Streamlined Method for Purifying Single-Stranded Dna from Pcr Products for Frequent or High-Throughput Needs

Kuo, Tai-Chih

doi:10.2144/05385bm04

Cited by 7 publications

(3 citation statements)

References 5 publications

(1 reference statement)

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“…Functional microparticles can be useful in multiple diverse applications. They can be used for capture, purification [21], aggregation assays [22], chromatography [23], flow cytometry assays [24], and much more. With the equipment presented here, a modest investment would allow a researcher to accomplish much more than by buying a single type of commercial microparticles.…”

Section: Discussionmentioning

confidence: 99%

Open source and DIY hardware for DNA nanotechnology labs

et al. 2015

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A set of instruments and specialized equipment is necessary to equip a laboratory to work with DNA. Reducing the barrier to entry for DNA manipulation should enable and encourage new labs to enter the field. We present three examples of open source/DIY technology with significantly reduced costs relative to commercial equipment. This includes a gel scanner, a horizontal PAGE gel mold, and a homogenizer for generating DNA-coated particles. The overall cost savings obtained by using open source/DIY equipment was between 50 and 90%.

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Section: Discussionmentioning

confidence: 99%

Open source and DIY hardware for DNA nanotechnology labs

et al. 2015

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“…Thus, dsDNA products synthetized by classical PCR require additional steps of separation and purification to produce ssDNA that can serve as a scaffold strand for DNA origami folding. To this end, as previously established, for example, for ssDNA aptamers synthesis, various methods have been further developed to obtain pure ssDNA scaffolds from dsDNA PCR products, such as denaturation and separation with streptavidin magnetic beads [ 76 , 77 , 78 ], capture electrophoresis [ 79 ], and preferential DNase digestion of one of the strands [ 80 , 81 , 82 , 83 ]. Alternatively, studies have used single-primer PCR [ 84 ] and asymmetric PCR (aPCR) [ 85 ] ( Figure 3 ), two variants of the PCR technique that allow for the direct production of ssDNA that can be isolated from dsDNA byproducts via agarose gel extraction and used without further purification.…”

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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“…Identification and isolation of the desired strand post-denaturation can be accomplished by, for example, asymmetric biotin modification using a variety of streptavidin (or avidin) selection systems [21,25,26] or agarose gel electrophoresis (AGE) [24,26,27]. NaOH and urea are the most commonly used chemical denaturants based on their high efficiency, and economy [21,27,28,30,31]. However, these methods can be somewhat dangerous, and extensive purification may be required to remove residual denaturants [21,26,28].…”

Section: Chemical Denaturationmentioning

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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Streamlined Method for Purifying Single-Stranded Dna from Pcr Products for Frequent or High-Throughput Needs

Cited by 7 publications

References 5 publications

Open source and DIY hardware for DNA nanotechnology labs

Open source and DIY hardware for DNA nanotechnology labs

Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies

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

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