메뉴 건너뛰기




Volumn 12, Issue 3, 2004, Pages 379-388

Anion binding to nucleic acids

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ANION; ASPARTIC ACID; GLUTAMIC ACID; HYDROXYL GROUP; IMINO ACID; NUCLEIC ACID; PHOSPHATE;

EID: 1542498400     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.02.015     Document Type: Article
Times cited : (109)

References (61)
  • 1
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: A quarter of a million crystal structures and rising
    • Allen F.H. The Cambridge Structural Database. a quarter of a million crystal structures and rising Acta Crystallogr. B. 58:2002;380-388.
    • (2002) Acta Crystallogr. B , vol.58 , pp. 380-388
    • Allen, F.H.1
  • 2
    • 0035800599 scopus 로고    scopus 로고
    • Structure-based analysis of protein-RNA interactions using the program ENTANGLE
    • Allers J., Shamoo Y. Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J. Mol. Biol. 311:2001;75-86.
    • (2001) J. Mol. Biol. , vol.311 , pp. 75-86
    • Allers, J.1    Shamoo, Y.2
  • 3
    • 14244271781 scopus 로고    scopus 로고
    • RNA solvation: A molecular dynamics simulation perspective
    • Auffinger P., Westhof E. RNA solvation. a molecular dynamics simulation perspective Biopolymers. 56:2000;266-274.
    • (2000) Biopolymers , vol.56 , pp. 266-274
    • Auffinger, P.1    Westhof, E.2
  • 4
    • 0035028632 scopus 로고    scopus 로고
    • An extended structural signature for the tRNA anticodon loop
    • Auffinger P., Westhof E. An extended structural signature for the tRNA anticodon loop. RNA. 7:2001;334-341.
    • (2001) RNA , vol.7 , pp. 334-341
    • Auffinger, P.1    Westhof, E.2
  • 5
    • 0038539610 scopus 로고    scopus 로고
    • 2+ binding sites of the 5S rRNA loop e motif as investigated by molecular dynamics simulations
    • 2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. Chem. Biol. 10:2003;551-561.
    • (2003) Chem. Biol. , vol.10 , pp. 551-561
    • Auffinger, P.1    Bielecki, L.2    Westhof, E.3
  • 6
    • 0346366808 scopus 로고    scopus 로고
    • 2+ ion binding sites in the 5S rRNA loop e inferred from molecular dynamics simulations
    • 2+ ion binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations. J. Mol. Biol. 335:2004;555-571.
    • (2004) J. Mol. Biol. , vol.335 , pp. 555-571
    • Auffinger, P.1    Bielecki, L.2    Westhof, E.3
  • 7
    • 0026279527 scopus 로고
    • Crystal structure of a barnase-d(GpC) complex at 1.9 a resolution
    • Baudet S., Janin J. Crystal structure of a barnase-d(GpC) complex at 1.9 A resolution. J. Mol. Biol. 219:1991;123-132.
    • (1991) J. Mol. Biol. , vol.219 , pp. 123-132
    • Baudet, S.1    Janin, J.2
  • 10
    • 0034098420 scopus 로고    scopus 로고
    • Tertiary core rearrangements in a tight binding transfer RNA aptamer
    • Bullock T.L., Sherlin L.D., Perona J.J. Tertiary core rearrangements in a tight binding transfer RNA aptamer. Nat. Struct. Biol. 7:2000;497-504.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 497-504
    • Bullock, T.L.1    Sherlin, L.D.2    Perona, J.J.3
  • 12
    • 0035963340 scopus 로고    scopus 로고
    • Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule
    • Changela A., DiGate R.J., Mondragon A. Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Nature. 411:2001;1077-1081.
