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Volumn 284, Issue 5, 1998, Pages 1453-1463

Structure determination and analysis of helix parameters in the DNA decamer d(CATGGCCATG)2 comparison of results from NMR and crystallography

Author keywords

Bendability of DNA; DNA structure; Flexibility of DNA; NMR of DNA; TG CA base pair steps

Indexed keywords

DOUBLE STRANDED DNA;

EID: 0032545156     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2261     Document Type: Article
Times cited : (36)

References (48)
  • 1
    • 0031238604 scopus 로고    scopus 로고
    • DNA recognition and bending
    • Allemann, R. K. & Egli, M. (1997). DNA recognition and bending. Chem. Biol. 4, 643-650.
    • (1997) Chem. Biol. , vol.4 , pp. 643-650
    • Allemann, R.K.1    Egli, M.2
  • 2
    • 0000265069 scopus 로고
    • Conformational analysis of nucleic acids. Determination of backbone geometry of single-helical RNA and DNA in aqueous solution
    • Altona, C. (1982). Conformational analysis of nucleic acids. Determination of backbone geometry of single-helical RNA and DNA in aqueous solution. Red. Trav. Chim. Pays-Bas. 101, 413-433.
    • (1982) Red. Trav. Chim. Pays-Bas. , vol.101 , pp. 413-433
    • Altona, C.1
  • 4
    • 0024996711 scopus 로고
    • Solution conformation of purine-pyrimidine DNA octamers using Nuclear Magnetic Resonance, restrained molecular dynamics and NOE-based refinement
    • Baleja, J. D., Germann, M. W., van de Sande, J. H. & Sykes, B. D. (1990). Solution conformation of purine-pyrimidine DNA octamers using Nuclear Magnetic Resonance, restrained molecular dynamics and NOE-based refinement. J. Mol. Biol. 215, 411-428.
    • (1990) J. Mol. Biol. , vol.215 , pp. 411-428
    • Baleja, J.D.1    Germann, M.W.2    Van De Sande, J.H.3    Sykes, B.D.4
  • 5
    • 0027078718 scopus 로고
    • In vitro evolution of intrinsically bent DNA
    • Beutel, B. A. & Gold, L. (1992). In vitro evolution of intrinsically bent DNA. J. Mol. Biol. 228, 803-812.
    • (1992) J. Mol. Biol. , vol.228 , pp. 803-812
    • Beutel, B.A.1    Gold, L.2
  • 7
    • 0000425457 scopus 로고
    • MARDIGRAS - A procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure
    • Borgias, B. A. & James, T. L. (1990). MARDIGRAS - a procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure. J. Magn. Reson. 87, 475-487.
    • (1990) J. Magn. Reson. , vol.87 , pp. 475-487
    • Borgias, B.A.1    James, T.L.2
  • 8
    • 0027209077 scopus 로고
    • Evidence for opposite groove-directed curvature of GGGCCC and AAAAA tracts
    • Brukner, I., Dlakic, M., Savic, A., Susic, S., Pongor, S. & Suck, D. (1993). Evidence for opposite groove-directed curvature of GGGCCC and AAAAA tracts. Nucl. Acids Res. 21, 1025-1029.
    • (1993) Nucl. Acids Res. , vol.21 , pp. 1025-1029
    • Brukner, I.1    Dlakic, M.2    Savic, A.3    Susic, S.4    Pongor, S.5    Suck, D.6
  • 9
    • 0032559372 scopus 로고    scopus 로고
    • CTG repeats associated with human genetic disease are inherently flexible
    • Chastain, P. D. & Sinden, R. R. (1998). CTG repeats associated with human genetic disease are inherently flexible. J. Mol. Biol. 275, 405-411.
    • (1998) J. Mol. Biol. , vol.275 , pp. 405-411
    • Chastain, P.D.1    Sinden, R.R.2
  • 10
    • 17544394367 scopus 로고    scopus 로고
    • Hairpin loops consisting of single adenine residues closed by sheared A·A and G·G pairs formed by the DNA triplets AAA and GAG: Solution structure of the d(GTACAAAGTAC) hairpin
    • Chou, S.-H., Zhu, L., Gao, Z., Cheng, J.-W. & Reid, B. R. (1996). Hairpin loops consisting of single adenine residues closed by sheared A·A and G·G pairs formed by the DNA triplets AAA and GAG: solution structure of the d(GTACAAAGTAC) hairpin. J. Mol. Biol. 264, 981-1001.
    • (1996) J. Mol. Biol. , vol.264 , pp. 981-1001
    • Chou, S.-H.1    Zhu, L.2    Gao, Z.3    Cheng, J.-W.4    Reid, B.R.5
