Facilitated diffusion of Argonaute-mediated target search

References

• Pauli A, Rinn JL, Schier AF. Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet. 2011;12(2):136–149.
   PubMed Web of Science ®Google Scholar
• Riggs AD, Bourgeois S, Cohn M, The lac represser-operator interaction: III. Kinetic studies. J Mol Biol [Internet]. 1970 Nov 14 [cited 2018 Sep 27];53(3):401–417. Available from: https://www.sciencedirect.com/science/article/pii/0022283670900744?via%3Dihub
   PubMed Web of Science ®Google Scholar
• Riggs AD, Suzuki H, Bourgeois S, Lac repressor-operator interaction: I. Equilibrium studies. J Mol Biol [Internet]. 1970 Feb 28 [cited 2018 Sep 27];48(1):67–83. Available from: https://www.sciencedirect.com/science/article/pii/0022283670902196?via%3Dihub
   PubMed Web of Science ®Google Scholar
• Berg OG, Winter RB, von Hippel PH. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry. 1981;20(24):6929–6948.
   PubMed Web of Science ®Google Scholar
• Slutsky M, Mirny LA. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys J. 2004;87(6):4021–4035.
   PubMed Web of Science ®Google Scholar
• Mirny L, Slutsky M, Wunderlich Z, et al. How a protein searches for its site on DNA: the mechanism of facilitated diffusion. J Phys A Math Theor [Internet]. 2009;42(43):434013. Available from: http://stacks.iop.org/1751-8121/42/i=43/a=434013?key=crossref.c3b19cfa3ebb32a80370e612c091028f
   Web of Science ®Google Scholar
• Stanford NP, Szczelkun MD, Marko JF, et al. One- and three-dimensional pathways for proteins to reach specific DNA sites. Embo J. 2000;19(23):6546–6557.
   PubMed Web of Science ®Google Scholar
• Shimamoto N. One-dimensional diffusion of proteins along DNA. J Biol Chem [Internet]. 1999 May 28;274(22):15293–15296. Available from: http://www.jbc.org/lookup/doi/10.1074/jbc.274.22.15293
   PubMed Web of Science ®Google Scholar
• Hammar P, Leroy P, Mahmutovic A, et al. The lac repressor displays facilitated diffusion in living cells. Science [Internet]. 2012 Jun 22;336(6088):1595–1598. Available from: http://science.sciencemag.org/content/sci/336/6088/1595.full.pdf
   PubMed Web of Science ®Google Scholar
• Gorman J, Chowdhury A, Surtees JA, et al. Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. Mol Cell. 2007;28(3):359–370.
   PubMed Web of Science ®Google Scholar
• Gorman J, Plys AJ, Visnapuu M-L, et al. Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice. Nat Struct Mol Biol [Internet]. 2010;17(8):932–938. Available from: http://www.nature.com/doifinder/10.1038/nsmb.1858
   PubMed Web of Science ®Google Scholar
• Zandarashvili L, Esadze A, Vuzman D, et al. Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble. Proc Natl Acad Sci [Internet]. 2015;112(37):E5142–9. Available from: http://www.pnas.org/lookup/doi/10.1073/pnas.1507726112
   PubMed Web of Science ®Google Scholar
• Cuculis L, Abil Z, Zhao H, et al. Direct observation of TALE protein dynamics reveals a two-state search mechanism. Nat Commun [Internet]. 2015;6:7277. Available from: http://www.nature.com/doifinder/10.1038/ncomms8277
   PubMed Web of Science ®Google Scholar
• Ragunathan K, Liu C, Ha T. RecA filament sliding on DNA facilitates homology search. Elife. 2012;2012(1):1–14.
   Google Scholar
• Qi Z, Redding S, Lee JY, et al. DNA sequence alignment by microhomology sampling during homologous recombination. Cell [Internet]. 2015;160(5):856–869. DOI:10.1016/j.cell.2015.01.029.
