Construction of a novel phagemid to produce custom DNA origami scaffolds.

Synth Biol (Oxf)

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.

Published: January 2018

AI Article Synopsis

  • DNA origami uses a long DNA strand as a scaffold to assemble shorter DNA pieces, enabling the creation of nanoscale objects.
  • Custom scaffold sequences improve design accuracy, allowing for greater control over the object's size and specific structural details.
  • The introduction of a new phagemid, pScaf, reduces the fixed DNA sequence needed for scaffold production, enhancing design flexibility for DNA origami applications.

Article Abstract

DNA origami, a method for constructing nanoscale objects, relies on a long single strand of DNA to act as the 'scaffold' to template assembly of numerous short DNA oligonucleotide 'staples'. The ability to generate custom scaffold sequences can greatly benefit DNA origami design processes. Custom scaffold sequences can provide better control of the overall size of the final object and better control of low-level structural details, such as locations of specific base pairs within an object. Filamentous bacteriophages and related phagemids can work well as sources of custom scaffold DNA. However, scaffolds derived from phages require inclusion of multi-kilobase DNA sequences in order to grow in host bacteria, and those sequences cannot be altered or removed. These fixed-sequence regions constrain the design possibilities of DNA origami. Here, we report the construction of a novel phagemid, pScaf, to produce scaffolds that have a custom sequence with a much smaller fixed region of 393 bases. We used pScaf to generate new scaffolds ranging in size from 1512 to 10 080 bases and demonstrated their use in various DNA origami shapes and assemblies. We anticipate our pScaf phagemid will enhance development of the DNA origami method and its future applications.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461039PMC
http://dx.doi.org/10.1093/synbio/ysy015DOI Listing

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