메뉴 건너뛰기




Volumn 52, Issue 38, 2013, Pages 6575-6583

Thermodynamics and kinetics of adaptive binding in the malachite green RNA aptamer

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE NATURES; BINDING POCKETS; COMPETITIVE BINDING; ISOTHERMAL TITRATION CALORIMETRY; MALACHITE GREEN; NON-PLANAR STRUCTURES; STOPPED-FLOW KINETICS; THERMODYNAMICS AND KINETICS;

EID: 84884833081     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi400549s     Document Type: Article
Times cited : (22)

References (40)
  • 1
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • Ellington, A. D. and Szostak, J. W. (1990) In vitro selection of RNA molecules that bind specific ligands Nature 346, 818-822
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 2
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 249, 505-510
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 3
    • 77952499429 scopus 로고    scopus 로고
    • Selecting RNA aptamers for synthetic biology: Investigating magnesium dependence and predicting binding affinity
    • Carothers, J. M., Goler, J. A., Kapoor, Y., Lara, L., and Keasling, J. D. (2010) Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity Nucleic Acids Res. 38, 2736-2747
    • (2010) Nucleic Acids Res. , vol.38 , pp. 2736-2747
    • Carothers, J.M.1    Goler, J.A.2    Kapoor, Y.3    Lara, L.4    Keasling, J.D.5
  • 4
    • 28444484636 scopus 로고    scopus 로고
    • Aptamers - Basic research, drug development, and clinical applications
    • Proske, D., Blank, M., Buhmann, R., and Resch, A. (2005) Aptamers-basic research, drug development, and clinical applications Appl. Microbiol. Biotechnol. 69, 367-374
    • (2005) Appl. Microbiol. Biotechnol. , vol.69 , pp. 367-374
    • Proske, D.1    Blank, M.2    Buhmann, R.3    Resch, A.4
  • 5
    • 0034604296 scopus 로고    scopus 로고
    • 2.8 angstrom crystal structure of the malachite green aptamer
    • Baugh, C., Grate, D., and Wilson, C. (2000) 2.8 angstrom crystal structure of the malachite green aptamer J. Mol. Biol. 301, 117-128
    • (2000) J. Mol. Biol. , vol.301 , pp. 117-128
    • Baugh, C.1    Grate, D.2    Wilson, C.3
  • 6
    • 0033033283 scopus 로고    scopus 로고
    • Laser-mediated, site-specific inactivation of RNA transcripts
    • Grate, D. and Wilson, C. (1999) Laser-mediated, site-specific inactivation of RNA transcripts Proc. Natl. Acad. Sci. U. S. A. 96, 6131-6136
    • (1999) Proc. Natl. Acad. Sci. U. S. A. , vol.96 , pp. 6131-6136
    • Grate, D.1    Wilson, C.2
  • 7
    • 0442311057 scopus 로고    scopus 로고
    • Dynamics studies of a malachite Green-RNA complex revealing the origin of the red-shift and energetic contributions of stacking interactions
    • Nguyen, D. H., Dieckmann, T., Colvin, M. E., and Fink, W. H. (2004) Dynamics studies of a malachite Green-RNA complex revealing the origin of the red-shift and energetic contributions of stacking interactions J. Phys. Chem. B 108, 1279-1286
    • (2004) J. Phys. Chem. B , vol.108 , pp. 1279-1286
    • Nguyen, D.H.1    Dieckmann, T.2    Colvin, M.E.3    Fink, W.H.4
  • 8
    • 24744465188 scopus 로고    scopus 로고
    • Binary malachite green aptamer for fluorescent detection of nucleic acids
    • Kolpashchikov, D. M. (2005) Binary malachite green aptamer for fluorescent detection of nucleic acids J. Am. Chem. Soc. 127, 12442-12443
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 12442-12443
    • Kolpashchikov, D.M.1
  • 9
    • 75649115391 scopus 로고    scopus 로고
    • Label-free fluorescent aptamer sensor based on regulation of malachite green fluorescence
    • Xu, W. C. and Lu, Y. (2010) Label-free fluorescent aptamer sensor based on regulation of malachite green fluorescence Anal. Chem. 82, 574-578
    • (2010) Anal. Chem. , vol.82 , pp. 574-578
    • Xu, W.C.1    Lu, Y.2
  • 10
    • 77950451235 scopus 로고    scopus 로고
    • An RNA-aptamer-based assay for the detection and analysis of malachite green and leucomalachite green residues in fish tissue
