메뉴 건너뛰기




Volumn 33, Issue 19, 2005, Pages 6258-6267

Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYINOSINE; DOUBLE STRANDED DNA; INOSINE;

EID: 28544447850     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki918     Document Type: Article
Times cited : (116)

References (49)
  • 1
    • 0013936167 scopus 로고
    • Codon-anticodon pairing: The wobble hypothesis
    • Crick,F.H.C. (1966) Codon-anticodon pairing: The wobble hypothesis. J. Mol. Biol., 19, 548-555.
    • (1966) J. Mol. Biol. , vol.19 , pp. 548-555
    • Crick, F.H.C.1
  • 2
    • 0017340307 scopus 로고
    • Genetic effects of nitrous acid
    • Zimmerman,F.K. (1977) Genetic effects of nitrous acid. Mutat. Res., 39, 127-148.
    • (1977) Mutat. Res. , vol.39 , pp. 127-148
    • Zimmerman, F.K.1
  • 3
    • 0019331557 scopus 로고
    • Hypoxanthine in deoxyribonucleic acid: Generation by heat-induced hydrolysis of adenine residues and release in free form by a deoxyribonucleic acid glycosylase from calf thymus
    • Karran,P. and Lindahl,T. (1980) Hypoxanthine in deoxyribonucleic acid: generation by heat-induced hydrolysis of adenine residues and release in free form by a deoxyribonucleic acid glycosylase from calf thymus. Biochemistry, 19, 6008-6011.
    • (1980) Biochemistry , vol.19 , pp. 6008-6011
    • Karran, P.1    Lindahl, T.2
  • 4
    • 20744459167 scopus 로고    scopus 로고
    • A bioinformatic screen for novel A-I RNA editing sites reveals recoding editing in BC10
    • Clutterbuck,D.R., Leroy,A., O'Connell,M.A. and Semple,C.A.M. (2005) A bioinformatic screen for novel A-I RNA editing sites reveals recoding editing in BC10. Bioinformatics, 21, 2590-2595.
    • (2005) Bioinformatics , vol.21 , pp. 2590-2595
    • Clutterbuck, D.R.1    Leroy, A.2    O'Connell, M.A.3    Semple, C.A.M.4
  • 5
    • 0022429804 scopus 로고
    • Base pairing involving deoxyinosine: Implications for probe design
    • Martin,F.H., Castro,M.M., Aboul-ela,F. and Tinoco,I.,Jr (1985) Base pairing involving deoxyinosine: Implications for probe design. Nucleic Acids Res., 13, 8927-8938.
    • (1985) Nucleic Acids Res. , vol.13 , pp. 8927-8938
    • Martin, F.H.1    Castro, M.M.2    Aboul-Ela, F.3    Tinoco Jr., I.4
  • 6
    • 0028231020 scopus 로고
    • Studies on the base pairing properties of deoxyinosine by solid phase hybridisation to oligonucleotides
    • Case-Green,S.C. and Southern,E.M. (1994) Studies on the base pairing properties of deoxyinosine by solid phase hybridisation to oligonucleotides. Nucleic Acids Res., 22, 131-136.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 131-136
    • Case-Green, S.C.1    Southern, E.M.2
  • 7
    • 0023664405 scopus 로고
    • Identification of I:A mismatch base-pairing structure in DNA
    • Uesugi,S., Oda,Y., Ikehara,M., Kawase,Y. and Ohtsuka,E. (1987) Identification of I:A mismatch base-pairing structure in DNA. J. Biol. Chem., 262, 6965-6968.
    • (1987) J. Biol. Chem. , vol.262 , pp. 6965-6968
    • Uesugi, S.1    Oda, Y.2    Ikehara, M.3    Kawase, Y.4    Ohtsuka, E.5
  • 9
    • 0028245297 scopus 로고
    • A universal nucleoside for use at ambiguous sites in DNA primers
    • Nichols,R., Andrews,P.C., Zhang,P. and Bergstrom,D.E. (1994) A universal nucleoside for use at ambiguous sites in DNA primers. Nature, 369, 492-493.