    • (2001) Nature , vol.411 , pp. 1077-1081
    • Changela, A.1    Digate, R.J.2    Mondragon, A.3
  • 14
    • 0030856333 scopus 로고    scopus 로고
    • Metals, motifs and recognition in the crystal structure of a 5S rRNA domain
    • Correll C.C., Freeborn B., Moore P.B., Steitz T.A. Metals, motifs and recognition in the crystal structure of a 5S rRNA domain. Cell. 91:1997;705-712.
    • (1997) Cell , vol.91 , pp. 705-712
    • Correll, C.C.1    Freeborn, B.2    Moore, P.B.3    Steitz, T.A.4
  • 16
    • 0345531092 scopus 로고    scopus 로고
    • The common and the distinctive features of the bulged-G motif based on a 1.04 Å resolution RNA structure
    • Correll C.C., Beneken J., Plantinga M.J., Lubbers M., Chan Y.L. The common and the distinctive features of the bulged-G motif based on a 1.04 Å resolution RNA structure. Nucleic Acids Res. 31:2003;6806-6818.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6806-6818
    • Correll, C.C.1    Beneken, J.2    Plantinga, M.J.3    Lubbers, M.4    Chan, Y.L.5
  • 17
    • 0029636784 scopus 로고
    • Mechanism and thermodynamics of ion selectivity in aqueous solutions of 18-crown-6 ether: A molecular dynamics study
    • Dang L.X. Mechanism and thermodynamics of ion selectivity in aqueous solutions of 18-crown-6 ether. a molecular dynamics study J. Am. Chem. Soc. 117:1995;6954-6960.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 6954-6960
    • Dang, L.X.1
  • 18
    • 0000358340 scopus 로고
    • + complex in water: A molecular dynamics simulation
    • + complex in water. a molecular dynamics simulation J. Am. Chem. Soc. 112:1990;5716-5720.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 5716-5720
    • Dang, L.X.1    Kollman, P.A.2
  • 19
    • 0033104039 scopus 로고    scopus 로고
    • New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations
    • Darden T., Perera L., Li P., Pedersen L. New tricks for modelers from the crystallography toolkit. the particle mesh Ewald algorithm and its use in nucleic acid simulations Structure. 7:1999;R55-R60.
    • (1999) Structure , vol.7
    • Darden, T.1    Perera, L.2    Li, P.3    Pedersen, L.4
  • 21
    • 0034332436 scopus 로고    scopus 로고
    • Transfer-RNA aminoacylation by arginyl-transfer-RNA synthetase - Induced conformations during substrates binding
    • Delagoutte B., Moras D., Cavarelli J. Transfer-RNA aminoacylation by arginyl-transfer-RNA synthetase - Induced conformations during substrates binding. EMBO J. 19:2000;5599-5610.
    • (2000) EMBO J. , vol.19 , pp. 5599-5610
    • Delagoutte, B.1    Moras, D.2    Cavarelli, J.3
  • 23
    • 0019318942 scopus 로고
    • High-salt d(CpGpCpG), a left-handed Z′ DNA double helix
    • Drew H., Takano T., Tanaka S., Itakura K., Dickerson R.E. High-salt d(CpGpCpG), a left-handed Z′ DNA double helix. Nature. 286:1980;567-573.
    • (1980) Nature , vol.286 , pp. 567-573
    • Drew, H.1    Takano, T.2    Tanaka, S.3    Itakura, K.4    Dickerson, R.E.5
  • 24
    • 0036009329 scopus 로고    scopus 로고
    • DNA-cation interactions: Quo vadis?
    • Egli M. DNA-cation interactions. quo vadis? Chem. Biol. 9:2002;277-286.
    • (2002) Chem. Biol. , vol.9 , pp. 277-286
    • Egli, M.1
  • 25
    • 0033571581 scopus 로고    scopus 로고
    • Synthesis of aspartyl-tRNA(Asp) in Escherichia coli - A snapshot of the second step
    • Eiler S., Dock-Bregeon A., Moulinier L., Thierry J.C., Moras D. Synthesis of aspartyl-tRNA(Asp) in Escherichia coli - a snapshot of the second step. EMBO J. 18:1999;6532-6541.
