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Volumn 32, Issue 17, 2004, Pages 5087-5095

DNA adopts normal B-form upon incorporation of highly flourescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE DERIVATIVE; DNA B; DNA BASE; DOUBLE STRANDED DNA; 1,3 DIAZA 2 OXOPHENOTHIAZIN 3 YLACETIC ACID; 1,3-DIAZA-2-OXOPHENOTHIAZIN-3-YLACETIC ACID; DNA; FLUORESCENT DYE; PHENOTHIAZINE DERIVATIVE;

EID: 4844229802     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh844     Document Type: Article
Times cited : (79)

References (40)
  • 1
    • 0035366378 scopus 로고    scopus 로고
    • Single-molecule fluorescence methods for the study of nucleic acids
    • Ha, T. (2001) Single-molecule fluorescence methods for the study of nucleic acids. Curr. Opin. Struct. Biol., 11, 287-292.
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 287-292
    • Ha, T.1
  • 2
    • 0036308302 scopus 로고    scopus 로고
    • Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions
    • Rist, M.J. and Marino, J.P. (2002) Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions. Curr. Org. Chem., 6, 775-793.
    • (2002) Curr. Org. Chem. , vol.6 , pp. 775-793
    • Rist, M.J.1    Marino, J.P.2
  • 3
    • 0014669561 scopus 로고
    • Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside, and their derivatives
    • Ward, D.C., Reich, E. and Stryer, L. (1969) Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside, and their derivatives. J. Biol. Chem., 244, 1228-1237.
    • (1969) J. Biol. Chem. , vol.244 , pp. 1228-1237
    • Ward, D.C.1    Reich, E.2    Stryer, L.3
  • 4
    • 0031011001 scopus 로고    scopus 로고
    • Electronic transition moments of 2-aminopurine
    • Holmén, A., Nordén, B. and Albinsson, B. (1997) Electronic transition moments of 2-aminopurine. J. Am. Chem. Soc., 119, 3114-3121.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 3114-3121
    • Holmén, A.1    Nordén, B.2    Albinsson, B.3
  • 5
    • 0030448581 scopus 로고    scopus 로고
    • Targeted base stacking disruption by the EcoRI DNA methyltransferase
    • Allan, B.W. and Reich, N.O. (1996) Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry, 35 14757-14762.
    • (1996) Biochemistry , vol.35 , pp. 14757-14762
    • Allan, B.W.1    Reich, N.O.2
  • 6
    • 0027493457 scopus 로고
    • Influence of 5′-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment
    • Bloom, L.B., Otto, M.R., Beechem, J.M. and Goodman,M.F. (1993) Influence of 5′-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment. Biochemistry, 32, 11247-11258.
    • (1993) Biochemistry , vol.32 , pp. 11247-11258
    • Bloom, L.B.1    Otto, M.R.2    Beechem, J.M.3    Goodman, M.F.4
  • 8
    • 0028143392 scopus 로고
    • Melting of a DNA helix terminus within the active site of a DNA polymerase
    • Hochstrasser,R.A., Carver,T.E., Sowers,L.C. and Millar,D.P. (1994) Melting of a DNA helix terminus within the active site of a DNA polymerase. Biochemistry, 33, 11971-11979.
    • (1994) Biochemistry , vol.33 , pp. 11971-11979
    • Hochstrasser, R.A.1    Carver, T.E.2    Sowers, L.C.3    Millar, D.P.4
  • 9
    • 0023651409 scopus 로고
    • Base pair opening dynamics of a 2-aminopurine substituted Eco RI restriction sequence and its unsubstituted counterpart in oligonucleotides
    • Lycksell,P.O., Gräslund,A., Claesens,F., McLaughlin,L.W., Larsson,U. and Rigler,R. (1987) Base pair opening dynamics of a 2-aminopurine substituted Eco RI restriction sequence and its unsubstituted counterpart in oligonucleotides. Nucleic Acids Res., 15, 9011-9025.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 9011-9025
    • Lycksell, P.O.1    Gräslund, A.2    Claesens, F.3    McLaughlin, L.W.4    Larsson, U.5    Rigler, R.6
  • 10
    • 0024456523 scopus 로고
    • Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: Fluorescence, molecular dynamics, and NMR studies
    • Nordlund,T.M., Andersson,S., Nilsson,L., Rigler,R., Gräslund,A. and McLaughlin,L.W. (1989) Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies. Biochemistry, 28, 9095-9103.
