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Fluorogenic RNA Aptamers: A Nano-platform for Fabrication of Simple and Combinatorial Logic Gates.

作者信息

Goldsworthy Victoria, LaForce Geneva, Abels Seth, Khisamutdinov Emil F

机构信息

Department of Chemistry, Ball State University, Muncie, IN 47304, USA.

出版信息

Nanomaterials (Basel). 2018 Nov 28;8(12):984. doi: 10.3390/nano8120984.


DOI:10.3390/nano8120984
PMID:30486495
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6315349/
Abstract

RNA aptamers that bind non-fluorescent dyes and activate their fluorescence are highly sensitive, nonperturbing, and convenient probes in the field of synthetic biology. These RNA molecules, referred to as light-up aptamers, operate as molecular nanoswitches that alter folding and fluorescence function in response to ligand binding, which is important in biosensing and molecular computing. Herein, we demonstrate a conceptually new generation of smart RNA nano-devices based on malachite green (MG)-binding RNA aptamer, which fluorescence output controlled by addition of short DNA oligonucleotides inputs. Four types of RNA switches possessing AND, OR, NAND, and NOR Boolean logic functions were created in modular form, allowing MG dye binding affinity to be changed by altering 3D conformation of the RNA aptamer. It is essential to develop higher-level logic circuits for the production of multi-task nanodevices for data processing, typically requiring combinatorial logic gates. Therefore, we further designed and synthetized higher-level half adder logic circuit by "in parallel" integration of two logic gates XOR and AND within a single RNA nanoparticle. The design utilizes fluorescence emissions from two different RNA aptamers: MG-binding RNA aptamer (AND gate) and Broccoli RNA aptamer that binds DFHBI dye (XOR gate). All computationally designed RNA devices were synthesized and experimentally tested in vitro. The ability to design smart nanodevices based on RNA binding aptamers offers a new route to engineer "label-free" ligand-sensing regulatory circuits, nucleic acid detection systems, and gene control elements.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af39/6315349/89daa7d4812c/nanomaterials-08-00984-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af39/6315349/554782a0368e/nanomaterials-08-00984-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af39/6315349/7e2caf1ca987/nanomaterials-08-00984-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af39/6315349/87deb39a70fd/nanomaterials-08-00984-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af39/6315349/89daa7d4812c/nanomaterials-08-00984-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af39/6315349/554782a0368e/nanomaterials-08-00984-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af39/6315349/7e2caf1ca987/nanomaterials-08-00984-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af39/6315349/87deb39a70fd/nanomaterials-08-00984-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af39/6315349/89daa7d4812c/nanomaterials-08-00984-g004.jpg

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Fluorogenic RNA Aptamers: A Nano-platform for Fabrication of Simple and Combinatorial Logic Gates.

Nanomaterials (Basel). 2018-11-28

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本文引用的文献

[1]
Structure and Composition Define Immunorecognition of Nucleic Acid Nanoparticles.

Nano Lett. 2018-6-20

[2]
Aptamer-based biosensors and nanosensors for the detection of vascular endothelial growth factor (VEGF): A review.

Biosens Bioelectron. 2018-3-19

[3]
RNA-Based Fluorescent Biosensors for Detecting Metabolites in vitro and in Living Cells.

Adv Pharmacol. 2018

[4]
Ribocomputing: Cellular Logic Computation Using RNA Devices.

Biochemistry. 2018-2-13

[5]
Programmable Nucleic Acid Based Polygons with Controlled Neuroimmunomodulatory Properties for Predictive QSAR Modeling.

Small. 2017-9-18

[6]
A review: Aptamer-based analytical strategies using the nanomaterials for environmental and human monitoring of toxic heavy metals.

Talanta. 2017-6-27

[7]
Development and characterization of Sindbis virus with encoded fluorescent RNA aptamer Spinach2 for imaging of replication and immune-mediated changes in intracellular viral RNA.

J Gen Virol. 2017-5

[8]
Functionally-interdependent shape-switching nanoparticles with controllable properties.

Nucleic Acids Res. 2017-2-28

[9]
Versatile RNA tetra-U helix linking motif as a toolkit for nucleic acid nanotechnology.

Nanomedicine. 2017-4

[10]
Fabrication of RNA 3D Nanoprisms for Loading and Protection of Small RNAs and Model Drugs.

Adv Mater. 2016-10-19

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