Volume 7 Issue 1
Feb.  2021
Turn off MathJax
Article Contents
Article Navigation >  Biophysics Reports  > 2021  >  7(1): 21-34
Kai Jiao, Yaya Hao, Fei Wang, Lihua Wang, Chunhai Fan, Jiang Li. Structurally reconfigurable designer RNA structures for nanomachines[J]. Biophysics Reports, 2021, 7(1): 21-34. doi: 10.52601/bpr.2021.200053
Citation: Kai Jiao, Yaya Hao, Fei Wang, Lihua Wang, Chunhai Fan, Jiang Li. Structurally reconfigurable designer RNA structures for nanomachines[J]. Biophysics Reports, 2021, 7(1): 21-34. doi: 10.52601/bpr.2021.200053
shu

Structurally reconfigurable designer RNA structures for nanomachines

doi: 10.52601/bpr.2021.200053
  • 1.

    Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; University of Chinese Academy of Sciences, Beijing 100049, China

  • 2.

    School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China

  • 3.

    The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China

Funds:  This work was supported by the National Key Research and Development Program (2020YFA0908900), the National Natural Science Foundation of China (21775157, 21775104, 11705270, 21834007), the Shanghai Municipal Science and Technology Commission (19JC1410300), the LU JIAXI International team program supported by the K.C. Wong Education Foundation, the National Major Special Project for the Development of Transgenic Organisms (2018ZX08011-04B), the Open Large Infrastructure Research and the Youth Innovation Promotion Association of CAS (2012205, 2016236).
More Information
    Abstract
  • Structurally reconfigurable RNA structures enable dynamic transitions of the functional states in response to diverse molecular stimuli, which are fundamental in genetic and epigenetic regulations. Inspired by nature, rationally designed RNA structures with responsively reconfigurable motifs have been developed to serve as switchable components for building engineered nanomachines, which hold promise in synthetic biological applications. In this review, we summarize recent progress in the design, synthesis, and integration of engineered reconfigurable RNA structures for nanomachines. We highlight recent examples of their targeted applications such as biocomputing and smart theranostics. We also discuss their advantages, challenges as well as possible solutions. We further provide an outlook of their potential in future synthetic biology.
    • FullText(HTML)
  • loading
    • References(105)
  • [1]
    Abbink TEM, Ooms M, Haasnoot PCJ, Berkhout B (2005) The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation. Biochemistry 44(25): 9058−9066 doi: 10.1021/bi0502588
    [2]
    Afonin KA, Viard M, Koyfman AY, Martins AN, Kasprzak WK, Panigaj M, Desai R, Santhanam A, Grabow WW, Jaeger L, Heldman E, Reiser J, Chiu W, Freed EO, Shapiro BA (2014) Multifunctional RNA nanoparticles. Nano Lett 14(10): 5662−5671 doi: 10.1021/nl502385k
    [3]
    Agapakis CM, Silver PA (2009) Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks. Mol Biosyst 5(7): 704−713 doi: 10.1039/b901484e
    [4]
    Bailor MH, Sun XY, Al-Hashimi HM (2010) Topology links RNA secondary structure with global conformation, dynamics, and adaptation. Science 327(5962): 202−206 doi: 10.1126/science.1181085
    [5]
    Batey RT, Gilbert SD, Montange RK (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432(7015): 411−415 doi: 10.1038/nature03037
    [6]
