RT Journal Article
SR Electronic
T1 3D DNA structural barcode copying and random access
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.11.27.401596
DO 10.1101/2020.11.27.401596
A1 Filip Bošković
A1 Alexander Ohmann
A1 Ulrich F. Keyser
A1 Kaikai Chen
YR 2020
UL http://biorxiv.org/content/early/2020/11/27/2020.11.27.401596.abstract
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.