    • (1989) Biochemistry , vol.28 , pp. 9095-9103
    • Nordlund, T.M.1    Andersson, S.2    Nilsson, L.3    Rigler, R.4    Gräslund, A.5    McLaughlin, L.W.6
  • 11
    • 0035969959 scopus 로고    scopus 로고
    • Probing structure and dynamics of DNA with 2-aminopurine: Effects of local environment on fluorescence
    • Rachofsky,E.L., Osman,R. and Ross,J.B.A. (2001) Probing structure and dynamics of DNA with 2-aminopurine: effects of local environment on fluorescence. Biochemistry, 40, 946-956.
    • (2001) Biochemistry , vol.40 , pp. 946-956
    • Rachofsky, E.L.1    Osman, R.2    Ross, J.B.A.3
  • 12
    • 0032529485 scopus 로고    scopus 로고
    • 2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: Metal-ion and base sequence effects
    • Stivers,J.T. (1998) 2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects. Nucleic Acids Res., 26, 3837-3844.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 3837-3844
    • Stivers, J.T.1
  • 13
    • 0033579953 scopus 로고    scopus 로고
    • Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase
    • Stivers,J.T., Pankiewicz,K.W. and Watanabe,K.A. (1999) Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase. Biochemistry, 38, 952-963.
    • (1999) Biochemistry , vol.38 , pp. 952-963
    • Stivers, J.T.1    Pankiewicz, K.W.2    Watanabe, K.A.3
  • 15
    • 0035754097 scopus 로고    scopus 로고
    • Fluorescent pteridine nucleoside analogs: A window on DNA interactions
    • Hawkins,M.E. (2001) Fluorescent pteridine nucleoside analogs: a window on DNA interactions. Cell Biochem. Biophys., 34, 257-281.
    • (2001) Cell Biochem. Biophys. , vol.34 , pp. 257-281
    • Hawkins, M.E.1
  • 16
    • 0029118594 scopus 로고
    • Incorporation of a fluorescent guanosine analog into oligonucleotides and its application to a real time assay for the Hiv-1 integrase 3′-processing reaction
    • Hawkins,M.E., Pfleiderer,W., Mazumder,A., Pommier,Y.G. and Falls,F.M. (1995) Incorporation of a fluorescent guanosine analog into oligonucleotides and its application to a real time assay for the Hiv-1 integrase 3′-processing reaction. Nucleic Acids Res., 23, 2872-2880.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 2872-2880
    • Hawkins, M.E.1    Pfleiderer, W.2    Mazumder, A.3    Pommier, Y.G.4    Falls, F.M.5
  • 17
    • 0031023096 scopus 로고    scopus 로고
    • Fluorescence properties of pteridine nucleoside analogs as monomers and incorporated into oligonucleotides
    • Hawkins,M.E., Pfleiderer,W., Balis,F.M., Porter,D. and Knutson,J.R. (1997) Fluorescence properties of pteridine nucleoside analogs as monomers and incorporated into oligonucleotides. Anal. Biochem., 244, 86-95.
    • (1997) Anal. Biochem. , vol.244 , pp. 86-95
    • Hawkins, M.E.1    Pfleiderer, W.2    Balis, F.M.3    Porter, D.4    Knutson, J.R.5
  • 18
    • 0035892607 scopus 로고    scopus 로고
    • Synthesis and fluorescence characterization of pteridine adenosine nucleoside analogs for DNA incorporation
    • Hawkins,M.E., Pfleiderer,W., Jungmann,O. and Balis,F.M. (2001) Synthesis and fluorescence characterization of pteridine adenosine nucleoside analogs for DNA incorporation. Anal. Biochem., 298 231-240.