   PubMed Web of Science ®Google Scholar
• Lau NC, Lim LP, Weinstein EG, et al. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science [Internet]. 2001 Oct 26;294(5543):858LP–862. Available from: http://science.sciencemag.org/content/294/5543/858.abstract
   Web of Science ®Google Scholar
• Lagos-Quintana M, Rauhut R, Lendeckel W, et al. Identification of novel genes coding for small expressed RNAs. Science [Internet]. 2001 Oct 26;294(5543):853LP–858. Available from: http://science.sciencemag.org/content/294/5543/853.abstract
   Web of Science ®Google Scholar
• Lee RC, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science [Internet]. 2001 Oct 26;294(5543):862LP–864. Available from: http://science.sciencemag.org/content/294/5543/862.abstract
   Web of Science ®Google Scholar
• Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science [Internet]. 2012 Aug 17;337(6096):816LP–821. Available from: http://science.sciencemag.org/content/337/6096/816.abstract
   Web of Science ®Google Scholar
• Brouns SJJ, Jore MM, Lundgren M, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science [Internet]. 2008 Aug 15;321(5891):960LP–964. Available from: http://science.sciencemag.org/content/321/5891/960.abstract
   Web of Science ®Google Scholar
• Greene EC, Wind S, Fazio T, et al. DNA curtains for high-throughput single-molecule optical imaging. Methods Enzymol [Internet]. 2010 Jan 1 [cited 2018 Sep 27];472:293–315. Available from: https://www.sciencedirect.com/science/article/pii/S0076687910720061?via%3Dihub
   PubMed Web of Science ®Google Scholar
• Joo C, Balci H, Ishitsuka Y, et al. Advances in single-molecule fluorescence methods for molecular biology. Annu Rev Biochem [Internet]. 2008 Jun 1;77(1):51–76. DOI:10.1146/annurev.biochem.77.070606.101543.
   PubMedGoogle Scholar
• Yu J. Single-molecule studies in live cells. Annu Rev Phys Chem [Internet]. 2016 May 23;67(1):565–585. DOI:10.1146/annurev-physchem-040215-112451.
   PubMedGoogle Scholar
• Neuman KC, Nagy A. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods [Internet]. 2008 May 29;5:491. DOI:10.1038/nmeth.1218.
   PubMed Web of Science ®Google Scholar
• Dulin D, Lipfert J, Moolman MC, et al. Studying genomic processes at the single-molecule level: introducing the tools and applications. Nat Rev Genet [Internet]. 2012 Oct 30;14:9. DOI:10.1038/nrg3316.
   PubMed Web of Science ®Google Scholar
• Fernández-Suárez M, Ting AY. Fluorescent probes for super-resolution imaging in living cells. Nat Rev Mol Cell Biol. 2008;9(12):929–943.
   PubMed Web of Science ®Google Scholar
• Gorman J, Greene EC. Visualizing one-dimensional diffusion of proteins along DNA. Nat Struct Mol Biol. 2008;15(8):768–774.
   PubMed Web of Science ®Google Scholar
• Blainey PC, van Oijen AM, Banerjee A, et al. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc Natl Acad Sci [Internet]. 2006;103(15):5752–5757. Available from: http://www.pnas.org/cgi/doi/10.1073/pnas.0509723103
   PubMed Web of Science ®Google Scholar
• Sternberg SH, LaFrance B, Kaplan M, et al. Conformational control of DNA target cleavage by CRISPR–cas9. Nature [Internet]. 2015 Oct 28;527:110. DOI:10.1038/nature15544.
   PubMed Web of Science ®Google Scholar
• Li G-W, Berg OG, Elf J. Effects of macromolecular crowding and DNA looping on gene regulation kinetics. Nat Phys [Internet]. 2009;5(4):294–297. DOI:10.1038/nphys1222.
   Web of Science ®Google Scholar
• Ha M, Kim VN. Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol Internet]. 2014;15(8):509–524. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25027649.
   PubMed Web of Science ®Google Scholar
• Carthew RW, Sontheimer EJ. Origins and mechanisms of miRNAs and siRNAs. Cell. 2009;136(4):642–655.
