메뉴 건너뛰기




Volumn 50, Issue 6, 2011, Pages 962-969

Molecular Recognition of 6′-N-5-Hexynoate kanamycin A and RNA 1x1 internal loops containing CA mismatches

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DEAMINASES; AMINOGLYCOSIDES; BINDING AFFINITIES; INTERNAL LOOPS; KANAMYCIN A; LIGAND AFFINITY; LOOP CLOSING; SMALL MOLECULES;

EID: 79851497250     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101724h     Document Type: Article
Times cited : (13)

References (56)
  • 1
    • 0035955361 scopus 로고    scopus 로고
    • An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
    • Lau, N. C., Lim, L. P., Weinstein, E. G., and Bartel, D. P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science 294, 858-862
    • (2001) Science , vol.294 , pp. 858
    • Lau, N.C.1    Lim, L.P.2    Weinstein, E.G.3    Bartel, D.P.4
  • 2
    • 0022649937 scopus 로고
    • The intervening sequence RNA of Tetrahymena is an enzyme
    • Zaug, A. J. and Cech, T. R. (1986) The intervening sequence RNA of Tetrahymena is an enzyme Science 231, 470-475
    • (1986) Science , vol.231 , pp. 470
    • Zaug, A.J.1    Cech, T.R.2
  • 3
    • 0021013526 scopus 로고
    • The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme
    • Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., and Altman, S. (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme Cell 35, 849-857
    • (1983) Cell , vol.35 , pp. 849
    • Guerrier-Takada, C.1    Gardiner, K.2    Marsh, T.3    Pace, N.4    Altman, S.5
  • 5
    • 0037206833 scopus 로고    scopus 로고
    • Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
    • Winkler, W., Nahvi, A., and Breaker, R. R. (2002) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression Nature 419, 952-956
    • (2002) Nature , vol.419 , pp. 952
    • Winkler, W.1    Nahvi, A.2    Breaker, R.R.3
  • 6
    • 0034783659 scopus 로고    scopus 로고
    • Targeting RNA with small-molecule drugs: Therapeutic promise and chemical challenges
    • Gallego, J. and Varani, G. (2001) Targeting RNA with small-molecule drugs: therapeutic promise and chemical challenges Acc. Chem. Res. 34, 836-843
    • (2001) Acc. Chem. Res. , vol.34 , pp. 836
    • Gallego, J.1    Varani, G.2
  • 7
    • 0027242380 scopus 로고
    • Footprinting the sites of interaction of antibiotics with catalytic group i intron RNA
    • von Ahsen, U. and Noller, H. F. (1993) Footprinting the sites of interaction of antibiotics with catalytic group I intron RNA Science 260, 1500-1503
    • (1993) Science , vol.260 , pp. 1500
    • Von Ahsen, U.1    Noller, H.F.2
  • 8
    • 67649197550 scopus 로고    scopus 로고
    • A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops
    • Chen, G., Kennedy, S. D., and Turner, D. H. (2009) A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops Biochemistry 48, 5738-5752
    • (2009) Biochemistry , vol.48 , pp. 5738
    • Chen, G.1    Kennedy, S.D.2    Turner, D.H.3
  • 9
    • 0037102491 scopus 로고    scopus 로고
    • The non-Watson-Crick base pairs and their associated isostericity matrices
    • Leontis, N. B., Stombaugh, J., and Westhof, E. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices Nucleic Acids Res. 30, 3497-3531
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3497
    • Leontis, N.B.1    Stombaugh, J.2    Westhof, E.3
  • 12
    • 0034232357 scopus 로고    scopus 로고
    • The G - U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems
    • Varani, G. and McClain, W. H. (2000) The G - U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems EMBO Rep. 1, 18-23
    • (2000) EMBO Rep. , vol.1 , pp. 18
    • Varani, G.1    McClain, W.H.2
  • 13
    • 0034974268 scopus 로고    scopus 로고
