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Volumn 37, Issue 14, 2009, Pages 4757-4763

The effects of unnatural base pairs and mispairs on DNA duplex stability and solvation

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; PYRIDINE; PYRIDINE DERIVATIVE; PYRIDINE DERIVATIVE 34DMPY; PYRIDINE DERIVATIVE 3MPY; PYRIDINE DERIVATIVE 45DMPY; PYRIDINE DERIVATIVE 4MPY; PYRIDINE DERIVATIVE 5MPY; UNCLASSIFIED DRUG;

EID: 69049104260     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp467     Document Type: Article
Times cited : (21)

References (39)
  • 1
    • 69049095804 scopus 로고    scopus 로고
    • Engineering nucleobases and polymerases for an expanded genetic alphabet
    • Köhrer,C. and RajBhandary,U.L, eds, Springer-Verlag, Berlin, pp
    • Leconte,A.M. and Romesberg,F.E. (2009) Engineering nucleobases and polymerases for an expanded genetic alphabet. In Köhrer,C. and RajBhandary,U.L. (eds), Protein Engineering, Springer-Verlag, Berlin, pp. 291-314.
    • (2009) Protein Engineering , pp. 291-314
    • Leconte, A.M.1    Romesberg, F.E.2
  • 2
    • 0025008851 scopus 로고
    • Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet
    • Piccirilli,J.A., Krauch,T., Moroney,S.E. and Benner,S.A. (1990) Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature, 343, 33-37.
    • (1990) Nature , vol.343 , pp. 33-37
    • Piccirilli, J.A.1    Krauch, T.2    Moroney, S.E.3    Benner, S.A.4
  • 4
    • 39549087460 scopus 로고    scopus 로고
    • Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet
    • Leconte,A.M., Hwang,G.T., Matsuda,S., Capek,P., Hari,Y. and Romesberg,F.E. (2008) Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet. J. Am. Chem. Soc., 130, 2336-2343.
    • (2008) J. Am. Chem. Soc , vol.130 , pp. 2336-2343
    • Leconte, A.M.1    Hwang, G.T.2    Matsuda, S.3    Capek, P.4    Hari, Y.5    Romesberg, F.E.6
  • 5
    • 55549129633 scopus 로고    scopus 로고
    • The unnatural substrate repertoire of A, B, and X family DNA polymerases
    • Hwang,G.T. and Romesberg,F.E. (2008) The unnatural substrate repertoire of A, B, and X family DNA polymerases. J. Am. Chem. Soc., 130 14872-14882.
    • (2008) J. Am. Chem. Soc , vol.130 , pp. 14872-14882
    • Hwang, G.T.1    Romesberg, F.E.2
  • 6
    • 67849129011 scopus 로고    scopus 로고
    • Optimization of an unnatural base pair towards natural-like replication
    • Seo,Y.J., Hwang,G.T., Ordoukhanian,P. and Romesberg,F.E. (2009) Optimization of an unnatural base pair towards natural-like replication. J. Am. Chem. Soc., 131, 3246-3252.
    • (2009) J. Am. Chem. Soc , vol.131 , pp. 3246-3252
    • Seo, Y.J.1    Hwang, G.T.2    Ordoukhanian, P.3    Romesberg, F.E.4
  • 7
    • 20944444039 scopus 로고    scopus 로고
    • An efficient unnatural base pair for a base-pair-expanded transcription system
    • Mitsui,T., Kimoto,M., Harada,Y., Yokoyama,S. and Hirao,I. (2005) An efficient unnatural base pair for a base-pair-expanded transcription system. J. Am. Chem. Soc., 127, 8652-8658.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 8652-8658
    • Mitsui, T.1    Kimoto, M.2    Harada, Y.3    Yokoyama, S.4    Hirao, I.5
  • 8
  • 9
    • 37849014324 scopus 로고    scopus 로고
    • An efficient unnatural base pair for PCR amplification
    • Hirao,I., Mitsui,T., Kimoto,M. and Yokoyama,S. (2007) An efficient unnatural base pair for PCR amplification. J. Am. Chem. Soc., 129, 15549-15555.