   PubMed Web of Science ®Google Scholar
• Ding L, Spencer A, Morita K, et al. The developmental timing regulator AIN-1 Interacts with miRISCs and may target the Argonaute protein ALG-1 to cytoplasmic P bodies in C. elegans. Mol Cell [Internet]. 2005 Aug 19 [cited 2018 Sep 27];19(4):437–447. Available from: https://www.sciencedirect.com/science/article/pii/S1097276505014772?via%3Dihub
   PubMed Web of Science ®Google Scholar
• Liu J, Rivas FV, Wohlschlegel J, et al. A role for the P-body component GW182 in microRNA function. Nat Cell Biol [Internet]. 2005 Nov 13;7:1261. DOI:10.1038/ncb1333.
   PubMed Web of Science ®Google Scholar
• Meister G, Landthaler M, Peters L, et al. Identification of novel Argonaute-associated proteins. Curr Biol [Internet]. 2005 Dec 6 [cited 2018 Sep 27];15(23):2149–2155. Available from: https://www.sciencedirect.com/science/article/pii/S0960982205013011?via%3Dihub
   PubMed Web of Science ®Google Scholar
• Chekulaeva M, Mathys H, Zipprich JT, et al. miRNA repression involves GW182-mediated recruitment of CCR4–NOT through conserved W-containing motifs. Nat Struct Mol Biol [Internet]. 2011 Oct 7;18:1218. DOI:10.1038/nsmb.2166.
   PubMed Web of Science ®Google Scholar
• Braun JE, Huntzinger E, Fauser M, et al. GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets. Mol Cell [Internet]. 2011 Oct 7 [cited 2018 Sep 28];44(1):120–133. Available from: https://www.sciencedirect.com/science/article/pii/S1097276511007246?via%3Dihub
   PubMed Web of Science ®Google Scholar
• Behm-Ansmant I, Rehwinkel J, Doerks T, et al. mRNA degradation by miRNAs and GW182 requires both CCR4: NOT deadenylase and DCP1: DCP2 decapping complexes. Genes Dev. 2006;20:1885–1898 ST–MRNA degradation by miRNAs and GW1.
   Web of Science ®Google Scholar
• Chen C-YA, Zheng D, Xia Z, et al. Ago–TNRC6 triggers microRNA-mediated decay by promoting two deadenylation steps. Nat Struct Mol Biol [Internet]. 2009 Oct 18;16:1160. DOI:10.1038/nsmb.1709.
   PubMed Web of Science ®Google Scholar
• Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136(2):215–233.
   PubMed Web of Science ®Google Scholar
• Bernstein E, Kim SY, Carmell MA, et al. Dicer is essential for mouse development. Nat Genet. 2003;35(3):215–217.
   PubMed Web of Science ®Google Scholar
• Chong MMW, Zhang G, Cheloufi S, et al. Canonical and alternate functions of the microRNA biogenesis machinery. Genes Dev. 2010;24(17):1951–1960.
   PubMed Web of Science ®Google Scholar
• Lin S, Gregory RI. MicroRNA biogenesis pathways in cancer. Nat Rev Cancer [Internet]. 2015 May 22;15(6):321. DOI:10.1038/nrc3932.
   PubMed Web of Science ®Google Scholar
• Bracken CP, Scott HS, Goodall GJ. A network-biology perspective of microRNA function and dysfunction in cancer. Nat Rev Genet [Internet]. 2016 Oct 31;17:719. DOI:10.1038/nrg.2016.134.
   PubMed Web of Science ®Google Scholar
• Takamizawa J, Konishi H, Yanagisawa K, et al. Reduced expression of the let-7 MicroRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res [Internet]. 2004 Jun 1;64(11):3753LP–3756. Available from: http://cancerres.aacrjournals.org/content/64/11/3753.abstract
   Web of Science ®Google Scholar
• Chakraborty C, Sharma AR, Sharma G, et al. Therapeutic miRNA and siRNA: moving from bench to clinic as next generation medicine. Mol Ther Nucleic Acids [Internet]. 2017 Sep 15 [[cited 2018 Sep 28]];8:132–143. Available from: https://www.sciencedirect.com/science/article/pii/S2162253117301907
   PubMedGoogle Scholar
• Wang Y, Sheng G, Juranek S, et al. Structure of the guide-strand-containing argonaute silencing complex. Nature [Internet]. 2008;456(7219):209–213. DOI:10.1038/nature07315.
   PubMed Web of Science ®Google Scholar
• Nakanishi K, Weinberg DE, Bartel DP, et al. Structure of yeast Argonaute with guide RNA. Nature [Internet]. 2012 May 18;486:368. DOI:10.1038/nature11211.
