Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers

Quarterly Reviews of Biophysics - Tập 52 - 2019
Robert J. Trachman1, A.R. Ferré-D′Amaré1
1Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA

Tóm tắt

AbstractFluorescence turn-on aptamers,in vitroevolved RNA molecules that bind conditional fluorophores and activate their fluorescence, have emerged as RNA counterparts of the fluorescent proteins. Turn-on aptamers have been selected to bind diverse fluorophores, and they achieve varying degrees of specificity and affinity. These RNA–fluorophore complexes, many of which exceed the brightness of green fluorescent protein and their variants, can be used as tags for visualizing RNA localization and transport in live cells. Structure determination of several fluorescent RNAs revealed that they have diverse, unrelated overall architectures. As most of these RNAs activate the fluorescence of their ligands by restraining their photoexcited states into a planar conformation, their fluorophore binding sites have in common a planar arrangement of several nucleobases, most commonly a G-quartet. Nonetheless, each turn-on aptamer has developed idiosyncratic structural solutions to achieve specificity and efficient fluorescence turn-on. The combined structural diversity of fluorophores and turn-on RNA aptamers has already produced combinations that cover the visual spectrum. Further molecular evolution and structure-guided engineering is likely to produce fluorescent tags custom-tailored to specific applications.

Từ khóa


Tài liệu tham khảo

10.1038/ncomms4626

10.1038/srep24793

10.1038/nchembio.2475

10.1021/bi00262a003

10.1039/c3sc50729g

10.1016/j.tibs.2007.08.005

10.1126/science.2200121

10.1002/chem.200600699

10.1073/pnas.95.16.9244

10.1021/ja0530319

10.1038/nsmb.2865

10.1016/S1359-0278(98)00059-5

10.1261/rna.5205404

10.1016/j.tips.2017.06.007

Arora, 2015, Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers, Nucleic Acids Research, 43, e144

10.1261/rna.051797.115

10.1021/ja508478x

10.1016/j.cell.2016.02.054

10.1016/S0968-0896(01)00031-1

10.1016/j.tibs.2015.02.004

10.1016/j.jsb.2018.09.013

10.1038/346818a0

10.3389/fchem.2016.00029

10.1021/ja037994o

10.1021/ja410819x

10.1093/nar/gkw083

10.1038/nsmb1327

10.1038/nmeth.4403

10.1021/jp981185n

10.1021/jacs.7b04211

10.1016/S1097-2765(00)80143-4

10.1021/acssynbio.7b00059

10.1093/nar/13.5.1717

10.1021/jacs.7b10724

Alam, 2019, Rapid, low-cost detection of water contaminants using regulated in vitro transcription, bioRxiv, 619296

10.1038/s41589-019-0267-9

10.1038/s41467-017-02435-x

10.1021/acs.biochem.8b00399

10.1016/j.cbpa.2011.10.006

10.1016/j.biochi.2019.04.018

10.1261/rna.063008.117

10.1261/rna.056325.116

10.1146/annurev-biochem-061516-044839

10.1261/rna.056226.116

10.1038/s41598-018-20960-7

10.1016/j.bbagrm.2014.02.012

10.1038/s41467-018-02993-8

10.1038/423689a

10.1002/cbic.200300701

10.1021/acs.accounts.6b00517

10.1038/348548a0

10.1073/pnas.96.11.6131

10.1126/science.1207339

10.3390/molecules23123178

10.1038/srep03615

10.1371/journal.pgen.1003569

10.1021/jacs.5b00275

10.1146/annurev-biochem-013118-110744

10.1038/nchembio.1561

10.1038/nchembio.2477

10.1002/wrna.1383

10.1021/cb500499x

10.1073/pnas.1515737112

10.1021/ja308629w

10.1201/b16869

10.1093/nar/gkx1292

10.1002/(SICI)1097-0282(199807)46:1<39::AID-BIP4>3.0.CO;2-Z

10.1006/jmbi.2000.3951

10.1021/acs.biochem.7b00529

10.1021/ja9016864

10.1038/nbt0102-83

10.1021/cb700248m

10.1039/B920865H

Troung, 2019, From fluorescent proteins to fluorogenic RNAs: tools for imaging cellular macromolecules, Protein Science, 28, 1374, 10.1002/pro.3632

10.1006/jmbi.2002.5422

10.1038/s41589-018-0103-7

10.1073/pnas.93.24.13617

10.1016/S1387-2656(05)11007-2

10.1002/chem.201805882

10.1002/anie.201306622

10.1021/ja411060p

10.1016/S0969-2126(01)00156-3

10.1021/ja027635d

10.1021/ja309588h

10.1126/science.1218298

You, 2015, Annual Review of Biophysics, 187

10.1073/pnas.91.26.12501

10.1093/nar/gku111

10.3390/genes3030344

10.1002/cbic.200500538

10.1073/pnas.0914365107

10.1021/ja101974k

10.1038/nsmb.2064

10.1021/ol702920e

10.1016/j.tibs.2016.09.010

10.1016/j.jsb.2011.02.004

10.1021/sb5000725

10.1016/j.sbi.2007.05.004

10.1038/s41467-018-06942-3

10.1021/ja3018972

Sjekloća, 2019, Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence, Cell Chem Biol, 30143

10.1021/ja070111z

10.1038/nmeth1023

10.1038/nmeth.3935

10.1038/nmeth.2701

10.2174/138161212799958477

10.1038/nchembio.138

10.1038/344467a0

10.1038/nchembio.2392

Thông tin
Thông tin xuất bản

Quarterly Reviews of Biophysics

Tập 52

Thông tin tác giả