Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures

Di Liu; Cody W Geary; Gang Chen; Yaming Shao; Mo Li; Chengde Mao; Ebbe S Andersen; Joseph A Piccirilli; Paul W K Rothemund; Yossi Weizmann

doi:10.1038/s41557-019-0406-7

Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures

Di Liu, Cody W Geary, Gang Chen, Yaming Shao, Mo Li, Chengde Mao, Ebbe S Andersen, Joseph A Piccirilli, Paul W K Rothemund, Yossi Weizmann

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

51 Citations (Scopus)

Abstract

In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy-homooligomerization-allows efficient genetic encoding of structures and avoids the need to control the stoichiometry of multiple distinct units. It also allows the minimal number of distinct subunits when designing artificial nucleic acid structures. Here, we present a robust self-assembly system in which homooligomerizable tiles are formed from intramolecularly folded RNA single strands. Tiles are linked through an artificially designed branched kissing-loop motif, involving Watson-Crick base pairing between the single-stranded regions of a bulged helix and a hairpin loop. By adjusting the tile geometry to gain control over the curvature, torsion and the number of helices, we have constructed 16 different linear and circular structures, including a finite-sized three-dimensional cage. We further demonstrate cotranscriptional self-assembly of tiles based on branched kissing loops, and show that tiles inserted into a transfer RNA scaffold can be overexpressed in bacterial cells.

Original language	English
Journal	Nature Chemistry
Volume	12
Issue	3
Pages (from-to)	249-259
Number of pages	11
ISSN	1755-4330
DOIs	https://doi.org/10.1038/s41557-019-0406-7
Publication status	Published - 2020

Keywords

COMPLEX
CRYSTAL-STRUCTURE
DESIGN
DNA ORIGAMI
EMERGING FIELD
METAL-IONS
NMR SOLUTION STRUCTURE
POTENTIAL PARTS
RECOMBINANT RNA
TRANSCRIPTION

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10.1038/s41557-019-0406-7

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title = "Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures",

abstract = "In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy-homooligomerization-allows efficient genetic encoding of structures and avoids the need to control the stoichiometry of multiple distinct units. It also allows the minimal number of distinct subunits when designing artificial nucleic acid structures. Here, we present a robust self-assembly system in which homooligomerizable tiles are formed from intramolecularly folded RNA single strands. Tiles are linked through an artificially designed branched kissing-loop motif, involving Watson-Crick base pairing between the single-stranded regions of a bulged helix and a hairpin loop. By adjusting the tile geometry to gain control over the curvature, torsion and the number of helices, we have constructed 16 different linear and circular structures, including a finite-sized three-dimensional cage. We further demonstrate cotranscriptional self-assembly of tiles based on branched kissing loops, and show that tiles inserted into a transfer RNA scaffold can be overexpressed in bacterial cells.",

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author = "Di Liu and Geary, {Cody W} and Gang Chen and Yaming Shao and Mo Li and Chengde Mao and Andersen, {Ebbe S} and Piccirilli, {Joseph A} and Rothemund, {Paul W K} and Yossi Weizmann",

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AU - Liu, Di

AU - Geary, Cody W

AU - Chen, Gang

AU - Shao, Yaming

AU - Li, Mo

AU - Mao, Chengde

AU - Andersen, Ebbe S

AU - Piccirilli, Joseph A

AU - Rothemund, Paul W K

AU - Weizmann, Yossi

PY - 2020

Y1 - 2020

N2 - In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy-homooligomerization-allows efficient genetic encoding of structures and avoids the need to control the stoichiometry of multiple distinct units. It also allows the minimal number of distinct subunits when designing artificial nucleic acid structures. Here, we present a robust self-assembly system in which homooligomerizable tiles are formed from intramolecularly folded RNA single strands. Tiles are linked through an artificially designed branched kissing-loop motif, involving Watson-Crick base pairing between the single-stranded regions of a bulged helix and a hairpin loop. By adjusting the tile geometry to gain control over the curvature, torsion and the number of helices, we have constructed 16 different linear and circular structures, including a finite-sized three-dimensional cage. We further demonstrate cotranscriptional self-assembly of tiles based on branched kissing loops, and show that tiles inserted into a transfer RNA scaffold can be overexpressed in bacterial cells.

AB - In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy-homooligomerization-allows efficient genetic encoding of structures and avoids the need to control the stoichiometry of multiple distinct units. It also allows the minimal number of distinct subunits when designing artificial nucleic acid structures. Here, we present a robust self-assembly system in which homooligomerizable tiles are formed from intramolecularly folded RNA single strands. Tiles are linked through an artificially designed branched kissing-loop motif, involving Watson-Crick base pairing between the single-stranded regions of a bulged helix and a hairpin loop. By adjusting the tile geometry to gain control over the curvature, torsion and the number of helices, we have constructed 16 different linear and circular structures, including a finite-sized three-dimensional cage. We further demonstrate cotranscriptional self-assembly of tiles based on branched kissing loops, and show that tiles inserted into a transfer RNA scaffold can be overexpressed in bacterial cells.

KW - COMPLEX

KW - CRYSTAL-STRUCTURE

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KW - EMERGING FIELD

KW - METAL-IONS

KW - NMR SOLUTION STRUCTURE

KW - POTENTIAL PARTS

KW - RECOMBINANT RNA

KW - TRANSCRIPTION

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SP - 249

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JO - Nature Chemistry

JF - Nature Chemistry

IS - 3

ER -

Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures

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Keywords

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