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Liposome membrane can induce self-cleavage of RNA that models the core fragments of hammerhead ribozyme
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  • 作者:Keishi Suga ; Seishiro Tanaka ; Hiroshi Umakoshi
  • 关键词:Hammerhead ribozyme ; Liposome ; Membranome ; Metal ion ; free ; RNA conformation
  • 刊名:European Biophysics Journal
  • 出版年:2016
  • 出版时间:January 2016
  • 年:2016
  • 卷:45
  • 期:1
  • 页码:55-62
  • 全文大小:1,127 KB
  • 参考文献:Ausländer S, Ketzer P, Hartig JS (2010) A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. Mol BioSyst 6:807–814PubMed CrossRef
    Bassi GS, Murchie AIH, Lilley DMJ (1996) The ion-induced folding of the hammerhead ribozyme: core sequence changes that perturb folding into the active conformation. RNA 2:756–768PubMed PubMedCentral
    Billinghurst BE, Oladepo SA, Loppnow GR (2009) pH-Dependent UV resonance Raman spectra of cytosine and uracil. J Phys Chem B 113:7392–7397PubMed CrossRef
    Boots JL, Canny MD, Azimi E, Pardi A (2008) Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme. RNA 14:2212–2222PubMed PubMedCentral CrossRef
    Carmona P, Rodriguez-Casado A, Molina M (1999) Conformational structure and bindingmode of glyceraldehydes-3-phosphate dehydrogenase to tRNA studied by Raman and CD spectroscopy. Biochim Biophys Acta 1432:222–233PubMed CrossRef
    Chen IA (2015) Replicating towards complexity. Nat Chem 7:191–192PubMed CrossRef
    Chen IA, Salehi-Ashtiani K, Szostak JW (2005) RNA catalysis in model protocell vesicles. J Am Chem Soc 127:13213–13219PubMed CrossRef
    Curtis EA, Bartel DP (2001) The hammerhead cleavage reaction in monovalent cations. RNA 7:546–552PubMed PubMedCentral CrossRef
    De Almeida RFM, Loura LMS, Fedorov A, Prieto M (2005) Lipid rafts have different sizes depending on membrane composition: a time-resolved fluorescence resonance energy transfer study. J Mol Biol 346:1109–1120PubMed CrossRef
    De la Peña M, Gago S, Flores R (2003) Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J 22:5561–5570PubMed PubMedCentral CrossRef
    Ferrari D, Peracchi A (2002) A continuous kinetic assay for RNA-cleaving deoxyribozymes, exploiting ethidium bromide as an extrinsic fluorescent probe. Nucleic Acid Res 30:e112PubMed PubMedCentral CrossRef
    Florián J, Baumruk V, Leszczyński J (1996) IR and Raman spectra, tautomeric stabilities, and scaled quantum mechanical force fields of protonated cytosine. J Phys Chem 100:5578–5589CrossRef
    Hammann C, Lilley DMJ (2002) Folding and activity of the hammerhead ribozyme. ChemBioChem 3:690–700PubMed CrossRef
    Janas T, Janas T, Yarus M (2006) Specific RNA binding to ordered phospholipid bilayers. Nucleic Acid Res 34:2128–2136PubMed PubMedCentral CrossRef
    Khvorova A, Lescoute A, Westhof E, Jayasena SD (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol 10:708–712PubMed CrossRef
    Lanir A, Yu NT (1979) A Raman spectroscopic study of the interaction of divalent metal ions with adenine moiety of adenosine 5′-triphosphate. J Biol Chem 254:5882–5887PubMed
    Lilley DMJ (2005) Structure, folding and mechanisms of ribozymes. Curr Opin Struct Biol 15:313–323PubMed CrossRef
    Liu Y, Nagle JF (2004) Diffuse scattering provides material parameters and electron density profiles of biomembranes. Phys Rev E 69:1–4. article id:040901
    MacDonald RC, MacDonald RI, Menco BP, Takeshita K, Subbarao NK, Hu LR (1991) Small-volume extrusion apparatus for preparation of large, unilamellar vesicles. Biochim Biophys Acta 1061:297–303PubMed CrossRef
    Marrink SJ, De Vries AH, Mark AE (2004) Coarse grained model for semiquantitative lipid simulations. J Phys Chem B 108:750–760CrossRef
    Mathlouthi M, Seuvre AM, Koenig JL (1983) FT-IR and laser-Raman spectra of d -ribose and 2-deoxy-d -erythro-pentose (“2-deoxy-d -ribose”). Carbohyd Res 122:31–47CrossRef