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 15549-15555
    • Hirao, I.1    Mitsui, T.2    Kimoto, M.3    Yokoyama, S.4
  • 10
    • 67849087122 scopus 로고    scopus 로고
    • Transcription of an expanded genetic alphabet
    • Seo,Y.J., Matsuda,S. and Romesberg,F.E. (2009) Transcription of an expanded genetic alphabet. J. Am. Chem. Soc., 131, 5046-5047.
    • (2009) J. Am. Chem. Soc , vol.131 , pp. 5046-5047
    • Seo, Y.J.1    Matsuda, S.2    Romesberg, F.E.3
  • 12
    • 59649091247 scopus 로고    scopus 로고
    • An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules
    • Kimoto,M., Kawai,R., Mitsui,T., Yokoyama,S. and Hirao,I. (2009) An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules. Nucleic Acids Res., 37, e14.
    • (2009) Nucleic Acids Res , vol.37
    • Kimoto, M.1    Kawai, R.2    Mitsui, T.3    Yokoyama, S.4    Hirao, I.5
  • 13
    • 0030939593 scopus 로고    scopus 로고
    • Enhanced discrimination of single nucleotide polymorphisms by artificial mismatch hybridization
    • Guo,Z., Liu,Q. and Smith,L.M. (1997) Enhanced discrimination of single nucleotide polymorphisms by artificial mismatch hybridization. Nat. Biotechnol., 15, 331-335.
    • (1997) Nat. Biotechnol , vol.15 , pp. 331-335
    • Guo, Z.1    Liu, Q.2    Smith, L.M.3
  • 14
    • 3142710035 scopus 로고    scopus 로고
    • Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch
    • Burgner,D., D'Amato,M., Kwiatkowski,D.P. and Loakes,D. (2004) Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch. Nucleosides, Nucleotides Nucleic Acids, 23, 755-765.
    • (2004) Nucleosides, Nucleotides Nucleic Acids , vol.23 , pp. 755-765
    • Burgner, D.1    D'Amato, M.2    Kwiatkowski, D.P.3    Loakes, D.4
  • 15
    • 0033572961 scopus 로고    scopus 로고
    • Efforts toward expansion of the genetic alphabet: Recognition of a highly stable, self-pairing hydrophobic base
    • McMinn,D.L., Ogawa,A.K., Wu,Y., Liu,J., Schultz,P.G. and Romesberg,F.E. (1999) Efforts toward expansion of the genetic alphabet: Recognition of a highly stable, self-pairing hydrophobic base. J. Am. Chem. Soc., 121, 11585-11586.
    • (1999) J. Am. Chem. Soc , vol.121 , pp. 11585-11586
    • McMinn, D.L.1    Ogawa, A.K.2    Wu, Y.3    Liu, J.4    Schultz, P.G.5    Romesberg, F.E.6
  • 16
    • 0034639916 scopus 로고    scopus 로고
    • Efforts toward the expansion of the genetic alphabet: Information storage and replication with unnatural hydrophobic base pairs
    • Ogawa,A.K., Wu,Y., McMinn,D.L., Liu,J., Schultz,P.G. and Romesberg,F.E. (2000) Efforts toward the expansion of the genetic alphabet: Information storage and replication with unnatural hydrophobic base pairs. J. Am. Chem. Soc., 122, 3274-3287.
    • (2000) J. Am. Chem. Soc , vol.122 , pp. 3274-3287
    • Ogawa, A.K.1    Wu, Y.2    McMinn, D.L.3    Liu, J.4    Schultz, P.G.5    Romesberg, F.E.6
  • 17
    • 0034675008 scopus 로고    scopus 로고
    • Efforts toward expansion of the genetic alphabet: Optimization of interbase hydrophobic interactions
    • Wu,Y., Ogawa,A.K., Berger,M., McMinn,D.L., Schultz,P.G. and Romesberg,F.E. (2000) Efforts toward expansion of the genetic alphabet: optimization of interbase hydrophobic interactions. J. Am. Chem. Soc. 122, 7621-7632.