    • Substrate recognition by ADAR1 and ADAR2
    • Wong, S. K., Sato, S., and Lazinski, D. W. (2001) Substrate recognition by ADAR1 and ADAR2 RNA 7, 846-858
    • (2001) RNA , vol.7 , pp. 846
    • Wong, S.K.1    Sato, S.2    Lazinski, D.W.3
  • 14
    • 0030914301 scopus 로고    scopus 로고
    • RNA editing and hypermutation by adenosine deamination
    • DOI 10.1016/S0968-0004(97)01035-9, PII S0968000497010359
    • Bass, B. L. (1997) RNA editing and hypermutation by adenosine deamination Trends Biochem. Sci. 22, 157-162 (Pubitemid 27199315)
    • (1997) Trends in Biochemical Sciences , vol.22 , Issue.5 , pp. 157-162
    • Bass, B.L.1
  • 15
    • 34248523195 scopus 로고    scopus 로고
    • ADAR editing wobbles the microRNA world
    • Das, A. K. and Carmichael, G. G. (2007) ADAR editing wobbles the microRNA world ACS Chem. Biol. 2, 217-220
    • (2007) ACS Chem. Biol. , vol.2 , pp. 217
    • Das, A.K.1    Carmichael, G.G.2
  • 16
    • 33748101596 scopus 로고    scopus 로고
    • RNA editing in hepatitis delta virus
    • Hepatitis Delta Virus
    • Casey, J. L. (2006) RNA editing in hepatitis delta virus, in Hepatits Delta Virus, pp 67 - 89, Springer-Verlag, Berlin. (Pubitemid 47400309)
    • (2006) Current Topics in Microbiology and Immunology , vol.307 , pp. 67-89
    • Casey, J.L.1
  • 17
    • 0034711082 scopus 로고    scopus 로고
    • Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities
    • Lehmann, K. A. and Bass, B. L. (2000) Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities Biochemistry 39, 12875-12884
    • (2000) Biochemistry , vol.39 , pp. 12875
    • Lehmann, K.A.1    Bass, B.L.2
  • 20
    • 57649129042 scopus 로고    scopus 로고
    • RNA editing as a therapeutic target for CNS disorders
    • Morabito, M. V. and Emeson, R. B. (2009) RNA editing as a therapeutic target for CNS disorders Neuropsychopharmacology 34, 246
    • (2009) Neuropsychopharmacology , vol.34 , pp. 246
    • Morabito, M.V.1    Emeson, R.B.2
  • 21
    • 0036312082 scopus 로고    scopus 로고
    • Dimerization of a pathogenic human mitochondrial tRNA
    • Wittenhagen, L. M. and Kelley, S. O. (2002) Dimerization of a pathogenic human mitochondrial tRNA Nat. Struct. Biol. 9, 586-590
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 586
    • Wittenhagen, L.M.1    Kelley, S.O.2
  • 22
    • 13944256506 scopus 로고    scopus 로고
    • Structural probing of a pathogenic tRNA dimer
    • Roy, M. D., Wittenhagen, L. M., and Kelley, S. O. (2005) Structural probing of a pathogenic tRNA dimer RNA 11, 254-260
    • (2005) RNA , vol.11 , pp. 254
    • Roy, M.D.1    Wittenhagen, L.M.2    Kelley, S.O.3
  • 23
    • 0346743541 scopus 로고    scopus 로고
    • Impact of disease-related mitochondrial mutations on tRNA structure and function
    • Wittenhagen, L. M. and Kelley, S. O. (2003) Impact of disease-related mitochondrial mutations on tRNA structure and function Trends Biochem. Sci. 28, 605-611
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 605
    • Wittenhagen, L.M.1    Kelley, S.O.2
  • 25
    • 76649144805 scopus 로고    scopus 로고
    • The role of flexibility in the rational design of modularly assembled ligands targeting the RNAs that cause the myotonic dystrophies
    • Disney, M. D., Lee, M. M., Pushechnikov, A., and Childs-Disney, J. L. (2010) The role of flexibility in the rational design of modularly assembled ligands targeting the RNAs that cause the myotonic dystrophies ChemBioChem 11, 375-382
    • (2010) ChemBioChem , vol.11 , pp. 375
    • Disney, M.D.1    Lee, M.M.2    Pushechnikov, A.3    Childs-Disney, J.L.4
  • 26
    • 67650506996 scopus 로고    scopus 로고
    • Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: Application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3
    • Pushechnikov, A., Lee, M. M., Childs-Disney, J. L., Sobczak, K., French, J. M., Thornton, C. A., and Disney, M. D. (2009) Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3 J. Am. Chem. Soc. 131, 9767-9779
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 9767
    • Pushechnikov, A.1    Lee, M.M.2    Childs-Disney, J.L.3    Sobczak, K.4    French, J.M.5    Thornton, C.A.6    Disney, M.D.7
  • 27
    • 72249122539 scopus 로고    scopus 로고
    • Controlling the specificity of modularly assembled small molecules for RNA via ligand module spacing: Targeting the RNAs that cause myotonic muscular dystrophy
    • Lee, M. M., Childs-Disney, J. L., Pushechnikov, A., French, J. M., Sobczak, K., Thornton, C. A., and Disney, M. D. (2009) Controlling the specificity of modularly assembled small molecules for RNA via ligand module spacing: targeting the RNAs that cause myotonic muscular dystrophy J. Am. Chem. Soc. 131, 17464-17472
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 17464
    • Lee, M.M.1    Childs-Disney, J.L.2    Pushechnikov, A.3    French, J.M.4    Sobczak, K.5    Thornton, C.A.6    Disney, M.D.7
  • 28
    • 65749087933 scopus 로고    scopus 로고
    • Rational and modular design of potent ligands targeting the RNA that causes myotonic dystrophy 2
    • Lee, M. M., Pushechnikov, A., and Disney, M. D. (2009) Rational and modular design of potent ligands targeting the RNA that causes myotonic dystrophy 2 ACS Chem. Biol. 4, 345-355
    • (2009) ACS Chem. Biol. , vol.4 , pp. 345
    • Lee, M.M.1    Pushechnikov, A.2    Disney, M.D.3
  • 29
    • 34250367088 scopus 로고    scopus 로고
    • Using selection to identify and chemical microarray to study the RNA internal loops recognized by 6â€- N -acylated kanamycin A
    • Disney, M. D. and Childs-Disney, J. L. (2007) Using selection to identify and chemical microarray to study the RNA internal loops recognized by 6â€- N -acylated kanamycin A ChemBioChem 8, 649-656
    • (2007) ChemBioChem , vol.8 , pp. 649
    • Disney, M.D.1    Childs-Disney, J.L.2
  • 30
    • 37349030751 scopus 로고    scopus 로고
    • A small molecule microarray platform to select RNA internal loop-ligand interactions
    • Childs-Disney, J. L., Wu, M., Pushechnikov, A., Aminova, O., and Disney, M. D. (2007) A small molecule microarray platform to select RNA internal loop-ligand interactions ACS Chem. Biol. 2, 745-754
    • (2007) ACS Chem. Biol. , vol.2 , pp. 745
    • Childs-Disney, J.L.1    Wu, M.2    Pushechnikov, A.3    Aminova, O.4    Disney, M.D.5
  • 31
    • 0033607261 scopus 로고    scopus 로고
    • Thermodynamics of single mismatches in RNA duplexes
    • Kierzek, R., Burkard, M. E., and Turner, D. H. (1999) Thermodynamics of single mismatches in RNA duplexes Biochemistry 38, 14214-14223
    • (1999) Biochemistry , vol.38 , pp. 14214
    • Kierzek, R.1    Burkard, M.E.2    Turner, D.H.3
  • 32
    • 36248936612 scopus 로고    scopus 로고
    • Thermodynamic characterization of single mismatches found in naturally occurring RNA
    • Davis, A. R. and Znosko, B. M. (2007) Thermodynamic characterization of single mismatches found in naturally occurring RNA Biochemistry 46, 13425-13436
    • (2007) Biochemistry , vol.46 , pp. 13425
    • Davis, A.R.1    Znosko, B.M.2
  • 33
    • 79951574446 scopus 로고    scopus 로고
    • Structural characterization of naturally occurring RNA single mismatches
    • in press, doi: 10.1093/NAR/gpk793
    • Davis, A. R. and Znosko, B. M. (2010) Structural characterization of naturally occurring RNA single mismatches. Nucleic Acids Res. (in press, doi: 10.1093/NAR/gpk793).
