Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds

Hamblin, Graham D.; Rahbani, Janane F.; Sleiman, Hanadi F.

doi:10.1038/ncomms8065

Cited by 41 publications

(45 citation statements)

References 31 publications

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“…In addition to PCR-based methods that usually involve purification steps and limited production yields, few alternative enzymatic methods have been developed for the production of full-length ssDNA scaffolds, with notable examples including rolling circle amplification (RCA) and sequential growth, among others [ 100 , 101 , 102 , 103 , 104 ].…”

Section: Current Methods For Ssdna Scaffold Productionmentioning

confidence: 99%

Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies

et al. 2020

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DNA origami nanocarriers have emerged as a promising tool for many biomedical applications, such as biosensing, targeted drug delivery, and cancer immunotherapy. These highly programmable nanoarchitectures are assembled into any shape or size with nanoscale precision by folding a single-stranded DNA scaffold with short complementary oligonucleotides. The standard scaffold strand used to fold DNA origami nanocarriers is usually the M13mp18 bacteriophage’s circular single-stranded DNA genome with limited design flexibility in terms of the sequence and size of the final objects. However, with the recent progress in automated DNA origami design—allowing for increasing structural complexity—and the growing number of applications, the need for scalable methods to produce custom scaffolds has become crucial to overcome the limitations of traditional methods for scaffold production. Improved scaffold synthesis strategies will help to broaden the use of DNA origami for more biomedical applications. To this end, several techniques have been developed in recent years for the scalable synthesis of single stranded DNA scaffolds with custom lengths and sequences. This review focuses on these methods and the progress that has been made to address the challenges confronting custom scaffold production for large-scale DNA origami assembly.

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Section: Current Methods For Ssdna Scaffold Productionmentioning

confidence: 99%

Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies

et al. 2020

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“…However, the applications of high-copy DNA repeats usually involve formations of many non-B DNA structures. [3][4][5][6] For example, the DNA hydrogel is composed of many inter-and intramolecular hybridization networks. [11,12] The dsDNA repeats are not in their perfect DNA duplex forms.…”

Section: A New Cost-effective Methods For the Synthesis Of High-copy Dmentioning

confidence: 99%

“…On the other hand, in the field of materials science, repetitive DNA has been frequently used as a building block of programmable nano-, micro-, macro-, and meso-structures. [3][4][5][6] For example, DNA repeats have been used to produce DNA hydrogels with unusual mechanical properties. [7][8][9][10] In general, DNA hydrogels are tunable, programmable, responsive to various stimuli, biocompatible, and biodegradable.…”

Section: Introductionmentioning

confidence: 99%

A Simple Blocking PCR‐Based Method for the Synthesis of High‐Copy dsDNA Tandem Repeats

Wang

Yang

2020

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DNA tandem repeats are frequently found in eukaryotic genomes. High-copy DNA repeats can serve as building blocks of complex DNA structures, but the in vitro synthesis of DNA repeats has been challenging due to complicated procedures and the high cost. Here, a new, simple method is developed using the strategy of blocking polymerase chain reaction for highly efficient DNA repeat expansion (BPRE). With BPRE, dsDNA fragments composed of more than 40 copies of the repeat sequence can be quickly produced, while the cost is reduced by at least 90%. As a typical application, reannealing of the dsDNA repeats generates elastic hydrogels, which shows a high capacity for doxycycline absorption and prolonged release.

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“…In enzymatic systems, ATP-dependent reactions are extremely sensitive to the exclusive use of ATP, such as for DNA and RNA ligases, as well as for protein kinases. [80,83,84] Consequently, enzymes are one particular avenue of choice to reach high selectivity and also catalytic control of the reaction rates. The challenges in the enzymatic system are however the limitations on available reactions and building blocks for such reactions and self-assemblies, possibilities for specific and non-specific inhibition, and potential stability issues requiring specific buffer systems and/or additives.…”

Section: Molecular Mechanisms For the Integration Of Atp In Self-assementioning

confidence: 99%

ATP‐Responsive and ATP‐Fueled Self‐Assembling Systems and Materials

2020

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his/her body weight in ATP each day, which is enabled through a very efficient ADP/ATP recycling system. [7] Aside of the fascinating non-equilibrium succeeded by exploiting ATP/GTP as chemical fuels to drive structures and functions, it is also important to realize that ATP and other nucleoside phosphates can be used as biological and chemical signals. [8-10] Lots of biological processes such as chromatin remodeler activation, [11] inflammatory signaling, [12] and cell differentiation [13] are mediated by ATP signaling. Additionally, cancer cells have a higher concentration of ATP, [14] which in turn provides a handle to develop new types of molecular therapies. This of course requires to develop sophisticated carriers or self-assembling structures that highly specifically react to ATP and potentially even to its concentration, ideally without any interference from other nucleoside phosphates. [15-20] For such cases, it is also important to realize that ATP is used as a chemical signal rather than a chemical fuel, as the primary objective may not be to harvest its energy from hydrolysis for functions, but just to use its chemical structure for a change of function. Overall, it becomes clear that the use of ATP (and similarly GTP) as a trigger or as a chemical fuel is of high relevance to interact with living systems and also to be able to create active devices in long term that can create work and allow for active communication in a biological environment using the fuels available therein. [21] In the scope of this review on ATP-dependent systems, and being set at the interface of near-equilibrium responsive materials versus non-equilibrium active materials, it is useful to begin Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-tocell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATPtriggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to nonequilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring ...

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Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds

Cited by 41 publications

References 31 publications

Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies

Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies

A Simple Blocking PCR‐Based Method for the Synthesis of High‐Copy dsDNA Tandem Repeats

ATP‐Responsive and ATP‐Fueled Self‐Assembling Systems and Materials

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