    Bayer TS, Smolke CD (2005) Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat Biotechnol 23(3): 337−343 doi: 10.1038/nbt1069
    [7]
    Beilstein K, Wittmann A, Grez M, Suess B (2015) Conditional control of mammalian gene expression by tetracycline-dependent hammerhead ribozymes. ACS Synth Biol 4(5): 526−534 doi: 10.1021/sb500270h
    [8]
    Birikh KR, Heaton PA, Eckstein F (1997) The structure, function and application of the hammerhead ribozyme. Eur J Biochem 245(1): 1−16 doi: 10.1111/j.1432-1033.1997.t01-3-00001.x
    [9]
    Broughton JP, Deng XD, Yu GX, Fasching CL, Servellita V, Singh J, Miao X, Streithorst JA, Granados A, Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan CY, Guevara H, Wadford DA, Chen JS, Chiu CY (2020) CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol 38(7): 870−U854 doi: 10.1038/s41587-020-0513-4
    [10]
    Callura JM, Cantor CR, Collins JJ (2012) Genetic switchboard for synthetic biology applications. Proc Natl Acad Sci USA 109(15): 5850−5855 doi: 10.1073/pnas.1203808109
    [11]
    Chakraborty K, Veetil AT, Jaffrey SR, Krishnan Y (2016) Nucleic acid-based nanodevices in biological imaging. Ann Rev Biochem 85(1): 349−373 doi: 10.1146/annurev-biochem-060815-014244
    [12]
    Chakraborty S, Mehtab S, Krishnan Y (2014) The predictive power of synthetic nucleic acid technologies in RNA biology. Acc Chem Res 47(6): 1710−1719 doi: 10.1021/ar400323d
    [13]
    Chan K, Ng TB (2015) In-vitro nanodiagnostic platform through nanoparticles and DNA–RNA nanotechnology. Appl Microbiol Biotechnol 99(8): 3359−3374 doi: 10.1007/s00253-015-6506-4
    [14]
    Chappell J, Takahashi MK, Lucks JB (2015) Creating small transcription activating RNAs. Nat Chem Biol 11(3): 214−U165 doi: 10.1038/nchembio.1737
    [15]
    Chen JS, Ma EB, Harrington LB, Da Costa M, Tian XR, Palefsky JM, Doudna JA (2018) CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360(6387): 436−439 doi: 10.1126/science.aar6245
    [16]
    Daniel R, Rubens JR, Sarpeshkar R, Lu TK (2013) Synthetic analog computation in living cells. Nature 497(7451): 619−623 doi: 10.1038/nature12148
    [17]
    Darmostuk M, Rimpelova S, Gbelcova H, Ruml T (2015) Current approaches in SELEX: an update to aptamer selection technology. Biotechnol Adv 33(6): 1141−1161 doi: 10.1016/j.biotechadv.2015.02.008
    [18]
    Delebecque CJ, Lindner AB, Silver PA, Aldaye FA (2011) Organization of intracellular reactions with rationally designed RNA assemblies. Science 333(6041): 470−474 doi: 10.1126/science.1206938
    [19]
    Durbin JK, Miller DK, Niekamp J, Khisamutdinov EF (2019) Modulating immune response with nucleic acid nanoparticles. Molecules 24(20
    [20]
    Dwidar M, Seike Y, Kobori S, Whitaker C, Matsuura T, Yokobayashi Y (2019) Programmable artificial cells using histamine-responsive synthetic riboswitch. J Am Chem Soc 141(28): 11103−11114 doi: 10.1021/jacs.9b03300
    [21]
    Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346(6287): 818−822 doi: 10.1038/346818a0
    [22]
    Gasiunas G, Barrangou R, Horvath P, Siksnys V (2012) Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci USA 109(39): E2579−E2586 doi: 10.1073/pnas.1208507109
    [23]
    Ge ZL, Gu HZ, Li Q, Fan CH (2018) Concept and development of framework nucleic acids. J Am Chem Soc 140(51): 17808−17819 doi: 10.1021/jacs.8b10529
    [24]
    Geary C, Rothemund PWK, Andersen ES (2014) A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Science 345(6198): 799−804 doi: 10.1126/science.1253920