    • Stead, S. L., Ashwin, H., Johnston, B., Tarbin, J. A., Sharman, M., Kay, J., and Keely, B. J. (2010) An RNA-aptamer-based assay for the detection and analysis of malachite green and leucomalachite green residues in fish tissue Anal. Chem. 82, 2652-2660
    • (2010) Anal. Chem. , vol.82 , pp. 2652-2660
    • Stead, S.L.1    Ashwin, H.2    Johnston, B.3    Tarbin, J.A.4    Sharman, M.5    Kay, J.6    Keely, B.J.7
  • 11
    • 77954946957 scopus 로고    scopus 로고
    • Design of bio-inspired multi-stage regulations for diagnostic molecular automata
    • Hirabayashi, M., Ohashi, H., and Kubo, T. (2010) Design of bio-inspired multi-stage regulations for diagnostic molecular automata J. Comput. Theor. Nanosci. 7, 831-839
    • (2010) J. Comput. Theor. Nanosci. , vol.7 , pp. 831-839
    • Hirabayashi, M.1    Ohashi, H.2    Kubo, T.3
  • 13
    • 66349133602 scopus 로고    scopus 로고
    • Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs
    • Gilbert, S. D., Reyes, F. E., Edwards, A. L., and Batey, R. T. (2009) Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs Structure 17, 857-868
    • (2009) Structure , vol.17 , pp. 857-868
    • Gilbert, S.D.1    Reyes, F.E.2    Edwards, A.L.3    Batey, R.T.4
  • 14
    • 0034603154 scopus 로고    scopus 로고
    • Biochemistry - Adaptive recognition by nucleic acid aptamers
    • Hermann, T. and Patel, D. J. (2000) Biochemistry-adaptive recognition by nucleic acid aptamers Science 287, 820-825
    • (2000) Science , vol.287 , pp. 820-825
    • Hermann, T.1    Patel, D.J.2
  • 15
    • 0030831668 scopus 로고    scopus 로고
    • Mutant ATP-binding RNA aptamers reveal the structural basis for ligand binding
    • Dieckmann, T., Butcher, S. E., Sassanfar, M., Szostak, J. W., and Feigon, J. (1997) Mutant ATP-binding RNA aptamers reveal the structural basis for ligand binding J. Mol. Biol. 273, 467-478
    • (1997) J. Mol. Biol. , vol.273 , pp. 467-478
    • Dieckmann, T.1    Butcher, S.E.2    Sassanfar, M.3    Szostak, J.W.4    Feigon, J.5
  • 16
    • 0029904020 scopus 로고    scopus 로고
    • Solution structure of an ATP-binding RNA aptamer reveals a novel fold
    • Dieckmann, T., Suzuki, E., Nakamura, G. K., and Feigon, J. (1996) Solution structure of an ATP-binding RNA aptamer reveals a novel fold RNA 2, 628-640
    • (1996) RNA , vol.2 , pp. 628-640
    • Dieckmann, T.1    Suzuki, E.2    Nakamura, G.K.3    Feigon, J.4
  • 17
    • 0346457132 scopus 로고    scopus 로고
    • Recognition of planar and nonplanar ligands in the malachite green-RNA aptamer complex
    • Flinders, J., DeFina, S. C., Brackett, D. M., Baugh, C., Wilson, C., and Dieckmann, T. (2004) Recognition of planar and nonplanar ligands in the malachite green-RNA aptamer complex ChemBioChem 5, 62-72
    • (2004) ChemBioChem , vol.5 , pp. 62-72
    • Flinders, J.1    Defina, S.C.2    Brackett, D.M.3    Baugh, C.4    Wilson, C.5    Dieckmann, T.6
  • 18
    • 33646802654 scopus 로고    scopus 로고
    • Aptamer to ribozyme: The intrinsic catalytic potential of a small RNA
    • Brackett, D. M. and Dieckmann, T. (2006) Aptamer to ribozyme: the intrinsic catalytic potential of a small RNA ChemBioChem 7, 839-843
    • (2006) ChemBioChem , vol.7 , pp. 839-843
    • Brackett, D.M.1    Dieckmann, T.2
  • 19
    • 79959192255 scopus 로고    scopus 로고
    • 2+ control ligand affinity and specificity in the malachite green binding RNA aptamer
    • 2+ control ligand affinity and specificity in the malachite green binding RNA aptamer Mol. Biosyst. 7, 2156-2163
    • (2011) Mol. Biosyst. , vol.7 , pp. 2156-2163
    • Bernard Da Costa, J.1    Dieckmann, T.2
  • 20
    • 0024819449 scopus 로고
    • Synthesis of small RNAs using T7 RNA polymerase
    • (Dahlberg, J. E. and Abelson, J. Eds.), pp, Academic Press, New York
    • Milligan, J. F. and Uhlenbeck, O. C. (1989) Synthesis of small RNAs using T7 RNA polymerase, in Methods in Enzymology (Dahlberg, J. E. and Abelson, J., Eds.), pp 51-62, Academic Press, New York.