   PubMed Web of Science ®Google Scholar
• Schirle NT, MacRae IJ. The crystal structure of human Argonaute2. Science [Internet]. 2012 May 25;336(6084):1037–1040. Available from: http://onlinelibrary.wiley.com/doi/10.1002/macp.1965.020830117/abstract
   PubMed Web of Science ®Google Scholar
• Wee LM, Flores-Jasso CF, Salomon WE, et al. Argonaute divides Its RNA guide into domains with distinct functions and RNA-binding properties. Cell. 2012;151(5):1055–1067.
   PubMed Web of Science ®Google Scholar
• Agarwal V, Bell GW, Nam JW, et al. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015;4(AUGUST2015):1–38.
   Google Scholar
• Grimson A, Farh KKH, Johnston WK, et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007;27(1):91–105.
   PubMed Web of Science ®Google Scholar
• Wang Y, Juranek S, Li H, et al. Nucleation, propagation and cleavage of target RNAs in ago silencing complexes. Nature [Internet]. 2009;461(7265):754–761. Available from: http://www.ncbi.nlm.nih.gov/pubmed/19812667
   PubMed Web of Science ®Google Scholar
• Olovnikov I, Chan K, Sachidanandam R, et al. Bacterial Argonaute samples the transcriptome to identify foreign DNA. Mol Cell [Internet]. 2013 Sep 12 [cited 2018 Sep 28]; 51(5):594–605. DOI:10.1016/j.molcel.2013.08.014.
   PubMed Web of Science ®Google Scholar
• Swarts DC, Jore MM, Westra ER, et al. DNA-guided DNA interference by a prokaryotic Argonaute. Nature [Internet]. 2014;507(7491):258–261. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24531762
   PubMed Web of Science ®Google Scholar
• Swarts DC, Hegge JW, Hinojo I, et al. Argonaute of the archaeon pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA. Nucleic Acids Res. 2015;43(10):5120–5129.
   PubMed Web of Science ®Google Scholar
• Willkomm S, Oellig CA, Zander A, et al. Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein. Nat Microbiol [Internet]. 2017;2(March):17035. Available from: http://www.nature.com/articles/nmicrobiol201735
   PubMedGoogle Scholar
• Zander A, Holzmeister P, Klose D, et al. Single-molecule FRET supports the two-state model of Argonaute action. RNA Biol [Internet]. 2014;11(1):45–56. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3929424&tool=pmcentrez&rendertype=abstract
   PubMed Web of Science ®Google Scholar
• Zander A, Willkomm S, Ofer S, et al. Guide-independent DNA cleavage by archaeal Argonaute from methanocaldococcus jannaschii. Nat Microbiol [Internet]. 2017;2(March):17034. Available from: http://www.nature.com/articles/nmicrobiol201734
   PubMedGoogle Scholar
• Reavy B, Swanson MM, Cock PJA, et al. Distinct circular single-stranded DNA viruses exist in different soil types. Appl Environ Microbiol. 2015;81(12):3934–3945.
   PubMed Web of Science ®Google Scholar
• Labonté JM, Suttle CA. Previously unknown and highly divergent ssDNA viruses populate the oceans. Isme J. 2013;7(11):2169–2177.
   PubMed Web of Science ®Google Scholar
• Yoshida M, Mochizuki T, Urayama SI, et al. Quantitative viral community DNA analysis reveals the dominance of single-stranded DNA viruses in offshore upper bathyal sediment from Tohoku, Japan. Front Microbiol. 2018;9(FEB):1–10.
   PubMedGoogle Scholar
• Kalodimos CG, Boelens R, Kaptein R. A residue-specific view of the association and dissociation pathway in protein-DNA recognition. Nat Struct Biol. 2002;9(3):193–197.
