Out-of-Plane Aptamer Functionalization of RNA Three-Helix Tiles

TY - JOUR

T1 - Out-of-Plane Aptamer Functionalization of RNA Three-Helix Tiles

AU - Chopra, Aradhana

AU - Sagredo, Sandra

AU - Grossi, Guido

AU - Andersen, Ebbe S

AU - Simmel, Friedrich C

PY - 2019/4

Y1 - 2019/4

N2 - Co-transcriptionally folding RNA nanostructures have great potential as biomolecular scaffolds, which can be used to organize small molecules or proteins into spatially ordered assemblies. Here, we develop an RNA tile composed of three parallel RNA double helices, which can associate into small hexagonal assemblies via kissing loop interactions between its two outer helices. The inner RNA helix is modified with an RNA motif found in the internal ribosome entry site (IRES) of the hepatitis C virus (HCV), which provides a 90° bend. This modification is used to functionalize the RNA structures with aptamers pointing perpendicularly away from the tile plane. We demonstrate modifications with the fluorogenic malachite green and Spinach aptamers as well with the protein-binding PP7 and streptavidin aptamers. The modified structures retain the ability to associate into larger assemblies, representing a step towards RNA hybrid nanostructures extending in three dimensions.

AB - Co-transcriptionally folding RNA nanostructures have great potential as biomolecular scaffolds, which can be used to organize small molecules or proteins into spatially ordered assemblies. Here, we develop an RNA tile composed of three parallel RNA double helices, which can associate into small hexagonal assemblies via kissing loop interactions between its two outer helices. The inner RNA helix is modified with an RNA motif found in the internal ribosome entry site (IRES) of the hepatitis C virus (HCV), which provides a 90° bend. This modification is used to functionalize the RNA structures with aptamers pointing perpendicularly away from the tile plane. We demonstrate modifications with the fluorogenic malachite green and Spinach aptamers as well with the protein-binding PP7 and streptavidin aptamers. The modified structures retain the ability to associate into larger assemblies, representing a step towards RNA hybrid nanostructures extending in three dimensions.

U2 - 10.3390/nano9040507

DO - 10.3390/nano9040507

M3 - Journal article

C2 - 30986942

SN - 2079-4991

VL - 9

JO - Nanomaterials (Basel, Switzerland)

JF - Nanomaterials (Basel, Switzerland)

IS - 4

M1 - 507

ER -