    • (1994) Nature , vol.369 , pp. 492-493
    • Nichols, R.1    Andrews, P.C.2    Zhang, P.3    Bergstrom, D.E.4
  • 10
    • 0029036729 scopus 로고
    • 3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR
    • Loakes,D., Brown,D.M., Linde,S. and Hill,F. (1995) 3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR. Nucleic Acids Res., 23, 2361-2366.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 2361-2366
    • Loakes, D.1    Brown, D.M.2    Linde, S.3    Hill, F.4
  • 12
    • 0021987215 scopus 로고
    • An alternative approach to deoxyoligonucleotides as hybridization probes by insertion of deoxyinosine at ambiguous codon positions
    • Ohtsuka,E., Matsuki,S., Ikehara,M., Takahashi,Y. and Matsubara,K. (1985) An alternative approach to deoxyoligonucleotides as hybridization probes by insertion of deoxyinosine at ambiguous codon positions. J. Biol. Chem., 260, 2605-2608.
    • (1985) J. Biol. Chem. , vol.260 , pp. 2605-2608
    • Ohtsuka, E.1    Matsuki, S.2    Ikehara, M.3    Takahashi, Y.4    Matsubara, K.5
  • 13
    • 0022371561 scopus 로고
    • Use of the deoxyinosine-containing probe to isolate and sequence cDNA encoding the fusion (F) glycoprotein of Sendai virus (HVJ)
    • Miura,N., Ohtsuka,E., Yamaberi,N., Ikehara,M., Uchida,T. and Okada,Y. (1985) Use of the deoxyinosine-containing probe to isolate and sequence cDNA encoding the fusion (F) glycoprotein of Sendai virus (HVJ). Gene, 38, 271-274.
    • (1985) Gene , vol.38 , pp. 271-274
    • Miura, N.1    Ohtsuka, E.2    Yamaberi, N.3    Ikehara, M.4    Uchida, T.5    Okada, Y.6
  • 14
    • 0025336615 scopus 로고
    • PCR amplification of an Escherichia Coli gene using mixed primers containing deoxyinosine at ambiguous positions in degenerate amino acid codons
    • Patil,R. and Dekkar,E. (1990) PCR amplification of an Escherichia Coli gene using mixed primers containing deoxyinosine at ambiguous positions in degenerate amino acid codons. Nucleic Acids Res., 18, 3080.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 3080
    • Patil, R.1    Dekkar, E.2
  • 15
    • 0028279949 scopus 로고
    • Application of PCR with oligonucleotide primers containing deoxyinosine for gene detection, isolation and sequencing
    • Palva,A., Vidgren,G. and Paulin,L. (1994) Application of PCR with oligonucleotide primers containing deoxyinosine for gene detection, isolation and sequencing. J. Microbiol. Methods, 19, 315-321.
    • (1994) J. Microbiol. Methods , vol.19 , pp. 315-321
    • Palva, A.1    Vidgren, G.2    Paulin, L.3
  • 17
    • 0019887733 scopus 로고
    • The use of synthetic oligonucleotides as hybridization probes. II. Hybridization of oligonucleotides of mixed sequence to rabbit beta-globin DNA
    • Wallace,R.B., Johnson,M.J., Hirose,T., Miyake,T., Kawashima,E.H. and Itakura,K. (1981) The use of synthetic oligonucleotides as hybridization probes. II. Hybridization of oligonucleotides of mixed sequence to rabbit beta-globin DNA. Nucleic Acids Res., 9, 879-894.
    • (1981) Nucleic Acids Res. , vol.9 , pp. 879-894
    • Wallace, R.B.1    Johnson, M.J.2    Hirose, T.3    Miyake, T.4    Kawashima, E.H.5    Itakura, K.6
  • 18
    • 0027981314 scopus 로고
    • Thermal denaturation of double-stranded nucleic acids: Prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction
    • Steger,G. (1994) Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res., 22, 2760-2768.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 2760-2768
    • Steger, G.1
  • 19
    • 0030804196 scopus 로고    scopus 로고
    • Oligodeoxyribonucleotide length and sequence effects on intramolecular and intermolecular G-quartet formation
    • Cheng,A. and Van Dyke,M.W. (1997) Oligodeoxyribonucleotide length and sequence effects on intramolecular and intermolecular G-quartet formation. Gene, 197, 253-260.
