Ramified rolling circle amplification for synthesis of nucleosomal DNA sequences

Emmerik, Clara L van; Gachulincova, Ivana; Lobbia, Vincenzo R.; Daniëls, Mark A.; Heus, Hans A.; Soufi, Abdenour; Nelissen, Frank H. T.; Ingen, Hugo van

doi:10.1016/j.ab.2019.113469

Cited by 17 publications

(15 citation statements)

References 27 publications

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“…The source of DNA material is an important factor as synthetically synthesized DNA can cost a few hundred to a few thousand dollars for a few milligrams required for milliliter scale DNA hydrogel synthesis [56]; typically requiring 2-4 milligrams (mg) of DNA per 100 µL, or 2-4 percent weight/volume (%w/v) of hydrogel. However, RCA is able to produce a few hundred micrograms of DNA per milliliter of overnight reaction [57][58][59], though it is currently limited to short tandem repeats (~100 nucleotides [nt]) without control over the repeat number. Multiprimed chain amplification (MCA) is the subsequent priming of the concatemeric strand produced by RCA (Figure 1a); this approach allows for a significant amount of DNA to be produced with a multitude of complementary domains enabling partial hybridization between multiple strands ranging from a few hundred to thousands of nucleotides in length.…”

Section: Entangled and Crosslinkedmentioning

confidence: 99%

Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials

Bush

Veneziano

2021

Applied Sciences

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DNA hydrogels are self-assembled biomaterials that rely on Watson–Crick base pairing to form large-scale programmable three-dimensional networks of nanostructured DNA components. The unique mechanical and biochemical properties of DNA, along with its biocompatibility, make it a suitable material for the assembly of hydrogels with controllable mechanical properties and composition that could be used in several biomedical applications, including the design of novel multifunctional biomaterials. Numerous studies that have recently emerged, demonstrate the assembly of functional DNA hydrogels that are responsive to stimuli such as pH, light, temperature, biomolecules, and programmable strand-displacement reaction cascades. Recent studies have investigated the role of different factors such as linker flexibility, functionality, and chemical crosslinking on the macroscale mechanical properties of DNA hydrogels. In this review, we present the existing data and methods regarding the mechanical design of pure DNA hydrogels and hybrid DNA hydrogels, and their use as hydrogels for cell culture. The aim of this review is to facilitate further study and development of DNA hydrogels towards utilizing their full potential as multifeatured and highly programmable biomaterials with controlled mechanical properties.

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Section: Entangled and Crosslinkedmentioning

confidence: 99%

Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials

Bush

Veneziano

2021

Applied Sciences

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“…To mitigate this situation, single-strand binding protein (SSB) can be included in the RCA reaction, but at additional cost and creating a need for additional post-synthesis purification steps [17]. Also, the reaction requires a circular template, nicked on the desired strand, which can be problematic DNA 2022, 2 in some instances [18] since the substrate for the reaction must contain one or more sites amenable to nicking by a relatively small pool of sequence-specific nicking endonucleases ("nickases") [16,17]. Finally, cleavage of concatemeric RCA products into monomeric ss-DNA is critical for the utilization of products for downstream applications [19].…”

Section: Rolling Circle Amplification (Rca)mentioning

confidence: 99%

A Comparison of Methods for the Production of Kilobase-Length Single-Stranded DNA

Henderson

2022

DNA

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DNA nanoengineering, in particular, DNA origami has potential applications in a variety of areas including, for example, nanoelectronics, biomedical diagnostics, and therapeutics. To fully realize the potential of DNA self-assembly in these and other areas, methods must be available for economical, scalable, and reliable production of single-stranded DNA (ssDNA) scaffolds from virtually any source. In this review, we will describe the virtues and liabilities of four strategies for generating ssDNA, including Rolling Circle Amplification (RCA), strand-specific exonuclease digestion, chemical denaturation, and asymmetric PCR (aPCR), with suggestions for approaches to optimize the use of each method.

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“…This is consistent with observations in previous studies showing that circularized DNA migrates slower than linear DNA of the same length in denaturing PAGE. 35,36 The unreacted L16 was removed by PAGE purification (Figure S3). Subsequently, CiD agonists with different linker lengths (C10-C26) were synthesized (Figure S3).…”

Section: Design and Synthesis Of Cid Agonists Targeting Metmentioning

confidence: 99%

CiD agonists: Circular DNA-based agonists for the fine-tuning of receptor signaling

Ueki

Watanabe

Akiyama

et al. 2022

Preprint

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Receptor dimerization geometry plays a significant role in signal transduction induced by growth factors and cytokines. A chemical strategy capable of controlling dimerization geometry provides a means for studying receptor activation mechanisms and designing novel agonists transducing fine-tuned receptor signaling. However, a generalized approach that can be applied to given receptors is still limited. In the present study, we propose a strategy using CiD agonists (circular DNA aptamer-based agonists), where circularized DNA is used as a rigid scaffold to present two receptor-binding aptamers from the duplex linker domain in a fixed distance and orientation. We targeted Met, a receptor for hepatocyte growth factor (HGF), and designed Met-binding CiD agonists with variable linker length. The designed CiD agonists demonstrated a distinctive periodic change in the receptor activation potential dependent on their linker length. This strategy represents a useful approach for the rational design of partial agonists that transduce fine-tuned receptor signaling and exert moderate biological activity.

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Ramified rolling circle amplification for synthesis of nucleosomal DNA sequences

Cited by 17 publications

References 27 publications

Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials

Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials

A Comparison of Methods for the Production of Kilobase-Length Single-Stranded DNA

CiD agonists: Circular DNA-based agonists for the fine-tuning of receptor signaling

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