    [25]
    Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F (2017) Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356(6336): 438−442 doi: 10.1126/science.aam9321
    [26]
    Grabow WW, Jaeger L (2014) RNA self-assembly and RNA nanotechnology. Acc Chem Res 47(6): 1871−1880 doi: 10.1021/ar500076k
    [27]
    Green AA, Kim JM, Ma D, Ilver PAS, Collins JJ, Yin P (2017) Complex cellular logic computation using ribocomputing devices. Nature 548(7665): 117−121 doi: 10.1038/nature23271
    [28]
    Green AA, Silver PA, Collins JJ, Yin P (2014) Toehold switches: de-novo-designed regulators of gene expression. Cell 159(4): 925−939 doi: 10.1016/j.cell.2014.10.002
    [29]
    Greider CW, Blackburn EH (1987) The telomere terminal transferase of tetrahymena is a ribonucleoprotein enzyme with 2 kinds of primer specificity. Cell 51(6): 887−898 doi: 10.1016/0092-8674(87)90576-9
    [30]
    Guo PX (2010) The emerging field of RNA nanotechnology. Nat Nanotech 5(12): 833−842 doi: 10.1038/nnano.2010.231
    [31]
    Guo S, Vieweger M, Zhang K, Yin H, Wang H, Li X, Li S, Hu S, Sparreboom A, Evers BM, Dong Y, Chiu W, Guo P (2020) Ultra-thermostable RNA nanoparticles for solubilizing and high-yield loading of paclitaxel for breast cancer therapy. Nat Commun 11(1): 972. https://doi.org/10.1038/s41467-020-14780-5
    [32]
    Han D, Qi X, Myhrvold C, Wang B, Dai M, Jiang S, Bates M, Liu Y, An B, Zhang F, Yan H, Yin P (2017) Single-stranded DNA and RNA origami. Science 358(6369): eaao2648. https://doi.org/10.1126/science.aao2648
    [33]
    Hao CH, Li X, Tian C, Jiang W, Wang GS, Mao CD (2014) Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage. Nat Commun 5: 3890. https://doi.org/10.1038/ncomms4890
    [34]
    Hao Y, Li J, Li Q, Zhang L, Shi JY, Zhang X, Aldalbahi A, Wang L, Fan C, Wang F (2020) Programmable live-cell CRISPR imaging with toehold-switch-mediated strand displacement. Angew Chem Int Ed Engl 59(46): 20612−20618 doi: 10.1002/anie.202009062
    [35]
    Hong F, Ma D, Wu K, Mina LA, Luiten RC, Liu Y, Yan H, Green AA (2020) Precise and programmable detection of mutations using ultraspecific riboregulators. Cell 180(5): 1018−1032 e1016 doi: 10.1016/j.cell.2020.02.011
    [36]
    Hu QQ, Li H, Wang LH, Gu HZ, Fan CH (2019) DNA nanotechnology-enabled drug delivery systems. Chem Rev 119(10): 6459−6506
    [37]
    Isaacs FJ, Dwyer DJ, Collins JJ (2006) RNA synthetic biology. Nat Biotechnol 24(5): 545−554 doi: 10.1038/nbt1208
    [38]
    Ishikawa J, Furuta H, Ikawa Y (2013) RNA tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology. Wiley Interdiscip Rev-RNA 4(6): 651−664 doi: 10.1002/wrna.1185
    [39]
    Jang M, Kim JH, Nam HY, Kwon IC, Ahn HJ (2015) Design of a platform technology for systemic delivery of siRNA to tumours using rolling circle transcription. Nat Commun 6: 7930. https://doi.org/10.1038/ncomms8930
    [40]
    Jasinski D, Haque F, Binzel DW, Guo PX (2017) Advancement of the emerging field of RNA nanotechnology. Acs Nano 11(2): 1142−1164 doi: 10.1021/acsnano.6b05737
    [41]
    Jepsen MDE, Sparvath SM, Nielsen TB, Langvad AH, Grossi G, Gothelf KV, Andersen ES (2018) Development of a genetically encodable FRET system using fluorescent RNA aptamers. Nat Commun 9(1): 18. https://doi.org/10.1038/s41467-017-02435-x
    [42]