    • (1997) Gene , vol.197 , pp. 253-260
    • Cheng, A.1    Van Dyke, M.W.2
  • 21
    • 0036308528 scopus 로고    scopus 로고
    • Detection and genotyping of human group a rotaviruses by oligonucleotide microarray hybridization
    • Chizhikov,V., Wagner,M., Ivshina,A., Hoshino,Y., Kapikian,A.Z. and Chumakov,K. (2002) Detection and genotyping of human group a rotaviruses by oligonucleotide microarray hybridization. J. Clin. Microbiol., 40, 2398-2407.
    • (2002) J. Clin. Microbiol. , vol.40 , pp. 2398-2407
    • Chizhikov, V.1    Wagner, M.2    Ivshina, A.3    Hoshino, Y.4    Kapikian, A.Z.5    Chumakov, K.6
  • 23
    • 0035875112 scopus 로고    scopus 로고
    • The applications of Universal DNA base analogues
    • Loakes,D. (2001) The applications of Universal DNA base analogues. Nucleic Acids Res., 29, 2437-2447.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2437-2447
    • Loakes, D.1
  • 24
    • 0027984280 scopus 로고
    • 5-Nitroindole as an universal base analogue
    • Loakes,D. and Brown,D.M. (1994) 5-Nitroindole as an universal base analogue. Nucleic Acids Res., 22, 4039-4043.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4039-4043
    • Loakes, D.1    Brown, D.M.2
  • 25
    • 0030788868 scopus 로고    scopus 로고
    • Comparison of the base pairing properties of a series of nitroazole nucleobase analogs in the oligodeoxyribonucleotide sequence 5′-d(CGCXAATTYGCG)-3′
    • Bergstrom,D.E., Zhang,P. and Johnson,W.T. (1997) Comparison of the base pairing properties of a series of nitroazole nucleobase analogs in the oligodeoxyribonucleotide sequence 5′-d(CGCXAATTYGCG)-3′. Nucleic Acids Res., 25, 1935-1942.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 1935-1942
    • Bergstrom, D.E.1    Zhang, P.2    Johnson, W.T.3
  • 26
    • 0030839743 scopus 로고    scopus 로고
    • The synthesis and stability of oligodeoxyribonucleotides containing the deoxyadenosine mimic 1-(2′-deoxy-β-D-ribofuranosyl) imidazole-4-carboxamide
    • Johnson,W.T., Zhang,P. and Bergstrom,D.E. (1997) The synthesis and stability of oligodeoxyribonucleotides containing the deoxyadenosine mimic 1-(2′-deoxy-β-D-ribofuranosyl) imidazole-4-carboxamide. Nucleic Acids Res., 25, 559-567.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 559-567
    • Johnson, W.T.1    Zhang, P.2    Bergstrom, D.E.3
  • 27
    • 0009761004 scopus 로고    scopus 로고
    • The use of spectroscopic techniques in the study of DNA stability
    • Gore,M.G. (ed.), University Press, Oxford, NY
    • SantaLucia,J.,Jr (2000) The use of spectroscopic techniques in the study of DNA stability. In Gore,M.G. (ed.), Spectrophotometry and Spectrofluorimetry. University Press, Oxford, NY, pp. 329-354.
    • (2000) Spectrophotometry and Spectrofluorimetry , pp. 329-354
    • SantaLucia Jr., J.1
  • 28
    • 0029968822 scopus 로고    scopus 로고
    • Improved nearest-neighbor parameters for predicting DNA duplex stability
    • SantaLucia,J.,Jr, Allawi,H.T. and Seneviratne,P.A. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry, 35, 3555-3562.
    • (1996) Biochemistry , vol.35 , pp. 3555-3562
    • SantaLucia Jr., J.1    Allawi, H.T.2    Seneviratne, P.A.3
  • 29
    • 0029805937 scopus 로고    scopus 로고
    • 2 by two-dimensional NMR and simulated annealing
    • 2 by two-dimensional NMR and simulated annealing. Biochemistry, 35, 14077-14089.