    Müller UF, Bartel DP (2008) Improved polymerase ribozyme efficiency on hydrophobic assemblies. RNA 14:552–562PubMed PubMedCentral CrossRef
    Nagatomo S, Nagai M, Kitagawa T (2011) A new way to understand quaternary structure changes of hemoglobin upon ligand binding on the basis of UV-resonance Raman evaluation of intersubunit interactions. J Am Chem Soc 133:10101–10110PubMed CrossRef
    Pley HW, Flaherty KM, McKay DB (1994) Three-dimensional structure of a hammerhead ribozyme. Nature 372:68–74PubMed CrossRef
    Ricardo A, Szostak JW (2009) Origin of life on earth. Sci Am 301:54–61PubMed CrossRef
    Riepe A, Beier H, Gross HJ (1999) Enhancement of RNA self-cleavage by micellar catalysis. FEBS Lett 457:193–199PubMed CrossRef
    Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Method 9:671–675CrossRef
    Singh JS (2012) FTIR and Raman spectra and fundamental frequencies of 5-halosubstituted uracils: 5-X-uracil (X = F, Cl, Br and I). Spectrochim Acta A 87:106–111CrossRef
    Strobel SA, Cochrane JC (2007) RNA catalysis: ribozymes, ribosomes, and riboswitches. Curr Opin Chem Biol 11:636–643PubMed PubMedCentral CrossRef
    Strulson CA, Molden RC, Keating CD, Bevilacqua PC (2012) RNA catalysis through compartmentalization. Nat Chem 4:941–946PubMed
    Suga K, Umakoshi H (2013) Detection of nanosized ordered domains in DOPC/DPPC and DOPC/Ch binary lipid mixture systems of large unilamellar vesicles using a TEMPO quenching method. Langmuir 29:4830–4837PubMed CrossRef
    Suga K, Umakoshi H, Tomita H et al (2010) Liposomes destabilize tRNA during heat stress. Biotechnol J 5:526–529PubMed CrossRef
    Suga K, Tanabe T, Tomita H et al (2011) Conformational change of single-stranded RNAs induced by liposome binding. Nucl Acid Res 39:8891–8900CrossRef
    Suga K, Tanabe T, Umakoshi H (2013) Heterogeneous cationic liposomes modified with 3β-{N-[(N′, N′-dimethylamino) ethyl] carbamoyl} cholesterol can induce partial conformational changes in messenger RNA and regulate translation in an Escherichia coli cell-free translation system. Langmuir 29:1899–1907PubMed CrossRef
    Tanaka Y, Kasai Y, Mochizuki S et al (2004) Nature of the chemical bond formed with the structural metal ion at the A9/G10.1 motif derived from hammerhead ribozymes. J Am Chem Soc 126:744–752PubMed CrossRef
    Tessera M (2009) Life began when evolution began: a lipidic vesicle-based scenario. Orig Life Evol Biosph 39:559–564PubMed CrossRef
    Tsuji A, Yoshikawa K (2010) Real-time monitoring of RNA synthesis in a phospholipid-coated microdroplet as a live-cell model. ChemBioChem 11:351–357PubMed CrossRef
    Veatch SL, Keller SL (2005) Miscibility phase diagrams of giant vesicles containing sphingomyelin. Phys Rev Lett 94:148101PubMed CrossRef
    Walde P, Umakoshi H, Stano P, Mavellid F (2014) Emergent proper-ties arising from the assembly of amphiphiles. Artificial vesicle membranes as reaction promoters and regulators. Chem Commun 50:10177–10197CrossRef
    Wang S, Karbstein K, Paracchi A et al (1999) Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate. Biochem 38:14363–14378CrossRef
    Wieland M, Ausländer D, Fussenegger M (2012) Engineering of ribozyme-based riboswitches for mammalian cells. Methods 56:351–357PubMed CrossRef
    Zhelyaskov V, Yue KT (1992) A Raman study of the binding of Fe(III) to ATP and AMP. Biochem J 287:561–566PubMed PubMedCentral CrossRef
    Zipper H, Brunner H, Bernhagen J, Vitzthum F (2004) Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucl Acid Res 32:e103CrossRef
  • 作者单位:Keishi Suga (1)
    Seishiro Tanaka (1)
    Hiroshi Umakoshi (1)

    1. Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyamacho, Toyonaka, Osaka, 560-8531, Japan
  • 刊物类别:Physics and Astronomy
  • 刊物主题:Physics
    Biophysics and Biomedical Physics
    Cell Biology
    Biochemistry
    Plant Physiology
    Animal Physiology
    Neurobiology
  • 出版者:Springer Berlin / Heidelberg
  • ISSN:1432-1017
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