Integrating DNA strand-displacement circuitry with DNA tile self-assembly

Abstract

DNA nanotechnology has emerged as a reliable and programmable way of controlling matter at the nanoscale through the specificity of Watson–Crick base pairing, allowing both complex self-assembled structures with nanometer precision and complex reaction networks implementing digital and analog behaviors. Here we show how two well-developed frameworks, DNA tile self-assembly and DNA strand-displacement circuits, can be systematically integrated to provide programmable kinetic control of self-assembly. We demonstrate the triggered and catalytic isothermal self-assembly of DNA nanotubes over 10 μm long from precursor DNA double-crossover tiles activated by an upstream DNA catalyst network. Integrating more sophisticated control circuits and tile systems could enable precise spatial and temporal organization of dynamic molecular structures.

Programmable disorder in random DNA tilings

“…15 Staples with extensions for creating patterns T-T1R06C3 TTAAGAGGGTCCAATACTGCGGATAGCGAGTTTTTTTTTTTTTTTTTTTT T-T1R06C5 GTCAGAAGATTGAATCCCCCTCAACCTCGTTTTTTTTTTTTTTTTTTTTTTT T-T1R08C3 AGGCTTTTCAGGTAGAAAGATTCAATTACCTTTTTTTTTTTTTTTTTTTT T-T1R08C5 ACCAGACGGAATACCACATTCAACGAGATGGTTTTTTTTTTTTTTTTTTTTT T-T1R09C1 CGAACTAAATTATACCAGTCAGGACATAGGCTGGCTGACCTTTGAAAGTTTTTTTTTTTTTTTTTTTT T-T1R10C3 TTATGCGATTGACAAGAACCGGAGGTCAATTTTTTTTTTTTTTTTTTTTT T-T1R10C5 TTAATTTCCAACGTAACAAAGCTGTCCATGTTTTTTTTTTTTTTTTTTTTTT T-T1R11C4 ACCCAAATAACTTTAATCATTGTGATCAGTTGTTTTTTTTTTTTTTTTTTTT T-T1R11C6 GTGAATATAGTAAATTGGGCTTTAATGCAGTTTTTTTTTTTTTTTTTTTT T-T1R13C2 AAAAGAATAACCGAACTGACCAACTTCATCAATTTTTTTTTTTTTTTTTTTT T-T1R13C4 CCCCAGCGGGAACGAGGCGCAGACTATTCATTTTTTTTTTTTTTTTTTTTTT T-T1R13C6 ACAACGGAAATCCGCGACCTGCCTCATTCATTTTTTTTTTTTTTTTTTTT T-T1R15C4 GAGTTAAATTCATGAGGAAGTTTCTCTTTGACTTTTTTTTTTTTTTTTTTTT T-T1R15C6 CTCAGCAGGCTACAGAGGCTTTAACAAAGTTTTTTTTTTTTTTTTTTTTT T-T2R06C3 GTCTCTGACACCCTCAGAGCCACATCAAAATTTTTTTTTTTTTTTTTTTT T-T2R06C5 AATCCTCAACCAGAACCACCACCAGCCCCCTTTTTTTTTTTTTTTTTTTTTT T-T2R08C3 TCACCGGAAACGTCACCAATGAATTATTCATTTTTTTTTTTTTTTTTTTT T-T2R08C5 ATTAGCGTCCGTAATCAGTAGCGAATTGAGGGTTTTTTTTTTTTTTTTTTTT T-T2R09C1 ACCATTACCGACTTGAGCCATTTGCAAACGTAGAAAATACCTGGCATGTTTTTTTTTTTTTTTTTTTT T-T2R10C3 TTAAAGGTACATATAAAAGAAACAAACGCATTTTTTTTTTTTTTTTTTTT T-T2R10C5 AGGGAAGGATAAGTTTATTTTGTCAGCCGAACTTTTTTTTTTTTTTTTTTTT T-T2R11C4 ACCACGGATAAATATTGACGGAAAACCATCGATTTTTTTTTTTTTTTTTTTT T-T2R11C6 TAGAAAAGGCGACATTCAACCGCAGAATCATTTTTTTTTTTTTTTTTTTT T-T2R13C2 CGCTAATAGGAATACCCAAAAGAAATACATAATTTTTTTTTTTTTTTTTTTT T-T2R13C4 TGAGTTAACAGAAGGAAACCGAGGGCAAAGACTTTTTTTTTTTTTTTTTTTT T-T2R13C6 ATGAAATGAAAAGTAAGCAGATACAATCAATTTTTTTTTTTTTTTTTTTT T-T2R15C4 TGCCAGTTATAACATAAAAACAGGACAAGAATTTTTTTTTTTTTTTTTTTTT T-T2R15C6 ATCCCAAAAAAATGAAAATAGCAAGAAACATTTTTTTTTTTTTTTTTTTT T-T3R06C3 TATATAACGTAAATCGTCGCTATATTTGAATTTTTTTTTTTTTTTTTTTT T-T3R06C5 CTACCTTTAGAATCCTTGAAAACAAGAAAACATTTTTTTTTTTTTTTTTTTT T-T3R08C3 TTACCTTTACAATAACGGATTCGCAAAATTTTTTTTTTTTTTTTTTTTTT T-T3R08C5 AAATTAATACCAAGTTACAAAATCCTGAATAATTTTTTTTTTTTTTTTTTTT T-T3R09C1 ACAGTACCGAAATTGCGTAGATTTGTTATTAATTTTAAAAAACAATTCTTTTTTTTTTTTTTTTTTTT T-T3R10C3 ATTTGCACCATTTTGCGGAACAAATTTGAGTTTTTTTTTTTTTTTTTTTT T-T3R10C5 TGGAAGGGAGCGGAATTATCATCAACTAATAGTTTTTTTTTTTTTTTTTTTT T-T3R11C4 C...…”

Nanotechnology and the Unique Role of DNA

“…This can be achieved by insertion of mismatched bps, thus allowing to tune the energy landscape of the reaction in a predictable way. A remarkable example of the extreme degree of control achievable using DNA nanotechnology tools is represented by the work of Winfree and coauthors [103]. There, they showed how two well-defined frameworks, i.e.…”

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

“…Multiple such reactions can be chained together into multi-step reaction cascades with a high degree of control over the order and timing of individual reaction steps 3 . DNA strand displacement cascades have been used to create digital and analog molecular circuits [4][5][6][7] , switchable nanostructures [8][9][10] , autonomous molecular motors [11][12][13][14][15] , and non-covalent catalytic amplifiers 13,[16][17][18][19][20][21] . Moreover, DNA devices using strand displacement reactions can be simulated and designed for diverse applications using computer-assisted design software [22][23][24] .…”