    • (1996) Biochemistry , vol.35 , pp. 14077-14089
    • McDowell, J.A.1    Turner, D.H.2
  • 30
    • 0034194135 scopus 로고    scopus 로고
    • Thermodynamic parameters for DNA sequences with dangling ends
    • Bommarito,S., Peyret,N. and SantaLucia,J.,Jr (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res., 28, 1929-1934.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1929-1934
    • Bommarito, S.1    Peyret, N.2    SantaLucia Jr., J.3
  • 31
    • 0030875847 scopus 로고    scopus 로고
    • Thermodynamics and NMR of internal G·T mismatches in DNA
    • Allawi,H.T. and SantaLucia,J.,Jr (1997) Thermodynamics and NMR of internal G·T mismatches in DNA. Biochemistry, 36, 10581-10594.
    • (1997) Biochemistry , vol.36 , pp. 10581-10594
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 32
    • 0017406554 scopus 로고
    • Characterization of a spectrophotometric assay for cAMP phosphodiesterase
    • Dedman,J.R. and Means,A.R. (1977) Characterization of a spectrophotometric assay for cAMP phosphodiesterase. J. Cyclic Nucleotide Res., 3, 139-152.
    • (1977) J. Cyclic Nucleotide Res. , vol.3 , pp. 139-152
    • Dedman, J.R.1    Means, A.R.2
  • 33
    • 0017379544 scopus 로고
    • Spectrometric determination of ribose-1-phosphate
    • Mura,U., Sgarella,F. and Ipaten,P. (1977) Spectrometric determination of ribose-1-phosphate. Anal. Biochem., 82, 210-216.
    • (1977) Anal. Biochem. , vol.82 , pp. 210-216
    • Mura, U.1    Sgarella, F.2    Ipaten, P.3
  • 34
    • 84873795297 scopus 로고
    • Differential spectrophotometry of purine compounds by means of specific enzymes
    • Kalckar,H.M. (1947) Differential spectrophotometry of purine compounds by means of specific enzymes. J. Biol. Chem., 167, 445.
    • (1947) J. Biol. Chem. , vol.167 , pp. 445
    • Kalckar, H.M.1
  • 35
    • 0035963677 scopus 로고    scopus 로고
    • Effect of the universal base 3-nitropyrrole on the selectivity of neighboring natural bases
    • Oliver,J.D., Parker,K.A. and Suggs,J.W. (2001) Effect of the universal base 3-nitropyrrole on the selectivity of neighboring natural bases. Org. Lett., 3, 1977-1980.
    • (2001) Org. Lett. , vol.3 , pp. 1977-1980
    • Oliver, J.D.1    Parker, K.A.2    Suggs, J.W.3
  • 36
    • 0020674698 scopus 로고
    • Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp
    • Petersheim,M. and Turner,D.H. (1983) Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry, 22, 256-263.
    • (1983) Biochemistry , vol.22 , pp. 256-263
    • Petersheim, M.1    Turner, D.H.2
  • 38
    • 0025082690 scopus 로고
    • Effects of GA mismatches on the structure and thermodynamics of RNA internal loops
    • SantaLucia,J.,Jr, Kierzek,R. and Turner,D.H. (1990) Effects of GA mismatches on the structure and thermodynamics of RNA internal loops. Biochemistry, 29, 8813-8819.
    • (1990) Biochemistry , vol.29 , pp. 8813-8819
    • SantaLucia Jr., J.1    Kierzek, R.2    Turner, D.H.3
  • 39
    • 0000014960 scopus 로고
    • Monte Carlo description of oligoelectrolyte properties of DNA oligomers: Range of the end effect and the approach of molecular and thermodynamic properties to the polyelectrolyte limits
    • Olmsted,M.C., Anderson,C.F. and Record,M.T.,Jr (1989) Monte Carlo description of oligoelectrolyte properties of DNA oligomers: Range of the end effect and the approach of molecular and thermodynamic properties to the polyelectrolyte limits. Proc. Natl Acad. Sci. USA, 86, 7766-7770.