    • (1989) Methods in Enzymology , pp. 51-62
    • Milligan, J.F.1    Uhlenbeck, O.C.2
  • 21
    • 0023651444 scopus 로고
    • Oligoribonucleotide synthesis using T7-RNA polymerase and synthetic DNA templates
    • Milligan, J. F., Groebe, D. R., Witherell, G. W., and Uhlenbeck, O. C. (1987) Oligoribonucleotide synthesis using T7-RNA polymerase and synthetic DNA templates Nucleic Acids Res. 15, 8783-8798
    • (1987) Nucleic Acids Res. , vol.15 , pp. 8783-8798
    • Milligan, J.F.1    Groebe, D.R.2    Witherell, G.W.3    Uhlenbeck, O.C.4
  • 22
    • 0000521134 scopus 로고
    • Spin-echo water suppression for the generation of pure-phase two-dimensional NMR spectra
    • Sklenar, V. and Bax, A. (1987) Spin-echo water suppression for the generation of pure-phase two-dimensional NMR spectra J. Magn. Reson. 74, 469-479
    • (1987) J. Magn. Reson. , vol.74 , pp. 469-479
    • Sklenar, V.1    Bax, A.2
  • 23
    • 0026951903 scopus 로고
    • Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions
    • Piotto, M., Saudek, V., and Sklenar, V. (1992) Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions J. Biomol. NMR 2, 661-665
    • (1992) J. Biomol. NMR , vol.2 , pp. 661-665
    • Piotto, M.1    Saudek, V.2    Sklenar, V.3
  • 25
    • 0019327003 scopus 로고
    • A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules
    • Kumar, A., Ernst, R. R., and Wüthrich, K. (1980) A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules Biochem. Biophys. Res. Commun. 95, 1-6
    • (1980) Biochem. Biophys. Res. Commun. , vol.95 , pp. 1-6
    • Kumar, A.1    Ernst, R.R.2    Wüthrich, K.3
  • 26
    • 0000221195 scopus 로고
    • Computer-optimized homonuclear TOCSY experiments with suppression of cross relaxation
    • Briand, J. and Ernst, R. R. (1991) Computer-optimized homonuclear TOCSY experiments with suppression of cross relaxation Chem. Phys. Lett. 185, 276-285
    • (1991) Chem. Phys. Lett. , vol.185 , pp. 276-285
    • Briand, J.1    Ernst, R.R.2
  • 27
    • 0005963761 scopus 로고
    • Multiple quantum filters for elucidating NMR coupling networks
    • Piantini, U., Sørensen, O. W., and Ernst, R. R. (1982) Multiple quantum filters for elucidating NMR coupling networks J. Am. Chem. Soc. 104, 6800-6801
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 6800-6801
    • Piantini, U.1    Sørensen, O.W.2    Ernst, R.R.3
  • 28
    • 0034650726 scopus 로고    scopus 로고
    • Exact analysis of competition ligand binding by displacement isothermal titration calorimetry
    • Sigurskjold, B. W. (2000) Exact analysis of competition ligand binding by displacement isothermal titration calorimetry Anal. Biochem. 277, 260-266
    • (2000) Anal. Biochem. , vol.277 , pp. 260-266
    • Sigurskjold, B.W.1
  • 29
    • 0028936571 scopus 로고
    • An exact mathematical expression for describing competitive binding of two different ligands to a protein molecule
    • Wang, Z. X. (1995) An exact mathematical expression for describing competitive binding of two different ligands to a protein molecule FEBS Lett. 360, 111-114