    Jiao K, Zhu B, Guo L, Zhou H, Wang F, Zhang X, Shi J, Li Q, Wang L, Li J, Fan C (2020) Programming switchable transcription of topologically constrained DNA. J Am Chem Soc 142(24): 10739−10746 doi: 10.1021/jacs.0c01962
    [43]
    Jin MK, de Loubresse NG, Kim Y, Kim J, Yin P (2019) Programmable CRISPR-Cas repression, activation, and computation with sequence-independent targets and triggers. ACS Synth Biol 8(7): 1583−1589 doi: 10.1021/acssynbio.9b00141
    [44]
    Kawazoe N, Teramoto N, Ichinari H, Imanishi Y, Ito Y (2001) In vitro selection of nonnatural ribozyme-catalyzing porphyrin metalation. Biomacromolecules 2(3): 681−686 doi: 10.1021/bm000148a
    [45]
    Kedde M, van Kouwenhove M, Zwart W, Vrielink JAFO, Elkon R, Agami R (2010) A Pumilio-induced RNA structure switch in p27-3' UTR controls miR-221 and miR-222 accessibility. Nat Cell Biol 12(10): 1014−1020 doi: 10.1038/ncb2105
    [46]
    Khaled A, Guo SC, Li F, Guo PX (2005) Controllable self-assembly of nanoparticles for specific delivery of multiple therapeutic molecules to cancer cells using RNA nanotechnology. Nano Lett 5(9): 1797−1808 doi: 10.1021/nl051264s
    [47]
    Khan AU (2006) Ribozyme: a clinical tool. Clin Chim Acta 367(1-2): 20−27 doi: 10.1016/j.cca.2005.11.023
    [48]
    Khisamutdinov EF, Jasinski DL, Guo P (2014) RNA as a boiling-resistant anionic polymer material to build robust structures with defined shape and stoichiometry. ACS Nano 8(5): 4771−4781 doi: 10.1021/nn5006254
    [49]
    Kim J, Zhou Y, Carlson PD, Teichmann M, Chaudhary S, Simmel FC, Silver PA, Collins JJ, Lucks JB, Yin P, Green AA (2019) De novo-designed translation-repressing riboregulators for multi-input cellular logic. Nat Chem Biol 15(12): 1173−1182 doi: 10.1038/s41589-019-0388-1
    [50]
    Krishnan Y, Bathe M (2012) Designer nucleic acids to probe and program the cell. Trends Cell Biol 22(12): 624−633 doi: 10.1016/j.tcb.2012.10.001
    [51]
    Lau MWL, Ferre-D'Amare AR (2016) In vitro evolution of coenzyme-independent variants from the glmS ribozyme structural scaffold. Methods 106: 76−81 doi: 10.1016/j.ymeth.2016.04.027
    [52]
    Lee JB, Hong J, Bonner DK, Poon Z, Hammond PT (2012) Self-assembled RNA interference microsponges for efficient siRNA delivery. Nat Mater 11(4): 316−322 doi: 10.1038/nmat3253
    [53]
    Li H, Zhang KM, Pi FM, Guo SJ, Shlyakhtenko L, Chiu W, Shu D, Guo PX (2016) Controllable self-assembly of RNA tetrahedrons with precise shape and size for cancer targeting. Adv Mater 28(34): 7501−7507 doi: 10.1002/adma.201601976
    [54]
    Li J, Green AA, Yan H, Fan C (2017) Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation. Nat Chem 9(11): 1056−1067 doi: 10.1038/nchem.2852
    [55]
    Li M, Zheng M, Wu S, Tian C, Liu D, Weizmann Y, Jiang W, Wang G, Mao C (2018) In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs. Nat Commun 9(1): 2196. https://doi.org/10.1038/s41467-018-04652-4
    [56]
    Li YL, Vergne J, Torchet C, Maurel MC (2009) In vitro selection of adenine-dependent ribozyme against Tpl2/Cot oncogene. Febs J 276(1): 303−314 doi: 10.1111/j.1742-4658.2008.06780.x
    [57]
    Liu SR, Hu CG, Zhang JZ (2016a) Regulatory effects of cotranscriptional RNA structure formation and transitions. Wiley Interdiscip Rev-RNA 7(5): 562−574 doi: 10.1002/wrna.1350
    [58]
    Liu XG, Zhang F, Jing XX, Pan MC, Liu P, Li W, Zhu BW, Li J, Chen H, Wang LH, Lin JP, Liu Y, Zhao DY, Yan H, Fan CH (2018) Complex silica composite nanomaterials templated with DNA origami. Nature 559(7715): 593−598 doi: 10.1038/s41586-018-0332-7