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 7766-7770
    • Olmsted, M.C.1    Anderson, C.F.2    Record Jr., M.T.3
  • 40
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and olignucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia,J.,Jr (1998) A unified view of polymer, dumbbell, and olignucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 1460-1465
    • SantaLucia Jr., J.1
  • 41
    • 84982401389 scopus 로고
    • A new approach to the study of sequence-dependent properties of polynucleotides
    • Gray,D.M. and Tinoco,I.,Jr (1970) A new approach to the study of sequence-dependent properties of polynucleotides. Biopolymers, 9, 223-244.
    • (1970) Biopolymers , vol.9 , pp. 223-244
    • Gray, D.M.1    Tinoco Jr., I.2
  • 43
    • 0032562140 scopus 로고    scopus 로고
    • Nearest-neighbor thermodynamic parameters for internal G·A mismatches in DNA
    • Allawi,H.T. and SantaLucia,J.,Jr (1998) Nearest-neighbor thermodynamic parameters for internal G·A mismatches in DNA. Biochemistry, 37, 2170-2179.
    • (1998) Biochemistry , vol.37 , pp. 2170-2179
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 44
    • 0033596964 scopus 로고    scopus 로고
    • Nearest-neighbor thermodynamics and NMR of data sequences of internal A·A, C·C, G·G, and T·T Mismatches
    • Peyret,N., Seneviratne,P.A., Allawi,H.T. and SantaLucia,J.,Jr (1999) Nearest-neighbor thermodynamics and NMR of data sequences of internal A·A, C·C, G·G, and T·T Mismatches. Biochemistry, 38, 3468-3477.
    • (1999) Biochemistry , vol.38 , pp. 3468-3477
    • Peyret, N.1    Seneviratne, P.A.2    Allawi, H.T.3    SantaLucia Jr., J.4
  • 45
    • 12044257509 scopus 로고
    • Functional group substitutions as probes of hydrogen bonding between GA mismatches in rna internal loops
    • SantaLucia,J.,Jr, Kierzek,R. and Turner,D.H. (1991) 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 Jr., J.1    Kierzek, R.2    Turner, D.H.3
  • 46
    • 0002458550 scopus 로고
    • The influence of the Purine 2-Amino Group on DNA Conformation and Stability
    • Gaffney,B.L., Marky,L.A. and Jones,R.A. (1984) The influence of the Purine 2-Amino Group on DNA Conformation and Stability. Tetrahedron, 40, 3-13.
    • (1984) Tetrahedron , vol.40 , pp. 3-13
    • Gaffney, B.L.1    Marky, L.A.2    Jones, R.A.3
  • 47
    • 0000789168 scopus 로고
    • Free energy increments for hydrogen bonds in nucleic acid base pairs
    • Turner,D.H., Sugimoto,N., Kierzek,R. and Dreiker,S.D. (1987) Free energy increments for hydrogen bonds in nucleic acid base pairs. J. Am. Chem. Soc., 109, 3783-3785.
    • (1987) J. Am. Chem. Soc. , vol.109 , pp. 3783-3785
    • Turner, D.H.1    Sugimoto, N.2    Kierzek, R.3    Dreiker, S.D.4
  • 48
    • 0023046290 scopus 로고
    • 2) and self-complementary d(GGGAAXYTTCCC) containing deoxyinosine and other mismatched bases
    • 2) and self-complementary d(GGGAAXYTTCCC) containing deoxyinosine and other mismatched bases. Nucleic Acids Res., 14, 7727-7736.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 7727-7736
    • Kawase, Y.1    Iwai, S.2    Inoue, H.3    Miura, K.4    Ohtsuka, E.5
  • 49
    • 0347064295 scopus 로고    scopus 로고
    • Folding of a stable DNA motif involves a highly cooperative network of interactions
    • Moody,E.M. and Bevilacqua,P.C. (2003) Folding of a stable DNA motif involves a highly cooperative network of interactions. J. Am. Chem. Soc., 125, 16285-16293.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 16285-16293
    • Moody, E.M.1    Bevilacqua, P.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.