    • (2000) J. Am. Chem. Soc , vol.122 , pp. 7621-7632
    • Wu, Y.1    Ogawa, A.K.2    Berger, M.3    McMinn, D.L.4    Schultz, P.G.5    Romesberg, F.E.6
  • 19
    • 7744230597 scopus 로고    scopus 로고
    • Optimization of interstrand hydrophobic packing interactions within unnatural DNA base pairs
    • Matsuda,S. and Romesberg,F.E. (2004) Optimization of interstrand hydrophobic packing interactions within unnatural DNA base pairs. J. Am. Chem. Soc., 126, 14419-14427.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 14419-14427
    • Matsuda, S.1    Romesberg, F.E.2
  • 20
    • 33845310537 scopus 로고    scopus 로고
    • Stability and polymerase recognition of pyridine nucleobase analogues: Role of minor groove H-bond acceptors
    • Kim,Y., Leconte,A.M., Hari,Y. and Romesberg,F.E. (2006) Stability and polymerase recognition of pyridine nucleobase analogues: Role of minor groove H-bond acceptors. Angew. Chem. Int. Ed., 45, 7809-7812.
    • (2006) Angew. Chem. Int. Ed , vol.45 , pp. 7809-7812
    • Kim, Y.1    Leconte, A.M.2    Hari, Y.3    Romesberg, F.E.4
  • 21
    • 33744818886 scopus 로고    scopus 로고
    • An efficiently extended class of unnatural base pairs
    • Leconte,A.M., Matsuda,S. and Romesberg,F.E. (2006) An efficiently extended class of unnatural base pairs. J. Am. Chem. Soc., 128 6780-6781.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 6780-6781
    • Leconte, A.M.1    Matsuda, S.2    Romesberg, F.E.3
  • 22
    • 58149385844 scopus 로고    scopus 로고
    • Optimization of the pyridyl nucleobase scaffold for polymerase recognition and unnatural base pair replication
    • Hari,Y., Hwang,G.T., Leconte,A.M., Joubert,N., Hocek,M. and Romesberg,F.E. (2008) Optimization of the pyridyl nucleobase scaffold for polymerase recognition and unnatural base pair replication. ChemBioChem, 9, 2796-2799.
    • (2008) ChemBioChem , vol.9 , pp. 2796-2799
    • Hari, Y.1    Hwang, G.T.2    Leconte, A.M.3    Joubert, N.4    Hocek, M.5    Romesberg, F.E.6
  • 23
    • 0023406843 scopus 로고
    • Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves
    • Marky,L.A. and Breslauer,K.J. (1987) Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers, 26, 1601-1620.
    • (1987) Biopolymers , vol.26 , pp. 1601-1620
    • Marky, L.A.1    Breslauer, K.J.2
  • 24
    • 0033524401 scopus 로고    scopus 로고
    • Effects of hydration, ion release, and excluded volume on the melting of triplex and duplex DNA
    • Spink,C.H. and Chaires,J.B. (1999) Effects of hydration, ion release, and excluded volume on the melting of triplex and duplex DNA. Biochemistry, 38, 496-508.
    • (1999) Biochemistry , vol.38 , pp. 496-508
    • Spink, C.H.1    Chaires, J.B.2
  • 25
  • 26
    • 0022423486 scopus 로고
    • Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y=A,C,G,D
    • Aboul-ela,F., Koh,D., Tinoco,I. Jr. and Martin,F.H. (1985) Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y=A,C,G,D. Nucleic Acids Res., 13, 4811-4824.
    • (1985) Nucleic Acids Res , vol.13 , pp. 4811-4824
    • Aboul-ela, F.1    Koh, D.2    Tinoco Jr., I.3    Martin, F.H.4
  • 27
    • 0029100232 scopus 로고
    • Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions
    • Breslauer,K.L. (1995) Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. Methods Enzymol., 259, 221-242.