  • 12
    • 0026702486 scopus 로고
    • DNA structure from A to Z
    • Dickerson, R. E. (1992). DNA structure from A to Z. Methods Enzymol. 211, 67-111.
    • (1992) Methods Enzymol. , vol.211 , pp. 67-111
    • Dickerson, R.E.1
  • 13
    • 0029978007 scopus 로고    scopus 로고
    • MPD and DNA bending in crystals and in solution
    • Dickerson, R. E., Goodsell, D. S. & Kopka, M. L. (1996). MPD and DNA bending in crystals and in solution. J. Mol. Biol. 256, 108-125.
    • (1996) J. Mol. Biol. , vol.256 , pp. 108-125
    • Dickerson, R.E.1    Goodsell, D.S.2    Kopka, M.L.3
  • 15
    • 0030003963 scopus 로고    scopus 로고
    • Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA
    • El Hassan, M. A. & Calladine, C. R. (1996). Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J. Biol. Chem. 259, 95-103.
    • (1996) J. Biol. Chem. , vol.259 , pp. 95-103
    • El Hassan, M.A.1    Calladine, C.R.2
  • 16
    • 49149148488 scopus 로고
    • Radiofrequency pulse sequences which compensate their own imperfections
    • Freeman, R., Kempsell, S. P. & Levitt, M. H. (1980). Radiofrequency pulse sequences which compensate their own imperfections. J. Magn. Reson. 38, 453-479.
    • (1980) J. Magn. Reson. , vol.38 , pp. 453-479
    • Freeman, R.1    Kempsell, S.P.2    Levitt, M.H.3
  • 17
    • 0027990236 scopus 로고
    • Structural study of a DNA-RNA hybrid duplex with a chiral phosphorothioate moeity by NMR: Extraction of distance and torsion angle constraints and imino proton exchange rates
    • Gonzáles, C., Stec, W., Kobylanska, A., Hogrefe, R. I., Reynolds, M. & James, T. L. (1994). Structural study of a DNA-RNA hybrid duplex with a chiral phosphorothioate moeity by NMR: Extraction of distance and torsion angle constraints and imino proton exchange rates. Biochemistry, 33, 11062-11072.
    • (1994) Biochemistry , vol.33 , pp. 11062-11072
    • Gonzáles, C.1    Stec, W.2    Kobylanska, A.3    Hogrefe, R.I.4    Reynolds, M.5    James, T.L.6
  • 18
    • 0027536101 scopus 로고
    • Crystal structure of CATGGCCATG and its implications for A-tract bending models
    • Goodsell, D. S., Kopka, M. L., Cascio, D. & Dickerson, R. E. (1993). Crystal structure of CATGGCCATG and its implications for A-tract bending models. Proc. Natl Acad. Sci. USA, 90, 2930-2934.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 2930-2934
    • Goodsell, D.S.1    Kopka, M.L.2    Cascio, D.3    Dickerson, R.E.4
  • 20
    • 0028931709 scopus 로고
    • B-DNA twisting correlates with base-pair morphology
    • Gorin, A. A., Zhurkin, V. B. & Olson, W. K. (1995). B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247, 34-48.
    • (1995) J. Mol. Biol. , vol.247 , pp. 34-48
    • Gorin, A.A.1    Zhurkin, V.B.2    Olson, W.K.3
  • 21
    • 33845378213 scopus 로고
    • Two-dimensional correlation of connected NMR transitions
    • Griesinger, C., Sorensen, O. W. & Ernst, R. R. (1985). Two-dimensional correlation of connected NMR transitions. J. Am. Chem. Soc. 107, 6394-6396.
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 6394-6396
    • Griesinger, C.1    Sorensen, O.W.2    Ernst, R.R.3
  • 22
    • 0030267032 scopus 로고    scopus 로고
    • Sequence-dependent structural variation in B-DNA
    • Grzeskowiak, K. (1996). Sequence-dependent structural variation in B-DNA. Chem. Biol. 3, 785-790.
    • (1996) Chem. Biol. , vol.3 , pp. 785-790
    • Grzeskowiak, K.1
  • 23
    • 0028864424 scopus 로고
    • Studies of base pair kinetics by NMR measurement of proton exchange
    • Guéron, M. & Leroy, J.-L. (1995). Studies of base pair kinetics by NMR measurement of proton exchange. Methods Enzymol. 261, 383-413.
    • (1995) Methods Enzymol. , vol.261 , pp. 383-413
    • Guéron, M.1    Leroy, J.-L.2
  • 24
    • 0026259488 scopus 로고
    • Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints
