메뉴 건너뛰기




Volumn 257, Issue 2, 1996, Pages 276-289

The influence of symmetric internal loops on the flexibility of RNA

Author keywords

Hydrodynamics; Ribozymes; RNA bulges; RNA structure; Transient electric birefringence

Indexed keywords

BUFFER;

EID: 0029913806     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0162     Document Type: Article
Times cited : (36)

References (46)
  • 1
    • 0022423486 scopus 로고
    • Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G and dCT3YT3G (X, Y = A, C, G, T)
    • Aboul-ela, F., Koh, D., Tinoco, I., Jr & Martin, F. H. (1985). Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G and dCT3YT3G (X, Y = A, C, G, T). Nucl. Acids Res. 13, 4811-4824.
    • (1985) Nucl. Acids Res. , vol.13 , pp. 4811-4824
    • Aboul-Ela, F.1    Koh, D.2    Tinoco I., Jr.3    Martin, F.H.4
  • 2
    • 84990485097 scopus 로고
    • Transport properties of rigid and flexible macromolecules by Brownian dynamics simulation
    • Allison, S. A. & McCammon, J. A. (1984). Transport properties of rigid and flexible macromolecules by Brownian dynamics simulation. Biopolymers, 23, 167-187.
    • (1984) Biopolymers , vol.23 , pp. 167-187
    • Allison, S.A.1    McCammon, J.A.2
  • 3
    • 0026736993 scopus 로고
    • Electric dichroism and birefringence decay of short DNA restriction fragments studied by Brownian dynamics simulation
    • Allison, S. A. & Nambi, P. (1992). Electric dichroism and birefringence decay of short DNA restriction fragments studied by Brownian dynamics simulation. Macromolecules, 25, 759-768.
    • (1992) Macromolecules , vol.25 , pp. 759-768
    • Allison, S.A.1    Nambi, P.2
  • 4
    • 0028004021 scopus 로고
    • Global structure of a self-cleaving hammerhead RNA
    • Amiri, K. M. A. & Hagerman, P. J. (1994). Global structure of a self-cleaving hammerhead RNA. Biochemistry, 33, 13172-13177.
    • (1994) Biochemistry , vol.33 , pp. 13172-13177
    • Amiri, K.M.A.1    Hagerman, P.J.2
  • 5
    • 0028902990 scopus 로고
    • Structure of an RNA double helix including uracil-uracil base-pairs in an internal loop
    • Baeyens, K. J., De Bondt, H. L. & Holbrook, S. R. (1995). Structure of an RNA double helix including uracil-uracil base-pairs in an internal loop. Nature Struct. Biol. 2, 56-62.
    • (1995) Nature Struct. Biol. , vol.2 , pp. 56-62
    • Baeyens, K.J.1    De Bondt, H.L.2    Holbrook, S.R.3
  • 6
    • 0024426629 scopus 로고
    • The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles)
    • Battacharyya, A. & Lilley D. M. J. (1989). The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). Nucl. Acids Res. 17, 6821-6840.
    • (1989) Nucl. Acids Res. , vol.17 , pp. 6821-6840
    • Battacharyya, A.1    Lilley, D.M.J.2
  • 7
    • 0025171938 scopus 로고
    • RNA bulges and the helical periodicity of double stranded RNA
    • Battacharyya, A., Murchie, A. I. H. & Lilley, D. M. J. (1990). RNA bulges and the helical periodicity of double stranded RNA. Nature, 343, 484-487.
    • (1990) Nature , vol.343 , pp. 484-487
    • Battacharyya, A.1    Murchie, A.I.H.2    Lilley, D.M.J.3
  • 10
    • 0000231785 scopus 로고
    • Geometry of a branched DNA structure in solution
    • Cooper, J. P. & Hagerman, P. J. (1989). Geometry of a branched DNA structure in solution. Proc. Natl Acad. Sci. USA, 86, 7336-7340.
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 7336-7340
    • Cooper, J.P.1    Hagerman, P.J.2
  • 12
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • Ermak, D. L. & McCammon, J. A. (1978). Brownian dynamics with hydrodynamic interactions. J. Chem. Phys. 69, 1352-1360.
    • (1978) J. Chem. Phys. , vol.69 , pp. 1352-1360
    • Ermak, D.L.1    McCammon, J.A.2
  • 13
    • 0029065694 scopus 로고
    • Determination of the angle between the anticodon and aminoacyl acceptor stems of yeast phenylalanyl tRNA in solution