    [59]
    Liu YC, Zhan YH, Chen ZC, He AB, Li JF, Wu HW, Liu L, Zhuang CL, Lin JH, Guo XQ, Zhang QX, Huang WR, Cai ZM (2016b) Directing cellular information flow via CRISPR signal conductors. Nat Meth 13(11): 938−944 doi: 10.1038/nmeth.3994
    [60]
    Ma SY, Tang N, Tian JD (2012) DNA synthesis, assembly and applications in synthetic biology. Curr Opin Chem Biol 16(3-4): 260−267 doi: 10.1016/j.cbpa.2012.05.001
    [61]
    Maniatis T, Reed R (1987) The role of small nuclear ribonucleoprotein-particles in pre-messenger-RNA splicing. Nature 325(6106): 673−678 doi: 10.1038/325673a0
    [62]
    Meyer S, Chappell J, Sankar S, Chew R, Lucks JB (2016) Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies. Biotechnol Bioeng 113(1): 216−225 doi: 10.1002/bit.25693
    [63]
    Munzar JD, Ng A, Juncker D (2019) Duplexed aptamers: history, design, theory, and application to biosensing. Chem Soc Rev 48(5): 1390−1419 doi: 10.1039/C8CS00880A
    [64]
    Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC, Durbin AF, Kellner MJ, Tan AL, Paul LM, Parham LA, Garcia KF, Barnes KG, Chak B, Mondini A, Nogueira ML, Isern S, Michael SF, Lorenzana I, Yozwiak NL, MacInnis BL, Bosch I, Gehrke L, Zhang F, Sabeti PC (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360(6387): 444−448 doi: 10.1126/science.aas8836
    [65]
    Neubacher S, Hennig S (2019) RNA structure and cellular applications of fluorescent light-up aptamers. Angew Chem Int Ed Engl 58(5): 1266−1279 doi: 10.1002/anie.201806482
    [66]
    Nudler E, Mironov AS (2004) The riboswitch control of bacterial metabolism. Trends Biochem Sci 29(1): 11−17 doi: 10.1016/j.tibs.2003.11.004
    [67]
    Oesinghaus L, Simme FC (2019) Switching the activity of Cas12a using guide RNA strand displacement circuits. Nat Commun 10(1): 2092. https://doi.org/10.1038/s41467-019-09953-w
    [68]
    Ogawa A, Maeda M (2008) An artificial aptazyme-based riboswitch and its cascading system in E. coli. Chembiochem 9(2): 206−209 doi: 10.1002/cbic.200700478
    [69]
    Ohno H, Kobayashi T, Kabata R, Endo K, Iwasa T, Yoshimura SH, Takeyasu K, Inoue T, Saito H (2011) Synthetic RNA-protein complex shaped like an equilateral triangle. Nat Nanotech 6(2): 115−119
    [70]
    Omabegho T, Gurel PS, Cheng CY, Kim LY, Ruijgrok PV, Das R, Alushin GM, Bryant Z (2017) Controllable molecular motors engineered from myosin and RNA. Nat Nanotechnol 13(1): 34−40
    [71]
    Osada E, Suzuki Y, Hidaka K, Ohno H, Sugiyama H, Endo M, Saito H (2014) Engineering RNA-protein complexes with different shapes for imaging and therapeutic applications. ACS Nano 8(8): 8130−8140 doi: 10.1021/nn502253c
    [72]
    Ozer A, Pagano JM, Lis JT (2014) New technologies provide quantum changes in the scale, speed, and success of SELEX methods and aptamer characterization. Mol TherNucleic Acids 3(8): e183. https://doi.org/10.1038/mtna.2014.34
    [73]
    Paige JS, Nguyen-Duc T, Song W, Jaffrey SR (2012) Fluorescence imaging of cellular metabolites with RNA. Science 335(6073): 1194. https://doi.org/10.1126/science.1218298
    [74]
    Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P, Collins JJ (2014) Paper-based synthetic gene networks. Cell 159(4): 940−954 doi: 10.1016/j.cell.2014.10.004
    [75]
    Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M, Daringer NM, Bosch I, Dudley DM, O'Connor DH, Gehrke L, Collins JJ (2016) Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165(5): 1255−1266 doi: 10.1016/j.cell.2016.04.059