    • (2010) Nucleic Acids Res.
    • Davis, A.R.1    Znosko, B.M.2
  • 34
    • 77957665011 scopus 로고    scopus 로고
    • Positional and neighboring base pair effects on the thermodynamic stability of RNA single mismatches
    • Davis, A. R. and Znosko, B. M. (2010) Positional and neighboring base pair effects on the thermodynamic stability of RNA single mismatches. Biochemistry 49, 8669 - 8679.
    • (2010) Biochemistry , vol.49 , pp. 8669-8679
    • Davis, A.R.1    Znosko, B.M.2
  • 35
    • 0033596964 scopus 로고    scopus 로고
    • Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A•A, C•C, G•G, and T•T mismatches
    • Peyret, N., Seneviratne, P. A., Allawi, H. T., and SantaLucia, J., Jr. (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A•A, C•C, G•G, and T•T mismatches Biochemistry 38, 3468-3477
    • (1999) Biochemistry , vol.38 , pp. 3468
    • Peyret, N.1    Seneviratne, P.A.2    Allawi, H.T.3    Santalucia Jr., J.4
  • 36
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia, J., Jr. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics Proc. Natl. Acad. Sci. U.S.A. 95, 1460-1465
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 1460-1465
    • Santalucia Jr., J.1
  • 37
    • 0024804759 scopus 로고
    • Absorbance melting curves of RNA
    • Puglisi, J. D. and Tinoco, I., Jr. (1989) Absorbance melting curves of RNA Methods Enzymol. 180, 304-325
    • (1989) Methods Enzymol. , vol.180 , pp. 304
    • Puglisi, J.D.1    Tinoco Jr., I.2
  • 38
    • 0029294539 scopus 로고
    • Specific binding of aminoglycoside antibiotics to RNA
    • Wang, Y. and Rando, R. R. (1995) Specific binding of aminoglycoside antibiotics to RNA Chem. Biol. 2, 281-290
    • (1995) Chem. Biol. , vol.2 , pp. 281
    • Wang, Y.1    Rando, R.R.2
  • 39
    • 0029805937 scopus 로고    scopus 로고
    • 2 by two-dimensional NMR and simulated annealing
    • 2 by two-dimensional NMR and simulated annealing Biochemistry 35, 14077-14089
    • (1996) Biochemistry , vol.35 , pp. 14077
    • McDowell, J.A.1    Turner, D.H.2
  • 40
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • Xia, T., SantaLucia, J., Jr., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., and Turner, D. H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs Biochemistry 37, 14719-14735
    • (1998) Biochemistry , vol.37 , pp. 14719
    • Xia, T.1    Santalucia Jr., J.2    Burkard, M.E.3    Kierzek, R.4    Schroeder, S.J.5    Jiao, X.6    Cox, C.7    Turner, D.H.8
  • 41
    • 0020674698 scopus 로고
    • Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp
    • Petersheim, M. and Turner, D. H. (1983) Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp Biochemistry 22, 256-263
    • (1983) Biochemistry , vol.22 , pp. 256
    • Petersheim, M.1    Turner, D.H.2
  • 43
    • 0015800196 scopus 로고
    • Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches
    • Gralla, J. and Crothers, D. M. (1973) Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches J. Mol. Biol. 78, 301-319
    • (1973) J. Mol. Biol. , vol.78 , pp. 301
    • Gralla, J.1    Crothers, D.M.2
  • 44
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J. Mol. Biol. 288, 911-940
    • (1999) J. Mol. Biol. , vol.288 , pp. 911
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 45
    • 0033524495 scopus 로고    scopus 로고
    • Aminoglycoside antibiotics are able to specifically bind the 5â€-untranslated region of thymidylate synthase messenger RNA
    • Tok, J. B., Cho, J., and Rando, R. R. (1999) Aminoglycoside antibiotics are able to specifically bind the 5â€-untranslated region of thymidylate synthase messenger RNA Biochemistry 38, 199-206
    • (1999) Biochemistry , vol.38 , pp. 199
    • Tok, J.B.1    Cho, J.2    Rando, R.R.3