    • (2001) Anal. Biochem. , vol.298 , pp. 231-240
    • Hawkins, M.E.1    Pfleiderer, W.2    Jungmann, O.3    Balis, F.M.4
  • 19
    • 0030823054 scopus 로고    scopus 로고
    • Fluorescence properties of a new guanosine analog incorporated into small oligonucleotides
    • Driscoll,S.L., Hawkins,M.E., Balis,F.M., Pfleiderer,W. and Laws,W.R. (1997) Fluorescence properties of a new guanosine analog incorporated into small oligonucleotides. Biophys. J., 73, 3277-3286.
    • (1997) Biophys. J. , vol.73 , pp. 3277-3286
    • Driscoll, S.L.1    Hawkins, M.E.2    Balis, F.M.3    Pfleiderer, W.4    Laws, W.R.5
  • 20
    • 0032578563 scopus 로고    scopus 로고
    • Benzoquinazoline derivatives as substitutes for thymine in nucleic acid complexes. Use of fluorescence emission of benzo[g]quinazoline-2,4-(1H,3H)-dione in probing duplex and triplex formation
    • Godde,F., Toulmé,J.J. and Moreau,S. (1998) Benzoquinazoline derivatives as substitutes for thymine in nucleic acid complexes. Use of fluorescence emission of benzo[g]quinazoline-2,4-(1H,3H)-dione in probing duplex and triplex formation. Biochemistry, 37, 13765-13775.
    • (1998) Biochemistry , vol.37 , pp. 13765-13775
    • Godde, F.1    Toulmé, J.J.2    Moreau, S.3
  • 22
    • 0034238088 scopus 로고    scopus 로고
    • 4-Amino-1H-benzo[g]quinazoline-2-one: A fluorescent analog of cytosine to probe protonation sites in triplex forming oligonucleotides
    • Godde,F., Toulmé,J.J. and Moreau,S. (2000) 4-Amino-1H-benzo[g]quinazoline-2-one: a fluorescent analog of cytosine to probe protonation sites in triplex forming oligonucleotides. Nucleic Acids Res., 28, 2977-2985.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2977-2985
    • Godde, F.1    Toulmé, J.J.2    Moreau, S.3
  • 23
    • 0034812469 scopus 로고    scopus 로고
    • A highly fluorescent DNA base analogue that forms Watson-Crick base pairs with guanine
    • Wilhelmsson,L.M., Holmén,A., Lincoln,P., Nielsen,P.E. and Nordén,B. (2001) A highly fluorescent DNA base analogue that forms Watson-Crick base pairs with guanine. J. Am. Chem. Soc., 123, 2434-2435.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 2434-2435
    • Wilhelmsson, L.M.1    Holmén, A.2    Lincoln, P.3    Nielsen, P.E.4    Nordén, B.5
  • 24
    • 0028908575 scopus 로고
    • Tricyclic 2′-deoxycytidine analogs: Syntheses and incorporation into oligodeoxynucleotides which have enhanced binding to complementary RNA
    • Lin,K., Jones,R.J. and Matteucci,M. (1995) Tricyclic 2′-deoxycytidine analogs: syntheses and incorporation into oligodeoxynucleotides which have enhanced binding to complementary RNA. J. Am. Chem. Soc., 117, 3873-3874.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 3873-3874
    • Lin, K.1    Jones, R.J.2    Matteucci, M.3
  • 27
    • 0026640147 scopus 로고
    • Purification of synthetic oligonucleotides
    • Brown,T. and Brown,D.J.S. (1992) Purification of synthetic oligonucleotides. Meth. Enzymol., 211, 20-35.