   PubMedGoogle Scholar
• Klein M, Chandradoss SD, Depken M, et al. Why Argonaute is needed to make microRNA target search fast and reliable. Semin Cell Dev Biol [Internet]. 2017 May;65:20–28. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1084952116301434
   PubMed Web of Science ®Google Scholar
• Schirle NT, Sheu-Gruttadauria J, MacRae IJ. Structural basis for microRNA targeting. Science [Internet]. 2014;346(6209):608–613. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4313529&tool=pmcentrez&rendertype=abstract
   PubMed Web of Science ®Google Scholar
• Klum SM, Chandradoss SD, Schirle NT, et al. Helix‐7 in Argonaute2 shapes the microRNA seed region for rapid target recognition. Embo J [ [Internet]]. 2017;e201796474. Available from: http://emboj.embopress.org/lookup/doi/10.15252/embj.201796474.
   Web of Science ®Google Scholar
• Chandradoss SD, Schirle NT, Szczepaniak M, et al. A dynamic search process underlies MicroRNA targeting. Cell [Internet]. 2015;162(1):96–107. DOI:10.1016/j.cell.2015.06.032.
   PubMed Web of Science ®Google Scholar
• Jo MH, Shin S, Jung SR, et al. Human Argonaute 2 has diverse reaction pathways on target RNAs. Mol Cell [Internet]. 2015;59(1):117–124. DOI:10.1016/j.molcel.2015.04.027.
   PubMed Web of Science ®Google Scholar
• Salomon WE, Jolly SM, Moore MJ, et al. Single-molecule imaging reveals that Argonaute reshapes the binding properties of its nucleic acid guides. Cell [Internet]. 2015;162(1):84–95. DOI:10.1016/j.cell.2015.06.029.
   PubMed Web of Science ®Google Scholar
• Yao C, Sasaki HM, Ueda T, et al. Single-molecule analysis of the target cleavage reaction by the drosophila RNAi enzyme complex. Mol Cell [Internet]. 2015;59(1):125–132. DOI:10.1016/j.molcel.2015.05.015.
   PubMed Web of Science ®Google Scholar
• Hegge JW, Swarts DC, Chandradoss SD, et al. DNA-guided DNA cleavage at moderate temperatures by clostridium butyricum Argonaute. 2019. DOI:10.1101/534206
   Google Scholar
• Cui TJ, Klein M, Hegge JW, et al. Argonaute bypasses cellular obstacles without hindrance during target search. 2019. DOI:10.1101/535575
   Google Scholar
• van Den Broek B, Lomholt MA, Kalisch S-MJ, et al. How DNA coiling enhances target localization by proteins. Proc Natl Acad Sci U S A [Internet]. 2008;105(41):15738–15742. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2572962&tool=pmcentrez&rendertype=abstract
   PubMed Web of Science ®Google Scholar
• Kolomeisky AB. Physics of protein-DNA interactions: mechanisms of facilitated target search. Phys Chem Chem Phys. 2011;13(6):2088–2095.
   PubMed Web of Science ®Google Scholar
• Song G, Chen H, Sheng G, et al. Argonaute facilitates the lateral diffusion of the guide along its target and prevents the guide from being pushed away by the ribosome. Biochemistry [Internet]. 2018 Apr 17;57(15):2179–2183. DOI:10.1021/acs.biochem.8b00213.
   PubMed Web of Science ®Google Scholar
• Wang YM, Austin RH, Cox EC. Single molecule measurements of repressor protein 1D diffusion on DNA. Phys Rev Lett [Internet]. 2006 Jul 27;97(4):48302. DOI:10.1103/PhysRevLett.97.048302.
   Web of Science ®Google Scholar
• Blainey PC, Luo G, Kou SC, et al. Nonspecifically bound proteins spin while diffusing along DNA. Nat Struct Mol Biol [Internet]. 2009;16(12):1224–1229. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2889498&tool=pmcentrez&rendertype=abstract
   PubMed Web of Science ®Google Scholar
• Elf J, Li G-W, Xie XS. Probing transcription factor dynamics at the single-molecule level in a living cell. Science [Internet]. 2007 May 25;316(5828):1191LP–1194. Available from: http://science.sciencemag.org/content/316/5828/1191.abstract
   Web of Science ®Google Scholar
• Ding Y, Tang Y, Kwok CK, et al. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature [Internet]. 2014;505(7485):696–700. DOI:10.1038/nature12756.