    • (1999) EMBO J. , vol.18 , pp. 6532-6541
    • Eiler, S.1    Dock-Bregeon, A.2    Moulinier, L.3    Thierry, J.C.4    Moras, D.5
  • 26
    • 0035184520 scopus 로고    scopus 로고
    • Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site
    • Ennifar E., Walter P., Ehresmann B., Ehresmann C., Dumas P. Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site. Nat. Struct. Biol. 8:2001;1064-1068.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 1064-1068
    • Ennifar, E.1    Walter, P.2    Ehresmann, B.3    Ehresmann, C.4    Dumas, P.5
  • 28
    • 0032851951 scopus 로고    scopus 로고
    • Sodium and chlorine ions as part of the DNA solvation shell
    • Feig M., Pettitt B.M. Sodium and chlorine ions as part of the DNA solvation shell. Biophys. J. 77:1999;1769-1781.
    • (1999) Biophys. J. , vol.77 , pp. 1769-1781
    • Feig, M.1    Pettitt, B.M.2
  • 29
    • 0032472205 scopus 로고    scopus 로고
    • Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb(III)
    • Feig A., Scott W.G., Uhlenbeck O.C. Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb(III). Science. 279:1998;81-84.
    • (1998) Science , vol.279 , pp. 81-84
    • Feig, A.1    Scott, W.G.2    Uhlenbeck, O.C.3
  • 30
    • 0038013670 scopus 로고    scopus 로고
    • Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit
    • Hansen J.L., Moore P.B., Steitz T.A. Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. J. Mol. Biol. 330:2003;1061-1075.
    • (2003) J. Mol. Biol. , vol.330 , pp. 1061-1075
    • Hansen, J.L.1    Moore, P.B.2    Steitz, T.A.3
  • 31
    • 0032532765 scopus 로고    scopus 로고
    • Exploration of metal ion binding sites in RNA folds with Brownian dynamics simulations
    • Hermann T., Westhof E. Exploration of metal ion binding sites in RNA folds with Brownian dynamics simulations. Structure. 6:1998;1303-1315.
    • (1998) Structure , vol.6 , pp. 1303-1315
    • Hermann, T.1    Westhof, E.2
  • 32
    • 0030849184 scopus 로고    scopus 로고
    • Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme
    • Hermann T., Auffinger P., Scott W.G., Westhof E. Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme. Nucleic Acids Res. 25:1997;3421-3427.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3421-3427
    • Hermann, T.1    Auffinger, P.2    Scott, W.G.3    Westhof, E.4
  • 33
    • 0031915278 scopus 로고    scopus 로고
    • Molecular dynamics investigations of the hammerhead ribozyme RNA
    • Hermann T., Auffinger P., Westhof E. Molecular dynamics investigations of the hammerhead ribozyme RNA. Eur. Biophy. J. 27:1998;153-165.
    • (1998) Eur. Biophy. J. , vol.27 , pp. 153-165
    • Hermann, T.1    Auffinger, P.2    Westhof, E.3
  • 34
    • 0035966271 scopus 로고    scopus 로고
    • Cocrystal structure of a tRNA Psi55 pseudouridine synthase. Nucleotide flipping by an RNA-modifying enzyme
    • Hoang C., Ferre-D'Amare A.R. Cocrystal structure of a tRNA Psi55 pseudouridine synthase. Nucleotide flipping by an RNA-modifying enzyme. Cell. 107:2001;929-939.
    • (2001) Cell , vol.107 , pp. 929-939
    • Hoang, C.1    Ferre-D'Amare, A.R.2
  • 35
    • 0030763137 scopus 로고    scopus 로고
    • Localization of divalent metal ions in the minor groove of DNA A-tracts
    • Hud N.V., Feigon J. Localization of divalent metal ions in the minor groove of DNA A-tracts. J. Am. Chem. Soc. 119:1997;5756-5757.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 5756-5757
    • Hud, N.V.1    Feigon, J.2
  • 38
    • 0035423087 scopus 로고    scopus 로고
    • The kink-turn: A new RNA secondary structure motif
    • Klein D.J., Schmeing T.M., Moore P.B., Steitz T.A. The kink-turn. a new RNA secondary structure motif EMBO J. 20:2001;4214-4221.