    • (1992) Meth. Enzymol. , vol.211 , pp. 20-35
    • Brown, T.1    Brown, D.J.S.2
  • 30
    • 0343459675 scopus 로고
    • The program XEASY for computer-supported NMR spectral-analysis of biological macromolecules
    • Bartels,C., Xia,T.H., Billeter,M., Güntert,P. and Wüthrich,K. (1995) The program XEASY for computer-supported NMR spectral-analysis of biological macromolecules. J. Biomol. NMR, 6, 1-10.
    • (1995) J. Biomol. NMR , vol.6 , pp. 1-10
    • Bartels, C.1    Xia, T.H.2    Billeter, M.3    Güntert, P.4    Wüthrich, K.5
  • 32
    • 0026696172 scopus 로고
    • Determination of nucleic-acid backbone conformation by 1H NMR
    • Kim,S.G., Lin,L.J. and Reid,B.R. (1992) Determination of nucleic-acid backbone conformation by 1H NMR. Biochemistry, 31 3564-3574.
    • (1992) Biochemistry , vol.31 , pp. 3564-3574
    • Kim, S.G.1    Lin, L.J.2    Reid, B.R.3
  • 33
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • Güntert,P., Mumenthaler,C. and Wüthrich,K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol., 273, 283-298.
    • (1997) J. Mol. Biol. , vol.273 , pp. 283-298
    • Güntert, P.1    Mumenthaler, C.2    Wüthrich, K.3
  • 36
    • 0023657705 scopus 로고
    • Refinement of the solution structure of the DNA hexamer 5′ d(Geatge)2: Combined use of nuclear magnetic resonance and restrained molecular dynamics
    • Nilges,M., Clore,G.M., Gronenborn,A.M., Brunger,A.T., Karplus,M. and Nilsson,L. (1987) Refinement of the solution structure of the DNA hexamer 5′ d(Geatge)2: combined use of nuclear magnetic resonance and restrained molecular dynamics. Biochemistry, 26 3718-3733.
    • (1987) Biochemistry , vol.26 , pp. 3718-3733
    • Nilges, M.1    Clore, G.M.2    Gronenborn, A.M.3    Brunger, A.T.4    Karplus, M.5    Nilsson, L.6
  • 37
    • 0023657747 scopus 로고
    • Refinement of the solution structure of the DNA decamer 5′ d(ctggatccag)2: Combined use of nuclear magnetic resonance and restrained molecular dynamics
    • Nilges,M., Clore,G.M., Gronenborn,A.M., Piel,N. and McLaughlin,L.W. (1987) Refinement of the solution structure of the DNA decamer 5′ d(ctggatccag)2: combined use of nuclear magnetic resonance and restrained molecular dynamics. Biochemistry, 26, 3734-3744.
    • (1987) Biochemistry , vol.26 , pp. 3734-3744
    • Nilges, M.1    Clore, G.M.2    Gronenborn, A.M.3    Piel, N.4    McLaughlin, L.W.5
  • 38
    • 0025339406 scopus 로고
    • Solution structure of phage lambda half-operator DNA by use of NMR, restrained molecular dynamics, and NOE-based refinement
    • Baleja,J.D., Pon,R.T. and Sykes,B.D. (1990) Solution structure of phage lambda half-operator DNA by use of NMR, restrained molecular dynamics, and NOE-based refinement. Biochemistry, 29 4828-4839.
    • (1990) Biochemistry , vol.29 , pp. 4828-4839
    • Baleja, J.D.1    Pon, R.T.2    Sykes, B.D.3
  • 39
    • 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 two-dimensional NMR spectra
    • Mujeeb,A., Kerwin,S.M., Kenyon,G.L. and 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 two-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
  • 40
    • 0028013525 scopus 로고
    • Solution structure of the octamer motif in immunoglobulin genos via restrained molecular-dynamics calculations
    • Weisz,K., Shafer,R.H.,Egan,W. and James,T.L. (1994) Solution structure of the octamer motif in immunoglobulin genos 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


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