    • Güntert, P. & Wüthrich, K. (1991). Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J. Biomol. NMR, 1, 447-456.
    • (1991) J. Biomol. NMR , vol.1 , pp. 447-456
    • Güntert, P.1    Wüthrich, K.2
  • 25
    • 0030034928 scopus 로고    scopus 로고
    • Chromosomal localization of long trinucleotide repeats in the human genome by fluorescence in situ hybridization
    • Haaf, T., Sirugo, G., Kidd, K. K. & Ward, D. C. (1996). Chromosomal localization of long trinucleotide repeats in the human genome by fluorescence in situ hybridization. Nature Genet. 12, 183-185.
    • (1996) Nature Genet. , vol.12 , pp. 183-185
    • Haaf, T.1    Sirugo, G.2    Kidd, K.K.3    Ward, D.C.4
  • 26
    • 48749149745 scopus 로고
    • Solvent suppression in Fourier transform nuclear magnetic resonance
    • Hore, P. J. (1983). Solvent suppression in Fourier transform nuclear magnetic resonance. J. Magn. Reson. 55, 283-300.
    • (1983) J. Magn. Reson. , vol.55 , pp. 283-300
    • Hore, P.J.1
  • 27
    • 0027318463 scopus 로고
    • Sequence-dependent DNA structure: The role of base stacking interactions
    • Hunter, C. A. (1993). Sequence-dependent DNA structure: the role of base stacking interactions. J. Mol. Biol. 230, 1025-1054.
    • (1993) J. Mol. Biol. , vol.230 , pp. 1025-1054
    • Hunter, C.A.1
  • 28
  • 30
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi, R., Billeter, M. & Wüthrich, K. (1996). MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55.
    • (1996) J. Mol. Graph. , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wüthrich, K.3
  • 31
    • 0024539180 scopus 로고
    • Defining the structure of irregular nucleic acids: Conventions and principles
    • Lavery, R. & Sklenar, H (1989). Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn. 6, 655-667.
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 655-667
    • Lavery, R.1    Sklenar, H.2
  • 32
    • 0029612258 scopus 로고
    • NMR studies and restrained-molecular-dynamics calculations of a long a + T-rich stretch in DNA. Effects of phosphate charge and solvent approximations
    • Leijon, M., Zdunek, J., Fritzsche, H., Sklenar, H. & Gräslund, A. (1995). NMR studies and restrained-molecular-dynamics calculations of a long A + T-rich stretch in DNA. Effects of phosphate charge and solvent approximations. Eur. J. Biochem. 234, 832-842.
    • (1995) Eur. J. Biochem. , vol.234 , pp. 832-842
    • Leijon, M.1    Zdunek, J.2    Fritzsche, H.3    Sklenar, H.4    Gräslund, A.5
  • 34
    • 0029785480 scopus 로고    scopus 로고
    • Preferential absorption of a 'kinked' DNA to a neutral curved surface: Comparisons to and implications for nonspecific DNA-protein interactions
    • Mahtab, R., Rogers, J. P., Singleton, C. P. & Murphy, C. J. (1996). Preferential absorption of a 'kinked' DNA to a neutral curved surface: comparisons to and implications for nonspecific DNA-protein interactions. J. Am. Chem. Soc. 118, 7028-7032.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 7028-7032
    • Mahtab, R.1    Rogers, J.P.2    Singleton, C.P.3    Murphy, C.J.4
  • 35
    • 0027751258 scopus 로고
    • Solution structure of a conserved DNA sequence from the HIV-1 genome-restrained molecular dynamics simulation with distance and torsion angle restraints derived from 2-dimensional NMR spectra
    • Mujeeb, A., Kerwin, S. M., Kenyon, G. L. & James, T. L. (1993). Solution structure of a conserved DNA sequence from the HIV-1 genome-restrained molecular dynamics simulation with distance and torsion angle restraints derived from 2-dimensional NMR spectra. Biochemistry, 32, 13419-13431.
    • (1993) Biochemistry , vol.32 , pp. 13419-13431
    • Mujeeb, A.1    Kerwin, S.M.2    Kenyon, G.L.3    James, T.L.4
  • 36
    • 0030798605 scopus 로고    scopus 로고
    • Clues and consequences of DNA bending in transcription