   PubMed Web of Science ®Google Scholar
• Beaudoin J-D, Novoa EM, Vejnar CE, et al. Analyses of mRNA structure dynamics identify embryonic gene regulatory programs. Nat Struct Mol Biol. [Internet]. 2018;1. Available from: http://www.nature.com/articles/s41594-018-0091-z
   Google Scholar
• Bevilacqua PC, Ritchey LE, Su Z, et al. Genome-wide analysis of RNA secondary structure. Annu Rev Genet [Internet]. 2016;50(1):235–266. DOI:10.1146/annurev-genet-120215-035034.
   PubMedGoogle Scholar
• Vandivier LE, Anderson SJ, Foley SW, et al. The conservation and function of RNA secondary structure in plants. Annu Rev Plant Biol [Internet]. 2016;67(1):463–488. DOI:10.1146/annurev-arplant-043015-111754.
   PubMedGoogle Scholar
• Warf MB, Berglund JA, Role of RNA structure in regulating pre-mRNA splicing. Trends Biochem Sci [Internet]. 2010 Mar 1 [cited 2018 Sep 28];35(3):169–178. Available from: https://www.sciencedirect.com/science/article/pii/S0968000409001960?via%3Dihub
   PubMed Web of Science ®Google Scholar
• Martin KC, Ephrussi A. mRNA localization: gene expression in the spatial dimension. Cell [Internet]. 2009 Feb 20 [cited 2018 Sep 28];136(4):719–730. Available from: https://www.sciencedirect.com/science/article/pii/S0092867409001263
   PubMed Web of Science ®Google Scholar
• Ray PS, Jia J, Yao P, et al. A stress-responsive RNA switch regulates VEGFA expression. Nature [Internet]. 2008 Dec 21;457:915. DOI:10.1038/nature07598.
   PubMed Web of Science ®Google Scholar
• Weingarten-Gabbay S, Elias-Kirma S, Nir R, et al. Systematic discovery of cap-independent translation sequences in human and viral genomes. Science [Internet]. 2016 Jan 15;351(6270). Available from: http://science.sciencemag.org/content/351/6270/aad4939.abstract
   PubMed Web of Science ®Google Scholar
• Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010;327(5962):167–170.
   PubMed Web of Science ®Google Scholar
• Sorek R, Lawrence CM, Wiedenheft B. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochem [Internet]. 2013;82(May):237–266. Available from: http://www.ncbi.nlm.nih.gov/pubmed/23495939
   PubMedGoogle Scholar
• Redding S, Sternberg SH, Marshall M, et al. Surveillance and processing of foreign DNA by the escherichia coli CRISPR-cas system. Cell [Internet]. 2015;163(4):854–865. DOI:10.1016/j.cell.2015.10.003.
   PubMed Web of Science ®Google Scholar
• Sternberg SH, Redding S, Jinek M, et al. DNA interrogation by the CRISPR RNA-guided endonuclease cas9. Nature [Internet]. 2014;507(7490):62–67. DOI:10.1038/nature13011.
   PubMed Web of Science ®Google Scholar
• Globyte V, Lee SH, Bae T, et al. CRISPR/cas9 searches for a protospacer adjacent motif by lateral diffusion. Embo J [Internet]. 2018 Dec 20;e99466. Available from: https://www.biorxiv.org/content/early/2018/02/13/264879
   Google Scholar
• Swarts DC, Makarova K, Wang Y, et al. The evolutionary journey of Argonaute proteins. Nat Struct Mol Biol [Internet]. 2014;21(9):743–753. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4691850&tool=pmcentrez&rendertype=abstract
   PubMed Web of Science ®Google Scholar
• Jones DL, Leroy P, Unoson C, et al. Kinetics of dCas9 target search in Escherichia coli. Science. 2017;357(6358):1420–1424.
   PubMed Web of Science ®Google Scholar
• Singh D, Sternberg SH, Fei J, et al. Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease cas9. Nat Commun. 2016;7:1–8.
   Web of Science ®Google Scholar
• Jung SR, Kim E, Shin S, et al. Mechanisms of the binding/dissociation Acceleration of the target–guide interaction by thermus thermophilus Argonaute. Bull Korean Chem Soc. 2018;39(2):167–173.