    • (2001) EMBO J. , vol.20 , pp. 4214-4221
    • Klein, D.J.1    Schmeing, T.M.2    Moore, P.B.3    Steitz, T.A.4
  • 39
    • 0036145653 scopus 로고    scopus 로고
    • Structures of the two 3D domain-swapped RNase a trimers
    • Liu Y., Gotte G., Libonati M., Eisenberg D. Structures of the two 3D domain-swapped RNase A trimers. Protein Sci. 11:2002;371-380.
    • (2002) Protein Sci. , vol.11 , pp. 371-380
    • Liu, Y.1    Gotte, G.2    Libonati, M.3    Eisenberg, D.4
  • 40
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
    • Luscombe N.M., Laskowski R.A., Thornton J.M. Amino acid-base interactions. a three-dimensional analysis of protein-DNA interactions at an atomic level Nucleic Acids Res. 29:2001;2860-2874.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 41
    • 0001630716 scopus 로고
    • The crystal structure of cytosine hydrochloride
    • Mandel N.S. The crystal structure of cytosine hydrochloride. Acta Crystallogr. B. 33:1977;1079-1082.
    • (1977) Acta Crystallogr. B , vol.33 , pp. 1079-1082
    • Mandel, N.S.1
  • 43
    • 0032879334 scopus 로고    scopus 로고
    • A sulfate pocket formed by three GoU pairs in the 0.97 Å resolution x-ray structure of a nonameric RNA
    • Masquida B., Sauter C., Westhof E. A sulfate pocket formed by three GoU pairs in the 0.97 Å resolution x-ray structure of a nonameric RNA. RNA. 5:1999;1384-1395.
    • (1999) RNA , vol.5 , pp. 1384-1395
    • Masquida, B.1    Sauter, C.2    Westhof, E.3
  • 45
    • 0018037939 scopus 로고
    • A 1:2 crystalline complex of apa:proflavine: A model for binding to single-stranded regions in rna
    • Neidle S., Taylor G., Sanderson M. A 1:2 crystalline complex of apa:proflavine. a model for binding to single-stranded regions in rna Nucleic Acids Res. 5:1978;4417-4422.
    • (1978) Nucleic Acids Res. , vol.5 , pp. 4417-4422
    • Neidle, S.1    Taylor, G.2    Sanderson, M.3
  • 47
    • 0033081413 scopus 로고    scopus 로고
    • Cys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA
    • Cys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. Structure. 7:1999;143-154.
    • (1999) Structure , vol.7 , pp. 143-154
    • Nissen, P.1    Thirup, S.2    Kjeldgaard, M.3    Nyborg, J.4
  • 48
    • 67049156092 scopus 로고    scopus 로고
    • Ionic solvation in aqueous and nonaqueous solutions
    • Ohtaki H. Ionic solvation in aqueous and nonaqueous solutions. Monatsh. Chem. 132:2001;1237-1268.
    • (2001) Monatsh. Chem. , vol.132 , pp. 1237-1268
    • Ohtaki, H.1
  • 49
    • 0142025560 scopus 로고
    • Structure and dynamics of hydrated ions
    • Ohtaki H., Radnai T. Structure and dynamics of hydrated ions. Chem. Rev. 93:1993;1157-1204.
    • (1993) Chem. Rev. , vol.93 , pp. 1157-1204
    • Ohtaki, H.1    Radnai, T.2
  • 51
    • 0030476765 scopus 로고    scopus 로고
    • Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
    • Scott W.G., Murray J.B., Arnold J.R.P., Stoddard B.L., Klug A. Capturing the structure of a catalytic RNA intermediate. the hammerhead ribozyme Science. 274:1996;2065-2069.