    • (1995) Methods Enzymol , vol.259 , pp. 221-242
    • Breslauer, K.L.1
  • 28
    • 1242264497 scopus 로고    scopus 로고
    • Hydration of short DNA, RNA and 2′-OMe oligonucleotides determined by osmotic stressing
    • Rozners,E. and Moulder,J. (2004) Hydration of short DNA, RNA and 2′-OMe oligonucleotides determined by osmotic stressing. Nucleic Acids Res., 32, 248-254.
    • (2004) Nucleic Acids Res , vol.32 , pp. 248-254
    • Rozners, E.1    Moulder, J.2
  • 29
    • 0024292414 scopus 로고
    • Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton
    • Leroy,J.L., Kochoyan,M., Huynh-Dinh,T. and Guéron,M. (1988) Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton. J. Mol. Biol., 200, 223-238.
    • (1988) J. Mol. Biol , vol.200 , pp. 223-238
    • Leroy, J.L.1    Kochoyan, M.2    Huynh-Dinh, T.3    Guéron, M.4
  • 30
    • 0029120978 scopus 로고
    • Terminal base pairs of oligodeoxynucleotides: Imino proton exchange and fraying
    • Nonin,S., Leroy,J.L. and Guéron,M. (1995) Terminal base pairs of oligodeoxynucleotides: Imino proton exchange and fraying. Biochemistry, 34, 10652-10659.
    • (1995) Biochemistry , vol.34 , pp. 10652-10659
    • Nonin, S.1    Leroy, J.L.2    Guéron, M.3
  • 31
    • 0031790169 scopus 로고    scopus 로고
    • Solution structure of a DNA duplex containing a replicable difluorotolueneadenine pair
    • Guckian,K.M., Krugh,T.R. and Kool,E.T. (1998) Solution structure of a DNA duplex containing a replicable difluorotolueneadenine pair. Nat. Struct. Biol., 5, 954-959.
    • (1998) Nat. Struct. Biol , vol.5 , pp. 954-959
    • Guckian, K.M.1    Krugh, T.R.2    Kool, E.T.3
  • 33
  • 34
    • 34147187253 scopus 로고    scopus 로고
    • Water clustering and percolation in low hydration DNA shells
    • Brovchenko,I., Krukau,A., Oleinikova,A. and Mazur,A.K. (2007) Water clustering and percolation in low hydration DNA shells. J. Phys. Chem. B, 111, 3258-3266.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 3258-3266
    • Brovchenko, I.1    Krukau, A.2    Oleinikova, A.3    Mazur, A.K.4
  • 35
    • 20144368902 scopus 로고    scopus 로고
    • Complicated water orientations in the minor groove of the B-DNA decamer d(CCATT AATGG)2 observed by neutron diffraction measurements
    • Arai,S., Chatake,T., Ohhara,T., Kurihara,K., Tanaka,I., Suzuki,N., Fujimoto,Z., Mizuno,H. and Niimura,S. (2005) Complicated water orientations in the minor groove of the B-DNA decamer d(CCATT AATGG)2 observed by neutron diffraction measurements. Nucleic Acids Res., 33, 3017-3024.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3017-3024
    • Arai, S.1    Chatake, T.2    Ohhara, T.3    Kurihara, K.4    Tanaka, I.5    Suzuki, N.6    Fujimoto, Z.7    Mizuno, H.8    Niimura, S.9
  • 36
    • 2442573712 scopus 로고    scopus 로고
    • Structural and dynamic variations in DNA hexamers containing T-T and F-F single and tandem internal mispairs
    • Sherer,E.C. and Cramer,C.J. (2004) Structural and dynamic variations in DNA hexamers containing T-T and F-F single and tandem internal mispairs. Theor. Chem. Acc., 111, 311-327.
    • (2004) Theor. Chem. Acc , vol.111 , pp. 311-327
    • Sherer, E.C.1    Cramer, C.J.2
  • 37
    • 33644844520 scopus 로고    scopus 로고
    • Microarray technology: Beyond transcript profiling and genotype analysis
    • Hoheisel,J.D. (2006) Microarray technology: Beyond transcript profiling and genotype analysis. Nat. Rev. Genet., 7, 200-210.
    • (2006) Nat. Rev. Genet , vol.7 , pp. 200-210
    • Hoheisel, J.D.1


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