section: Discussionmentioning

confidence: 99%

Folding double-stranded DNA into designed shapes with triplex-forming oligonucleotides

Samanta

Mandrup

et al. 2023

Preprint

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The folding of double-stranded DNA around histones is a central mechanism in eukaryotic cells for compacting the genetic information into chromosomes. Very few artificial methods are available for controlling the shape of dsDNA at any level, whereas several artificial methods have been developed to efficiently organize single-stranded DNA and RNA into a variety of well-defined nanostructures by programmed self-assembly. Here, we show how long double-stranded DNA sequences can be spatially organized by triplex-forming oligonucleotides (TFOs), which bridge two or more encoded polypurine domains. The linearized or plasmid dsDNA is compacted into antiparallel folds, which enables the formation of raster-filled 2D shapes and 3D structures with either square or hexagonal organizations. Contrary to ssDNA, dsDNA has inherent rigidity which alleviates the requirement to saturate a structure with TFO strands, yet the TFOs are still able to bend the dsDNA controllably and steeply up to 180° over 6 bp. The majority of structures investigated here are formed by Hoogsteen interactions which require pH = 5-6, however, the methodology is also applied with reverse Hoogsteen interactions at physiological pH. In both cases, the DNA triplexes render pure polypurine scaffolded structures resistant to DNase I.

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Section: Discussionmentioning

confidence: 99%

Folding double-stranded DNA into designed shapes with triplex-forming oligonucleotides

Samanta

Mandrup

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Here, we fold dsDNA scaffolds of up to 18000 nt (9 kbp). While other DNA-based methodologies have yielded even larger non-periodic structures 20,35,36,53,54,55 , triplex origami is the first to require fewer unique starting materials and thus substantially decreases the cost-of-entry to this assembly size. The work presented here ensures that each staple recognition domain is sequentially unique by a margin of at least two mismatches, in addition to a number of other assumed restrictions on sequence design.…”

Section: Discussionmentioning

confidence: 99%

Folding double stranded DNA into designed shapes with triplex forming oligonucleotides

Samanta

Mandrup

et al. 2022

Preprint

View full text Add to dashboard Cite

The folding of double-stranded DNA around histones is a central mechanism in eukaryotic cells for compacting the genetic information into chromosomes. Very few artificial methods are available for controlling the shape of dsDNA at any level, whereas several artificial methods have been developed to efficiently organize single-stranded DNA and RNA into a variety of well-defined nanostructures by programmed self-assembly , . Here, we show how long double-stranded DNA sequences can be spatially organized by triplex forming oligonucleotides (TFOs), which bridge two or more embedded polypurine domains. The linearized or plasmid dsDNA is compacted into antiparallel folds, which enables the formation of raster-filled 2D shapes and 3D structures with either square or hexagonal organizations. Contrary to ssDNA, dsDNA has inherent rigidity which alleviates the requirement to saturate a structure with TFO strands, yet the TFOs are still able to bend the dsDNA controllably and steeply up to 180° over 6 bp. The majority of structures investigated here are formed by Hoogsteen interactions which require pH = 5-6, however, the methodology is also applied with reverse Hoogsteen interactions at physiological pH. In both cases, the DNA triplexes render pure polypurine scaffolded structures resistant to DNase I.

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“…This allows experimental groups designing DNA origami to quickly test their designs and return to the drawing board if significant undesired bending or twisting is predicted. The more recent SNUPI model improves upon the CanDo model by adding electrostatic interactions and has been shown to work well for computing the equilibrium conformations of hierarchical superstructures consisting of many DNA origami, , a task that has proven quite challenging for both AAMD and CGMD simulations. Continuum mechanics provides additional value to DNA nanotechnology by providing practically useful quasi-analytical scaling behavior of new systems.…”

Section: Resolutions Of Modeling and Simulation Techniquesmentioning

confidence: 99%

Prediction and Control in DNA Nanotechnology

DeLuca

Sensale

Lin

et al. 2023

ACS Appl. Bio Mater.

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DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.

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Multi-micron crisscross structures grown from DNA-origami slats

Cited by 60 publications

References 51 publications

Folding double-stranded DNA into designed shapes with triplex-forming oligonucleotides

Folding double-stranded DNA into designed shapes with triplex-forming oligonucleotides

Folding double stranded DNA into designed shapes with triplex forming oligonucleotides

Prediction and Control in DNA Nanotechnology

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