PT  - JOURNAL ARTICLE
AU  - Bošković, Filip
AU  - Ohmann, Alexander
AU  - Keyser, Ulrich F.
AU  - Chen, Kaikai
TI  - 3D DNA structural barcode copying and random access
AID  - 10.1101/2020.11.27.401596
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.11.27.401596
4099  - http://biorxiv.org/content/early/2020/11/27/2020.11.27.401596.short
4100  - http://biorxiv.org/content/early/2020/11/27/2020.11.27.401596.full
AB  - Three-dimensional (3D) DNA nanostructures built via DNA self-assembly have established recent applications in multiplexed biosensing and storing digital information. However, a key challenge is that 3D DNA structures are not easily copied which is of vital importance for their large-scale production and for access to desired molecules by target-specific amplification. Here, we build 3D DNA structural barcodes and demonstrate the copying and random access of the barcodes from a library of molecules using a modified polymerase chain reaction (PCR). The 3D barcodes were assembled by annealing a single-stranded DNA scaffold with complementary short oligonucleotides containing 3D protrusions at defined locations. DNA nicks in these structures are ligated to facilitate barcode copying using PCR. To randomly access a target from a library of barcodes, we employ a non-complementary end in the DNA construct that serves as a barcode-specific primer template. Readout of the 3D DNA structural barcodes was performed with nanopore measurements. Our study provides a roadmap for convenient production of large quantities of self-assembled 3D DNA nanostructures. In addition, this strategy offers access to specific targets, a crucial capability for multiplexed single-molecule sensing and for DNA data storage.Competing Interest StatementThe authors have declared no competing interest.