  • 46
    • 0032126750 scopus 로고    scopus 로고
    • Specificity of aminoglycoside antibiotics for the A-site of the decoding region of ribosomal RNA
    • Wong, C. H., Hendrix, M., Priestley, E. S., and Greenberg, W. A. (1998) Specificity of aminoglycoside antibiotics for the A-site of the decoding region of ribosomal RNA Chem. Biol. 5, 397-406
    • (1998) Chem. Biol. , vol.5 , pp. 397
    • Wong, C.H.1    Hendrix, M.2    Priestley, E.S.3    Greenberg, W.A.4
  • 47
    • 0032212026 scopus 로고    scopus 로고
    • Deciphering RNA recognition: Aminoglycoside binding to the hammerhead ribozyme
    • Tor, Y., Hermann, T., and Westhof, E. (1998) Deciphering RNA recognition: aminoglycoside binding to the hammerhead ribozyme Chem. Biol. 5, R277-283
    • (1998) Chem. Biol. , vol.5 , pp. 277
    • Tor, Y.1    Hermann, T.2    Westhof, E.3
  • 48
    • 57049107410 scopus 로고    scopus 로고
    • Two-dimensional combinatorial screening identifies specific 6â€-acylated kanamycin A- and 6â€-acylated neamine-RNA hairpin interactions
    • Aminova, O., Paul, D. J., Childs-Disney, J. L., and Disney, M. D. (2008) Two-dimensional combinatorial screening identifies specific 6â€- acylated kanamycin A- and 6â€-acylated neamine-RNA hairpin interactions Biochemistry 47, 12670-12679
    • (2008) Biochemistry , vol.47 , pp. 12670
    • Aminova, O.1    Paul, D.J.2    Childs-Disney, J.L.3    Disney, M.D.4
  • 50
    • 73049117567 scopus 로고    scopus 로고
    • Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside-RNA hairpin loop interactions
    • Paul, D. J., Seedhouse, S. J., and Disney, M. D. (2009) Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside-RNA hairpin loop interactions Nucleic Acids Res. 37, 5894-5907
    • (2009) Nucleic Acids Res. , vol.37 , pp. 5894
    • Paul, D.J.1    Seedhouse, S.J.2    Disney, M.D.3
  • 51
    • 77749255506 scopus 로고    scopus 로고
    • Two-dimensional combinatorial screening of a bacterial rRNA A-site-like motif library: Defining privileged asymmetric internal loops that bind aminoglycosides
    • Tran, T. and Disney, M. D. (2010) Two-dimensional combinatorial screening of a bacterial rRNA A-site-like motif library: defining privileged asymmetric internal loops that bind aminoglycosides Biochemistry 49, 1833-1842
    • (2010) Biochemistry , vol.49 , pp. 1833
    • Tran, T.1    Disney, M.D.2
  • 52
    • 0030747007 scopus 로고    scopus 로고
    • a shift at the active site of a lead-dependent ribozyme
    • a shift at the active site of a lead-dependent ribozyme J. Am. Chem. Soc. 119, 6621-6628
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 6621
    • Legault, P.1    Pardi, A.2
  • 54
    • 0034712097 scopus 로고    scopus 로고
    • General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
    • Nakano, S., Chadalavada, D. M., and Bevilacqua, P. C. (2000) General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme Science 287, 1493-1497
    • (2000) Science , vol.287 , pp. 1493
    • Nakano, S.1    Chadalavada, D.M.2    Bevilacqua, P.C.3
  • 56
    • 0037424612 scopus 로고    scopus 로고
    • Coupling of drug protonation to the specific binding of aminoglycosides to the A site of 16 S rRNA: Elucidation of the number of drug amino groups involved and their identities
    • Kaul, M., Barbieri, C. M., Kerrigan, J. E., and Pilch, D. S. (2003) Coupling of drug protonation to the specific binding of aminoglycosides to the A site of 16 S rRNA: elucidation of the number of drug amino groups involved and their identities J. Mol. Biol. 326, 1373-1387
    • (2003) J. Mol. Biol. , vol.326 , pp. 1373
    • Kaul, M.1    Barbieri, C.M.2    Kerrigan, J.E.3    Pilch, D.S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.