    • Friederich, M. W., Gast, F.-U., Vacano, E. & Hagerman, P. J. (1995). Determination of the angle between the anticodon and aminoacyl acceptor stems of yeast phenylalanyl tRNA in solution. Proc. Natl Acad. Sci. USA, 92, 4803-4807.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 4803-4807
    • Friederich, M.W.1    Gast, F.-U.2    Vacano, E.3    Hagerman, P.J.4
  • 14
    • 0025906148 scopus 로고
    • Electrophoretic and hydrodynamic properties of duplex ribonucleic acid molecules transcribed in vitro: Evidence that A-tracts do not generate curvature in RNA
    • Gast, F.-U. & Hagerman, P. J. (1991). Electrophoretic and hydrodynamic properties of duplex ribonucleic acid molecules transcribed in vitro: evidence that A-tracts do not generate curvature in RNA. Biochemistry, 30, 4268-4277.
    • (1991) Biochemistry , vol.30 , pp. 4268-4277
    • Gast, F.-U.1    Hagerman, P.J.2
  • 15
    • 0028331914 scopus 로고
    • Interhelix geometry of stems I and II of a self-cleaving hammerhead RNA
    • Gast, F.-U., Amiri, K. M. A. & Hagerman, P. J. (1994). Interhelix geometry of stems I and II of a self-cleaving hammerhead RNA. Biochemistry, 33, 1788-1796.
    • (1994) Biochemistry , vol.33 , pp. 1788-1796
    • Gast, F.-U.1    Amiri, K.M.A.2    Hagerman, P.J.3
  • 16
    • 0019588074 scopus 로고
    • Investigation of the flexibility of DNA using transient electric birefringence
    • Hagerman, P. J. (1981). Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers, 20, 1503-1535.
    • (1981) Biopolymers , vol.20 , pp. 1503-1535
    • Hagerman, P.J.1
  • 17
    • 0000935665 scopus 로고
    • Evidence for the existence of stable curvature of DNA in solution
    • Hagerman, P. J. (1984). Evidence for the existence of stable curvature of DNA in solution. Proc. Natl Acad. Sci. USA, 81, 4632-4636.
    • (1984) Proc. Natl Acad. Sci. USA , vol.81 , pp. 4632-4636
    • Hagerman, P.J.1
  • 19
    • 84985720098 scopus 로고
    • Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains
    • Hagerman, P. J. & Zimm, B. (1981). Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains. Biopolymers, 20, 1481-1502.
    • (1981) Biopolymers , vol.20 , pp. 1481-1502
    • Hagerman, P.J.1    Zimm, B.2
  • 20
    • 0026000848 scopus 로고
    • Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base-pairs
    • Holbrook, S. R., Cheong, C., Tinoco, I. & Kim, S.-H. (1991). Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base-pairs. Nature, 353, 579-581.
    • (1991) Nature , vol.353 , pp. 579-581
    • Holbrook, S.R.1    Cheong, C.2    Tinoco, I.3    Kim, S.-H.4
  • 21
    • 0001690587 scopus 로고
    • Deletions of bases in one strand of duplex DNA, in contrast to single-base mismatches, produce highly kinked molecules: Possible relevance to the folding of single-stranded nucleic acids
    • Hsieh, C.-H. & Griffith, J. D. (1989). Deletions of bases in one strand of duplex DNA, in contrast to single-base mismatches, produce highly kinked molecules: possible relevance to the folding of single-stranded nucleic acids. Proc. Natl Acad. Sci. USA, 86, 4833-4837.
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 4833-4837
    • Hsieh, C.-H.1    Griffith, J.D.2
  • 22
    • 0002672054 scopus 로고
    • International Mathematical and Statistical Libraries, Inc., IMSL LIB3-0005, Houston, TX
    • IMSL (1980). International Mathematical and Statistical Libraries, Inc., IMSL Library 3 Reference Manual, IMSL LIB3-0005, Houston, TX.
    • (1980) IMSL Library 3 Reference Manual
  • 23
    • 0027165550 scopus 로고
    • Determination of RNA structure and thermodynamics
    • Jaeger, J. A., SantaLucia, J. & Tinoco, I. (1993). Determination of RNA structure and thermodynamics. Annu. Rev. Biochem. 62, 255-287.
    • (1993) Annu. Rev. Biochem. , vol.62 , pp. 255-287
    • Jaeger, J.A.1    Santalucia, J.2    Tinoco, I.3
  • 24
    • 0028289189 scopus 로고
    • Detection of localized DNA flexibility