    • (1995) FEBS Lett. , vol.360 , pp. 111-114
    • Wang, Z.X.1
  • 30
    • 3042828266 scopus 로고    scopus 로고
    • The development of a continuous isothermal titration calorimetric method for equilibrium studies
    • Markova, N. and Hallen, D. (2004) The development of a continuous isothermal titration calorimetric method for equilibrium studies Anal. Biochem. 331, 77-88
    • (2004) Anal. Biochem. , vol.331 , pp. 77-88
    • Markova, N.1    Hallen, D.2
  • 31
    • 84856929468 scopus 로고    scopus 로고
    • Thermodynamics of ligand binding to a heterogeneous RNA population in the malachite green aptamer
    • Sokoloski, J. E., Dombrowski, S. E., and Bevilacqua, P. C. (2012) Thermodynamics of ligand binding to a heterogeneous RNA population in the malachite green aptamer Biochemistry 51, 565-572
    • (2012) Biochemistry , vol.51 , pp. 565-572
    • Sokoloski, J.E.1    Dombrowski, S.E.2    Bevilacqua, P.C.3
  • 32
    • 37549033509 scopus 로고    scopus 로고
    • Isothermal titration calorimetry at very low c
    • Tellinghuisen, J. (2008) Isothermal titration calorimetry at very low c Anal. Biochem. 373, 395-397
    • (2008) Anal. Biochem. , vol.373 , pp. 395-397
    • Tellinghuisen, J.1
  • 33
    • 84894523713 scopus 로고    scopus 로고
    • Conformational readout of RNA by small ligands
    • Kligun, E. and Mandel-Gutfreund, Y. (2013) Conformational readout of RNA by small ligands RNA Biol. 10
    • (2013) RNA Biol. , pp. 10
    • Kligun, E.1    Mandel-Gutfreund, Y.2
  • 36
    • 33748936869 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain
    • Gilbert, S. D., Stoddard, C. D., Wise, S. J., and Batey, R. T. (2006) Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain J. Mol. Biol. 363, 624-624
    • (2006) J. Mol. Biol. , vol.363 , pp. 624-624
    • Gilbert, S.D.1    Stoddard, C.D.2    Wise, S.J.3    Batey, R.T.4
  • 37
    • 26444620938 scopus 로고    scopus 로고
    • The kinetics of ligand binding by an adenine-sensing riboswitch
    • Wickiser, J. K., Cheah, M. T., Breaker, R. R., and Crothers, D. M. (2005) The kinetics of ligand binding by an adenine-sensing riboswitch Biochemistry 44, 13404-13414
    • (2005) Biochemistry , vol.44 , pp. 13404-13414
    • Wickiser, J.K.1    Cheah, M.T.2    Breaker, R.R.3    Crothers, D.M.4
  • 38
    • 34548761368 scopus 로고    scopus 로고
    • Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach
    • Lang, K., Rieder, R., and Micura, R. (2007) Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach Nucleic Acids Res. 35, 5370-5378
    • (2007) Nucleic Acids Res. , vol.35 , pp. 5370-5378
    • Lang, K.1    Rieder, R.2    Micura, R.3
  • 39
    • 77954627972 scopus 로고    scopus 로고
    • Folding of a transcriptionally acting PreQ(1) riboswitch
    • Rieder, U., Kreutz, C., and Micura, R. (2010) Folding of a transcriptionally acting PreQ(1) riboswitch Proc. Natl. Acad. Sci. U. S. A. 107, 10804-10809
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 10804-10809
    • Rieder, U.1    Kreutz, C.2    Micura, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.