    • Perez-Martin, J. & De Lorenzo, V. (1997). Clues and consequences of DNA bending in transcription. Annu. Rev. Microbiol. 51, 593-628.
    • (1997) Annu. Rev. Microbiol. , vol.51 , pp. 593-628
    • Perez-Martin, J.1    De Lorenzo, V.2
  • 39
    • 0342601355 scopus 로고    scopus 로고
    • Structure of an RNA hairpin loop with a 5′-CGUUUCG-3′ loop motif by heteronuclear NMR spectroscopy and distance geometry
    • Sich, C., Ohlenschläger, O., Ramachandran, R., Görlach, M. & Brown, L. R. (1997). Structure of an RNA hairpin loop with a 5′-CGUUUCG-3′ loop motif by heteronuclear NMR spectroscopy and distance geometry. Biochemistry, 36, 13989-14002.
    • (1997) Biochemistry , vol.36 , pp. 13989-14002
    • Sich, C.1    Ohlenschläger, O.2    Ramachandran, R.3    Görlach, M.4    Brown, L.R.5
  • 41
    • 0023041681 scopus 로고
    • 2 via complete relaxation matrix analysis of two-dimensional Nuclear Overhauser Effect spectra and molecular mechanics calculations: Evidence for a hydration tunnel
    • 2 via complete relaxation matrix analysis of two-dimensional Nuclear Overhauser Effect spectra and molecular mechanics calculations: evidence for a hydration tunnel. Biochemistry, 25, 6854-6865.
    • (1986) Biochemistry , vol.25 , pp. 6854-6865
    • Suzuki, E.1    Pattabiraman, N.2    Zon, G.3    James, T.L.4
  • 42
    • 0026726087 scopus 로고
    • Furanose sugar conformations in DNA from NMR coupling constants
    • Van Wijk, J., Huckriede, B. D., Ippel, J. H. & Altona, C. (1992). Furanose sugar conformations in DNA from NMR coupling constants. Methods Enzymol. 211, 286-306.
    • (1992) Methods Enzymol. , vol.211 , pp. 286-306
    • Van Wijk, J.1    Huckriede, B.D.2    Ippel, J.H.3    Altona, C.4
  • 43
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • Weiner, S. J., Kollmann, P. A., Nguyen, D. T. & Case, D. A. (1986). An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7, 230-252.
    • (1986) J. Comput. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollmann, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 44
    • 0028013525 scopus 로고
    • Solution structure of the octamer motif in immunoglobulin genes via restrained molecular dynamics calculations
    • Weisz, K., Shafer, R. H., Egan, W. & James, T. L. (1994). Solution structure of the octamer motif in immunoglobulin genes via restrained molecular dynamics calculations. Biochemistry, 33, 354-366.
    • (1994) Biochemistry , vol.33 , pp. 354-366
    • Weisz, K.1    Shafer, R.H.2    Egan, W.3    James, T.L.4
  • 45
    • 0001123057 scopus 로고
    • NMR of nucleic acids: From spectrum to structure
    • (Roberts, G. C. K., ed.), Oxford University Press
    • Wijmenga, S. S., Mooren, M. W. & Hilbers, C. W. (1993). NMR of nucleic acids: from spectrum to structure. In NMR of Macromolecules (Roberts, G. C. K., ed.), pp. 217-357, Oxford University Press.
    • (1993) NMR of Macromolecules , pp. 217-357
    • Wijmenga, S.S.1    Mooren, M.W.2    Hilbers, C.W.3
  • 47
    • 0024282738 scopus 로고
    • 2: An analysis of vicinal proton-proton coupling constants from two-dimensional proton nuclear magnetic resonance
    • 2: an analysis of vicinal proton-proton coupling constants from two-dimensional proton nuclear magnetic resonance. Biochemistry, 27, 6013-6020.
    • (1988) Biochemistry , vol.27 , pp. 6013-6020
    • Zhou, N.1    Manogaran, S.2    Zon, G.3    James, T.L.4
  • 48
    • 0025800219 scopus 로고
    • Static and statistical bending of DNA evaluated by Monte Carlo simulations
    • Zhurkin, V. B., Ulyanov, N. B., Gorin, A. A. & Jernigan, R. L. (1991). Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proc. Natl Acad. Sci. USA, 88, 7046-7050.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 7046-7050
    • Zhurkin, V.B.1    Ulyanov, N.B.2    Gorin, A.A.3    Jernigan, R.L.4


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