    • Kahn, J. D., Yun, E. & Crothers, D. M. (1994). Detection of localized DNA flexibility Nature, 368, 163-166.
    • (1994) Nature , vol.368 , pp. 163-166
    • Kahn, J.D.1    Yun, E.2    Crothers, D.M.3
  • 26
    • 0024841809 scopus 로고
    • Enzymatic approaches to probing of RNA secondary and tertiary structure
    • Knapp, G. (1989). Enzymatic approaches to probing of RNA secondary and tertiary structure. Methods Enzymol. 180, 192-212.
    • (1989) Methods Enzymol. , vol.180 , pp. 192-212
    • Knapp, G.1
  • 27
    • 0000305475 scopus 로고
    • Brownian dynamics simulations of a three-subunit and a ten-subunit worm-like chain: Comparison of results with trumbell theory and with experimental results from DNA
    • Lewis, R. J., Allison, S. A., Eden, D. & Pecora R. (1988). Brownian dynamics simulations of a three-subunit and a ten-subunit worm-like chain: comparison of results with trumbell theory and with experimental results from DNA. J. Chem. Phys. 89, 2490-2503.
    • (1988) J. Chem. Phys. , vol.89 , pp. 2490-2503
    • Lewis, R.J.1    Allison, S.A.2    Eden, D.3    Pecora, R.4
  • 28
    • 0028301832 scopus 로고
    • Electrophoretic evidence that single-stranded regions of one or more nucleotides dramatically increase the flexibility of DNA
    • Mills, J. B., Cooper, J. P. & Hagerman, P. J. (1994). Electrophoretic evidence that single-stranded regions of one or more nucleotides dramatically increase the flexibility of DNA. Biochemistry, 3, 1797-1803.
    • (1994) Biochemistry , vol.3 , pp. 1797-1803
    • Mills, J.B.1    Cooper, J.P.2    Hagerman, P.J.3
  • 29
    • 0021754242 scopus 로고
    • Deoxyguanosine-deoxyadenosine pairing in the d(CGAGAATTCGCG) duplex: Conformation and dynamics at and adjacent to the dGdA mismatch site
    • Patel, D. J., Kozlowski, S. A., Ikuta, S. & Itakura, K. (1984a). Deoxyguanosine-deoxyadenosine pairing in the d(CGAGAATTCGCG) duplex: conformation and dynamics at and adjacent to the dGdA mismatch site. Biochemistry, 23, 3207-3217.
    • (1984) Biochemistry , vol.23 , pp. 3207-3217
    • Patel, D.J.1    Kozlowski, S.A.2    Ikuta, S.3    Itakura, K.4
  • 30
    • 0021754249 scopus 로고
    • Deoxyadenosine-deoxycyytidine pairing in the d(CGCGAATTCACG) duplex: Conformation and dynamics at and adjacent to the dAdC mismatch site
    • Patel, D. J., Kozlowski, S. A., Ikuta, S. & Itakura, K. (1984b). Deoxyadenosine-deoxycyytidine pairing in the d(CGCGAATTCACG) duplex: conformation and dynamics at and adjacent to the dAdC mismatch site. Biochemistry, 23, 3218-3226.
    • (1984) Biochemistry , vol.23 , pp. 3218-3226
    • Patel, D.J.1    Kozlowski, S.A.2    Ikuta, S.3    Itakura, K.4
  • 32
    • 36549099033 scopus 로고
    • An elastic hinge model for dynamics of stiff chains. III. Viscoelastic and Kerr-effect behavior of bent molecules
    • Roitman, D. B. (1984). An elastic hinge model for dynamics of stiff chains. III. Viscoelastic and Kerr-effect behavior of bent molecules. J. Chem. Phys. 81, 6356-6360.
    • (1984) J. Chem. Phys. , vol.81 , pp. 6356-6360
    • Roitman, D.B.1
  • 33
    • 36549093861 scopus 로고
    • An elastic hinge model for dynamics of stiff chains. I. Viscoelastic properties
    • Roitman, D. B. & Zimm, B. (1984a). An elastic hinge model for dynamics of stiff chains. I. Viscoelastic properties. J. Chem. Phys. 81, 6340-6347.
    • (1984) J. Chem. Phys. , vol.81 , pp. 6340-6347
    • Roitman, D.B.1    Zimm, B.2
  • 34
    • 36549093751 scopus 로고
    • An elastic hinge model for dynamics of stiff chains. II. Transient electro-optical properties
    • Roitman, D. B. & Zimm, B. (1984b). An elastic hinge model for dynamics of stiff chains. II. Transient electro-optical properties. J. Chem. Phys. 81, 6348-6354.
    • (1984) J. Chem. Phys. , vol.81 , pp. 6348-6354
    • Roitman, D.B.1    Zimm, B.2
  • 35
    • 84933517499 scopus 로고
    • Variational treatment of hydrodynamic interaction in polymers