    • (1996) Science , vol.274 , pp. 2065-2069
    • Scott, W.G.1    Murray, J.B.2    Arnold, J.R.P.3    Stoddard, B.L.4    Klug, A.5
  • 52
    • 0000942976 scopus 로고
    • The crystal and molecular structure of adenosine hydrochloride
    • Shikata K., Ueki T., Mitsui T. The crystal and molecular structure of adenosine hydrochloride. Acta Crystallogr. B. 29:1973;31-38.
    • (1973) Acta Crystallogr. B , vol.29 , pp. 31-38
    • Shikata, K.1    Ueki, T.2    Mitsui, T.3
  • 53
    • 85047699292 scopus 로고    scopus 로고
    • Metal-modified nucleobase sextet: Joining four linear metal fragments (trans-a2PtII) and six model nucleobases to an exceedingly stable entity
    • Sigel R.K., Thompson S.M., Freisinger E., Glahe F., Lippert B. Metal-modified nucleobase sextet. joining four linear metal fragments (trans-a2PtII) and six model nucleobases to an exceedingly stable entity Chemistry. 7:2001;1968-1980.
    • (2001) Chemistry , vol.7 , pp. 1968-1980
    • Sigel, R.K.1    Thompson, S.M.2    Freisinger, E.3    Glahe, F.4    Lippert, B.5
  • 54
    • 0033010932 scopus 로고    scopus 로고
    • Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot
    • Su L., Chen L., Egli M., Berger J.M., Rich A. Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nat. Struct. Biol. 6:1999;285-292.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 285-292
    • Su, L.1    Chen, L.2    Egli, M.3    Berger, J.M.4    Rich, A.5
  • 57
    • 0034823943 scopus 로고    scopus 로고
    • Statistical analysis of atomic contacts at RNA-protein interfaces
    • Treger M., Westhof E. Statistical analysis of atomic contacts at RNA-protein interfaces. J. Mol. Recognit. 14:2001;199-214.
    • (2001) J. Mol. Recognit. , vol.14 , pp. 199-214
    • Treger, M.1    Westhof, E.2
  • 58
    • 0034624023 scopus 로고    scopus 로고
    • Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase
    • Vilkaitis G., Dong A., Weinhold E., Cheng X., Klimasauskas S. Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J. Biol. Chem. 275:2000;38722-38730.
    • (2000) J. Biol. Chem. , vol.275 , pp. 38722-38730
    • Vilkaitis, G.1    Dong, A.2    Weinhold, E.3    Cheng, X.4    Klimasauskas, S.5
  • 59
    • 0034626729 scopus 로고    scopus 로고
    • Structure and assembly of the Alu domain of the mammalian signal recognition particle
    • Weichenrieder O., Wild K., Strub K., Cusack S. Structure and assembly of the Alu domain of the mammalian signal recognition particle. Nature. 408:2000;167-173.
    • (2000) Nature , vol.408 , pp. 167-173
    • Weichenrieder, O.1    Wild, K.2    Strub, K.3    Cusack, S.4
  • 60
    • 0000521158 scopus 로고
    • Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals
    • Westhof E., Dumas P., Moras D. Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals. Acta Crystallogr. A. 44:1988;112-123.
    • (1988) Acta Crystallogr. a , vol.44 , pp. 112-123
    • Westhof, E.1    Dumas, P.2    Moras, D.3
  • 61
    • 0031047279 scopus 로고    scopus 로고
    • Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
    • Young M.A., Jayaram B., Beveridge D.L. Intrusion of counterions into the spine of hydration in the minor groove of B-DNA. fractional occupancy of electronegative pockets J. Am. Chem. Soc. 119:1997;59-69.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 59-69
    • Young, M.A.1    Jayaram, B.2    Beveridge, D.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.