    [76]
    Pothoulakis G, Ceroni F, Reeve B, Ellis T (2014) The spinach RNA aptamer as a characterization tool for synthetic biology. ACS Synth Biol 3(3): 182−187 doi: 10.1021/sb400089c
    [77]
    Purnick PEM, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10(6): 410−422
    [78]
    Qiu M, Khisamutdinov E, Zhao Z, Pan C, Choi J-W, Leontis NB, Guo P (2013) RNA nanotechnology for computer design and in vivo computation. Philos Trans AMath Phys Eng Sci 371(2000): 20120310. https://doi.org/10.1098/rsta.2012.0310
    [79]
    Ray PS, Jia J, Yao P, Majumder M, Hatzoglou M, Fox PL (2009) A stress-responsive RNA switch regulates VEGFA expression. Nature 457(7231): 915−919 doi: 10.1038/nature07598
    [80]
    Regev A, Shapiro E (2002) Cellular abstractions: cells as computation. Nature 419(6905): 343−343 doi: 10.1038/419343a
    [81]
    Saper G, Hess H (2020) Synthetic systems powered by biological molecular motors. Chem Rev 120(1): 288−309 doi: 10.1021/acs.chemrev.9b00249
    [82]
    Shapiro BA, Bindewald E, Kasprzak W, Yingling Y (2008) Protocols for the in silico design of RNA nanostructures. Methods Mol Biol 474: 93−115
    [83]
    Shi Y-Z, Wu Y-Y, Wang F-H, Tan Z-J (2014) RNA structure prediction: progress and perspective. ChinesePhys B 23(7): 078701. https://doi.org/10.1088/1674-1056/23/7/078701
    [84]
    Shibata T, Fujita Y, Ohno H, Suzuki Y, Hayashi K, Komatsu KR, Kawasaki S, Hidaka K, Yonehara S, Sugiyama H, Endo M, Saito H (2017) Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate. Nat Commun 8(1): 540. https://doi.org/10.1038/s41467-017-00459-x
    [85]
    Shu D, Li H, Shu Y, Xiong GF, Carson WE, Haque F, Xu R, Guo PX (2015) Systemic delivery of anti-miRNA for suppression of triple negative breast cancer utilizing RNA nanotechnology. Acs Nano 9(10): 9731−9740 doi: 10.1021/acsnano.5b02471
    [86]
    Shu D, Shu Y, Haque F, Abdelmawla S, Guo P (2011) Thermodynamically stable RNA three-way junction for constructing multifunctional nanoparticles for delivery of therapeutics. Nat Nano 6(10): 658−667 doi: 10.1038/nnano.2011.105
    [87]
    Sigel RKO, Pyle AM (2007) Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry. Chem Rev 107(1): 97−113 doi: 10.1021/cr0502605
    [88]
    Simmel FC, Yurke B, Singh HR (2019) Principles and applications of nucleic acid strand displacement reactions. Chem Rev 119(10): 6326−6369
    [89]
    Slomovic S, Pardee K, Collins JJ (2015) Synthetic biology devices for in vitro and in vivo diagnostics. Proc Natl Acad Sci US A 112(47): 14429−14435 doi: 10.1073/pnas.1508521112
    [90]
    Song WJ, Strack RL, Svensen N, Jaffrey SR (2014) Plug-and-play fluorophores extend the spectral properties of spinach. J Am Chem Soc 136(4): 1198−1201 doi: 10.1021/ja410819x
    [91]
    Takahashi MK, Tan X, Dy AJ, Braff D, Akana RT, Furuta Y, Donghia N, Ananthakrishnan A, Collins JJ (2018) A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers. Nat Commun 9(1): 3347. https://doi.org/10.1038/s41467-018-05864-4
    [92]
    Tang WX, Hu JH, Liu DR (2017) Aptazyme-embedded guide RNAs enable ligand-responsive genome editing and transcriptional activation. Nat Commun 8: 15939. https://doi.org/10.1038/ncomms15939
    [93]
