DNA Beyond Genes by Vadim V. Demidov

Author:Vadim V. Demidov
Language: eng
Format: epub
ISBN: 9783030364342
Publisher: Springer International Publishing

Another trio of scientists, from the same German research group that developed bacteriophage production of oligonucleotides described above, have made 3D DNA origami structures at sizes up to the micrometer scale by a different hierarchical self-assembly approach [88]. They used 50-nm-sized V-shaped DNA origami building blocks (called V-bricks), in which the angle of the V could be varied. By controlling the geometry and interactions between the building blocks, a large variety of higher order assemblies can be constructed. By using this method, the micrometer-long thick-wall tubes with 350 nm diameter, and polyhedrons up to 450 nm in diameter—the largest 3D objects obtained from DNA so far—were constructed of hundreds of DNA scaffolds and thousands of DNA staples (see Fig. 3.25b).

Alternative way to get DNA origami structures in the submicrometer and micrometer size ranges is to employ for their assembly longer DNA scaffold strands, other than those generally produced by bacteriophage M13, which could be generated by a variety of diverse approaches both in vivo and in vitro. For example, the team of academia researchers from North Carolina, USA, created hybrid bacteriophage from the two E. coli viruses, bacteriophages λ and M13, which replicates in special species of E. coli bacteria with single-stranded DNA more than 50 kb long [89]. Using these DNA single strands as origami scaffold, which is seven times longer than M13 DNA scaffold, both flat and non-flat 2D asymmetric origami sheets with shapes of notched rectangles and with controlled global curvature have been assembled. The largest sizes of these sheets were close to 300 nm and their surface area was over seven times larger than that obtained with M13 DNA scaffold.

Assembly of such large DNA origami sheets required over 1600 distinct DNA staple strands so that researchers developed new inexpensive process for DNA synthesis, which reduced the cost of staples by more than an order of magnitude. The thousand-plus pool of all necessary staple strands was made via an inkjet-printing process on a single chip embossed with functionalized micropillars made from cyclic olefin copolymer [89]. An alternative method for cost-reduced synthesis of oligonucleotides was a second achievement of this innovation in the DNA origami field.

A different, cell-free approach was utilized by the group of Chinese scientists who obtained in vitro a single-stranded scaffold DNA almost four times longer than M13 DNA by first producing the 26-kb-long double-stranded DNA with the well-developed molecular biotechnology polymerase chain reaction (PCR) followed by a selective enzymatic digestion of one of the two DNA strands [90]. Such a long DNA scaffold was folded by this research team into a 2D rectangular shape with the sizes of 238 × 108 nm using nearly 800 staple strands.

In 2009, the pioneer of DNA origami William Shih with two colleagues added a new twist on the DNA origami path to practice. Though before only the single-stranded scaffolds were used for DNA origami assemblies to avoid competitive reannealing with the complementary strand, Shih and co-workers have now demonstrated that successful assemblies could be achieved with a DNA scaffold provided initially in the double-stranded (ds) form [91].

Download

Copyright Disclaimer:
This site does not store any files on its server. We only index and link to content provided by other sites. Please contact the content providers to delete copyright contents if any and email us, we'll remove relevant links or contents immediately.