    • Rotne, J. & Prager, S. (1969). Variational treatment of hydrodynamic interaction in polymers. J. Chem. Phys. 50, 4831-4837.
    • (1969) J. Chem. Phys. , vol.50 , pp. 4831-4837
    • Rotne, J.1    Prager, S.2
  • 37
    • 0025925206 scopus 로고
    • Stabilities of consecutive AC, CC, GG, UC, and UU mismatches in RNA internal loops: Evidence for stable hydrogen-bonded UU and CC + pairs
    • SantaLucia, J., Kierzek, R. & Turner, D. H. (1991a). Stabilities of consecutive AC, CC, GG, UC, and UU mismatches in RNA internal loops: evidence for stable hydrogen-bonded UU and CC + pairs. Biochemistry, 30, 8242-8251.
    • (1991) Biochemistry , vol.30 , pp. 8242-8251
    • Santalucia, J.1    Kierzek, R.2    Turner, D.H.3
  • 38
    • 12044257509 scopus 로고
    • Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops
    • SantaLucia, J., Kierzek, R. & Turner, D. H. (1991b). Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops. J. Am. Chem. Soc. 113, 4313-4322.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 4313-4322
    • Santalucia, J.1    Kierzek, R.2    Turner, D.H.3
  • 39
    • 0027146665 scopus 로고
    • 2 in solution from NMR and restrained molecular dynamics
    • 2 in solution from NMR and restrained molecular dynamics. Biochemistry, 32, 12612-12623.
    • (1993) Biochemistry , vol.32 , pp. 12612-12623
    • Santalucia, S.L.1    Turner, D.T.2
  • 40
    • 0027982008 scopus 로고
    • Geometry of the central branch of the 5S ribosomal RNA of sulfolobus acidocaldarius
    • Shen, Z. & Hagerman, P. J. (1994). Geometry of the central branch of the 5S ribosomal RNA of sulfolobus acidocaldarius. J. Mol. Biol. 241, 415-430.
    • (1994) J. Mol. Biol. , vol.241 , pp. 415-430
    • Shen, Z.1    Hagerman, P.J.2
  • 41
    • 0025336457 scopus 로고
    • Bulge loops used to measure the helical twist of RNA in solution
    • Tang, R. S. & Draper, D. E. (1990). Bulge loops used to measure the helical twist of RNA in solution. Biochemistry, 29, 5232-5237.
    • (1990) Biochemistry , vol.29 , pp. 5232-5237
    • Tang, R.S.1    Draper, D.E.2
  • 42
    • 0028231951 scopus 로고
    • On the use of phasing experiments to measure helical repeat and bulge loop-associated twist in RNA
    • Tang, R. S. & Draper, D. E. (1994). On the use of phasing experiments to measure helical repeat and bulge loop-associated twist in RNA. Nucl. Acids Res. 22, 835-841.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 835-841
    • Tang, R.S.1    Draper, D.E.2
  • 43
    • 0024974083 scopus 로고
    • Conformation and dynamics of an RNA internal loop
    • Varani, G., Wimberly, B. & Tinoco, I. (1989). Conformation and dynamics of an RNA internal loop. Biochemistry, 28, 7760-7772.
    • (1989) Biochemistry , vol.28 , pp. 7760-7772
    • Varani, G.1    Wimberly, B.2    Tinoco, I.3
  • 44
    • 0027439912 scopus 로고
    • The conformation of loop E in eukaryotic 5 S ribosomal RNA
    • Wimberly, B., Varani, G. & Tinoco, I. (1993). The conformation of loop E in eukaryotic 5 S ribosomal RNA. Biochemistry, 32, 1078-1087.
    • (1993) Biochemistry , vol.32 , pp. 1078-1087
    • Wimberly, B.1    Varani, G.2    Tinoco, I.3
  • 45
    • 0028969693 scopus 로고
    • Bulge-nduced bends in RNA: Quantification by transient electric birefringence
    • Zacharias, M. & Hagerman, P. J. (1995a). Bulge-nduced bends in RNA: quantification by transient electric birefringence. J. Mol. Biol. 247, 486-500.
    • (1995) J. Mol. Biol. , vol.247 , pp. 486-500
    • Zacharias, M.1    Hagerman, P.J.2
  • 46
    • 0029032837 scopus 로고
    • The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide
    • Zacharias, M. & Hagerman, P. J. (1995b). The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide. Proc. Natl Acad. Sci. USA, 92, 6052-6056.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 6052-6056
    • Zacharias, M.1    Hagerman, P.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.