   Web of Science ®Google Scholar
• Obmolova G, Ban C, Hsieh P, et al. Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature [Internet]. 2000 Oct 12;407:703. DOI:10.1038/35037509.
   PubMed Web of Science ®Google Scholar
• Schumacher MA, Choi KY, Zalkin H, et al. Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. Science [Internet]. 1994 Nov 4;266(5186):763LP–770. Available from: http://science.sciencemag.org/content/266/5186/763.abstract
   Web of Science ®Google Scholar
• Dillard KE, Brown MW, Johnson NV, et al. Assembly and translocation of a CRISPR-cas primed acquisition complex. Cell [Internet]. 2018;175(4):934–946. DOI:10.1016/j.cell.2018.09.039.
   PubMed Web of Science ®Google Scholar
• Jeon Y, Choi YH, Jang Y, et al. Direct observation of DNA target searching and cleavage by CRISPR-cas12a. Nat Commun [Internet]. 2018;9(1). DOI:10.1038/s41467-018-05245-x
   Google Scholar
• Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges. Nature [Internet]. 2013;495(7441):384–388. Available from: http://www.nature.com/doifinder/10.1038/nature11993
   PubMed Web of Science ®Google Scholar
• Mandal M, Breaker RR. Gene regulation by riboswitches. Nat Rev Mol Cell Biol. 2004;5(6):451–463.
   PubMed Web of Science ®Google Scholar
• Kedde M, Van Kouwenhove M, Zwart W, et al. A pumilio-induced RNA structure switch in p27-3′2 UTR controls miR-221 and miR-222 accessibility. Nat Cell Biol [Internet]. 2010;12(10):1014–1020. DOI:10.1038/ncb2105.
   PubMed Web of Science ®Google Scholar
• Ameres SL, Martinez J, Schroeder R. Molecular basis for target RNA recognition and cleavage by human RISC. Cell. 2007;130(1):101–112.
   PubMed Web of Science ®Google Scholar
• Scheel TKH, Luna JM, Liniger M, et al. A broad RNA virus survey reveals both miRNA dependence and functional sequestration. Cell Host Microbe [Internet]. 2016 Mar 9 [cited 2018 Sep 28];19(3):409–423. Available from: https://www.sciencedirect.com/science/article/pii/S1931312816300488?via%3Dihub
   PubMed Web of Science ®Google Scholar
• Jopling CL, Schütz S, Sarnow P, Position-dependent function for a tandem MicroRNA miR-122-binding site located in the hepatitis C virus RNA genome. Cell Host Microbe [Internet]. 2008 Jul 17 [cited 2018 Sep 28];4(1):77–85. Available from: https://www.sciencedirect.com/science/article/pii/S193131280800173X?via%3Dihub
   PubMed Web of Science ®Google Scholar
• Zheng Z, Reichel M, Deveson I, et al. Target RNA secondary structure is a major determinant of miR159 efficacy. Plant Physiol [Internet]. 2017 Jul 1;174(3):1764LP–1778. Available from: http://www.plantphysiol.org/content/174/3/1764.abstract
   Web of Science ®Google Scholar
• Gebert LFR, MacRae IJ. Regulation of microRNA function in animals. Nat Rev Mol Cell Biol [Internet]. 2018;(Mid). Available from: http://www.nature.com/articles/s41580-018-0045-7
   Google Scholar
• Nuñez JK, Kranzusch PJ, Noeske J, et al. Cas1-cas2 complex formation mediates spacer acquisition during CRISPR-cas adaptive immunity. Nat Struct Mol Biol [Internet]. 2014;21(6):528–534. Available from: http://www.nature.com/nsmb/journal/v21/n6/pdf/nsmb.2820.pdf
   PubMed Web of Science ®Google Scholar
• Jonas S, Izaurralde E. Towards a molecular understanding of microRNA-mediated gene silencing. Nat Rev Genet [Internet]. 2015;16(7):421–433. DOI:10.1038/nrg3965.
   PubMed Web of Science ®Google Scholar
• Sheu-Gruttadauria J, MacRae IJ. Phase transitions in the assembly and function of human miRISC. Cell [Internet]. 2018;173(4):946–957.e16. DOI:10.1016/j.cell.2018.02.051.
   PubMed Web of Science ®Google Scholar