    Thavarajah W, Silverman AD, Verosloff MS, Kelley-Loughnane N, Jewett MC, Lucks JB (2020) Point-of-use detection of environmental fluoride via a cell-free riboswitch-based biosensor. Acs Synth Biol 9(1): 10−18 doi: 10.1021/acssynbio.9b00347
    [94]
    Ueno K, Sakai Y, Shono C, Sakamoto I, Tsukakoshi K, Hihara Y, Sode K, Ikebukuro K (2017) Applying a riboregulator as a new chromosomal gene regulation tool for higher glycogen production in Synechocystis sp. PCC 6803. Appl Microbiol Biotechnol 101(23-24): 8465−8474 doi: 10.1007/s00253-017-8570-4
    [95]
    Ueno K, Tsukakoshi K, Ikebukuro K (2018) Riboregulator elements as tools to engineer gene expression in cyanobacteria. Appl Microbiol Biotechnol 102(18): 7717−7723 doi: 10.1007/s00253-018-9221-0
    [96]
    Wang F, Lv H, Li Q, Li J, Zhang XL, Shi JY, Wang LH, Fan CH (2020) Implementing digital computing with DNA-based switching circuits. Nat Commun 11(1): 121. https://doi.org/10.1038/s41467-019-13980-y
    [97]
    Wang J, Wang H, Yang L, Lv L, Zhang Z, Ren B, Dong L, Li N (2018a) A novel riboregulator switch system of gene expression for enhanced microbial production of succinic acid. J Ind Microbiol Biotechnol 45(4): 253−269 doi: 10.1007/s10295-018-2019-3
    [98]
    Wang XW, Hu LF, Hao J, Liao LQ, Chiu YZ, Shi M, Wang YM (2019) A microRNA-inducible CRISPR-Cas9 platform serves as a microRNA sensor and cell-type-specific genome regulation tool. Nat Cell Biol 21(4): 522−530 doi: 10.1038/s41556-019-0292-7
    [99]
    Wang ZJ, Luo Y, Xie XD, Hu XJ, Song HY, Zhao Y, Shi JY, Wang LH, Glinsky G, Chen N, Lal R, Fan CH (2018b) In situ spatial complementation of aptamer-mediated recognition enables live-cell imaging of native RNA transcripts in real time. Angew Chem Int Ed Engl 57(4): 972−976 doi: 10.1002/anie.201707795
    [100]
    Winkler W, Nahvi A, Breaker RR (2002) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419(6910): 952−956 doi: 10.1038/nature01145
    [101]
    Winkler WC, Breaker RR (2005) Regulation of bacterial gene expression by riboswitches. Ann Rev Microbiol 59: 487−517 doi: 10.1146/annurev.micro.59.030804.121336
    [102]
    Yu JW, Liu ZY, Jiang W, Wang GS, Mao CD (2015) De novo design of an RNA tile that self-assembles into a homo-octameric nanoprism. Nat Commun 6: 5724. https://doi.org/10.1038/ncomms6724
    [103]
    Yuan Y, Gu Z, Yao C, Luo D, Yang DY (2019) Nucleic acid-based functional nanomaterials as advanced cancer therapeutics. Small 15(26): e1900172. https://doi.org/10.1002/smll.201900172
    [104]
    Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA (2015) Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160(1-2): 339−350 doi: 10.1016/j.cell.2014.11.052
    [105]
    Zhu CS, Liu CY, Qiu XY, Xie SS, Li WY, Zhu LY, Zhu LY (2020) Novel nucleic acid detection strategies based on CRISPR-Cas systems: from construction to application. Biotechnol Bioeng 117(7): 2279−2294 doi: 10.1002/bit.27334
    • Supplements(0)
    • Relative Articles
    • Cited By
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(6)

    Get Citation
    PDF
    XML

    Article Metrics

    Article views (1200) PDF downloads(70) Cited by()
    Proportional views
    Related

    Contact us

    (86-10) 64888458

    biophysics-reports@ibp.ac.cn

    Institute of Biophysics, Chinese Academy of Sciences,15 Datun Road, Chaoyang Beijing 100101, China

    E-mail alert RSS

    Supported by Beijing Renhe Information Technology Co. Ltd.   京ICP备05002793号-4

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return