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Volumn 3, Issue 1, 2011, Pages 69-78

Concepts and software for a rational design of polynucleotide probes

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EID: 78249281491     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/j.1758-2229.2010.00189.x     Document Type: Article
Times cited : (17)

References (34)
  • 1
    • 42349093774 scopus 로고    scopus 로고
    • Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques
    • Amann, R., and Fuchs, B.M. (2008) Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 6: 339-348.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 339-348
    • Amann, R.1    Fuchs, B.M.2
  • 2
    • 0001908644 scopus 로고
    • Quantitative filter hybridisation
    • Hames, B.D., and Higgins, S.J. (eds). Oxford, UK: Oxford University Press
    • Anderson, M.L.M., and Young, B.D. (1985) Quantitative filter hybridisation. In Nucleic Acid Hybridisation - A Practical Approach. Hames, B.D., and Higgins, S.J. (eds). Oxford, UK: Oxford University Press, pp. 73-110.
    • (1985) Nucleic Acid Hybridisation - A Practical Approach , pp. 73-110
    • Anderson, M.L.M.1    Young, B.D.2
  • 4
    • 0015764063 scopus 로고
    • Reduction in the rate of DNA reassociation by sequence divergence
    • Bonner, T.I., Brenner, D.J., Neufeld, B.R., and Britten, R.J. (1973) Reduction in the rate of DNA reassociation by sequence divergence. J Mol Biol 81: 123-135.
    • (1973) J Mol Biol , vol.81 , pp. 123-135
    • Bonner, T.I.1    Brenner, D.J.2    Neufeld, B.R.3    Britten, R.J.4
  • 5
    • 0023928082 scopus 로고
    • Calibration of the change in thermal stability of DNA duplexes and degree of base pair mismatch
    • Caccone, A., DeSalle, R., and Powell, J. (1988) Calibration of the change in thermal stability of DNA duplexes and degree of base pair mismatch. J Mol Evol 27: 212-216.
    • (1988) J Mol Evol , vol.27 , pp. 212-216
    • Caccone, A.1    Desalle, R.2    Powell, J.3
  • 6
    • 0017396845 scopus 로고
    • Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplexes at high concentrations of formamide
    • Casey, J., and Davidson, N. (1977) Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplexes at high concentrations of formamide. Nucleic Acids Res 4: 1539-1552.
    • (1977) Nucleic Acids Res , vol.4 , pp. 1539-1552
    • Casey, J.1    Davidson, N.2
  • 7
    • 0032729451 scopus 로고    scopus 로고
    • Visualization and enumeration of marine planktonic Archaea and Bacteria by using polyribonucleotide probes and fluorescent in situ hybridization
    • DeLong, E.F., Taylor, L.T., Marsh, T.L., and Preston, C.M. (1999) Visualization and enumeration of marine planktonic Archaea and Bacteria by using polyribonucleotide probes and fluorescent in situ hybridization. Appl Environ Microbiol 65: 5554-5563.
    • (1999) Appl Environ Microbiol , vol.65 , pp. 5554-5563
    • Delong, E.F.1    Taylor, L.T.2    Marsh, T.L.3    Preston, C.M.4
  • 8
    • 79953739860 scopus 로고
    • Stabilizing effectiveness of alkali metals toward ribonucleic acid from the bacterial virus R17
    • Gordon, J.A. (1965) Stabilizing effectiveness of alkali metals toward ribonucleic acid from the bacterial virus R17. Biopolymers 3: 5-14.
    • (1965) Biopolymers , vol.3 , pp. 5-14
    • Gordon, J.A.1
  • 9
    • 0014981036 scopus 로고
    • The effects of aqueous neutral-salt solution on the melting temperatures of deoxyribonucleic acids
    • Gruenwedel, D.W., Hsu, C.-H., and Lu, D.S. (1971) The effects of aqueous neutral-salt solution on the melting temperatures of deoxyribonucleic acids. Biopolymers 10: 47-68.
    • (1971) Biopolymers , vol.10 , pp. 47-68
    • Gruenwedel, D.W.1    Hsu, C.-H.2    Lu, D.S.3
  • 10
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
    • (1999) Nucleic Acids Symp Ser , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 11
    • 0017672103 scopus 로고
    • Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea
    • Hutton, J.R. (1977) Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea. Nucleic Acids Res 4: 3538-3555.
    • (1977) Nucleic Acids Res , vol.4 , pp. 3538-3555
    • Hutton, J.R.1
  • 12
    • 0015939401 scopus 로고
    • Effect of chemical modification on the rate of renaturation of deoxyribonucleic acid. Deaminated and glyoxalated deoxyribonucleic acid
    • Hutton, J.R., and Wetmur, J.G. (1973) Effect of chemical modification on the rate of renaturation of deoxyribonucleic acid. Deaminated and glyoxalated deoxyribonucleic acid. Biochemistry 12: 558-563.
    • (1973) Biochemistry , vol.12 , pp. 558-563
    • Hutton, J.R.1    Wetmur, J.G.2
  • 13
    • 0029121625 scopus 로고
    • Relative thermodynamic stability of DNA, RNA, and DNA:RNA hybrid duplexes: Relationship with base composition and structure
    • Lesnik, E.A., and Freier, S.M. (1995) Relative thermodynamic stability of DNA, RNA, and DNA:RNA hybrid duplexes: relationship with base composition and structure. Biochemistry 34: 10807-10815.
    • (1995) Biochemistry , vol.34 , pp. 10807-10815
    • Lesnik, E.A.1    Freier, S.M.2
  • 14
    • 0028015963 scopus 로고
    • PCR-based preparation of 23S rRNA-targeted group-specific polynucleotide probes
    • Ludwig, W., Dorn, S., Springer, N., Kirchhof, G., and Schleifer, K.H. (1994) PCR-based preparation of 23S rRNA-targeted group-specific polynucleotide probes. Appl Environ Microbiol 69: 3236-3244.
    • (1994) Appl Environ Microbiol , vol.69 , pp. 3236-3244
    • Ludwig, W.1    Dorn, S.2    Springer, N.3    Kirchhof, G.4    Schleifer, K.H.5
  • 16
    • 78249268816 scopus 로고    scopus 로고
    • GeneFISH - an in situ technique for linking gene presence and cell identity in environmental microorganisms
    • (in press): doi:10.1111/j.1462-2920.2010.02281.x
    • Moraru, C., Lam, P., Fuchs, B.M., Kuypers, M.M.M., and Amann, R. (2010) GeneFISH - an in situ technique for linking gene presence and cell identity in environmental microorganisms. Environ Microbiol (in press): doi:10.1111/j.1462-2920.2010.02281.x.
    • (2010) Environ Microbiol
    • Moraru, C.1    Lam, P.2    Fuchs, B.M.3    Kuypers, M.M.M.4    Amann, R.5
  • 17
    • 0030768426 scopus 로고    scopus 로고
    • Subcellular distribution of actively partitioning F plasmid during the cell division cycle in E. coli
    • Niki, H., and Hiraga, S. (1997) Subcellular distribution of actively partitioning F plasmid during the cell division cycle in E. coli. Cell 90: 951-957.
    • (1997) Cell , vol.90 , pp. 951-957
    • Niki, H.1    Hiraga, S.2
  • 18
    • 4644226321 scopus 로고    scopus 로고
    • Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria
    • Pernthaler, A., and Amann, R. (2004) Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl Environ Microbiol 70: 5426-5433.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 5426-5433
    • Pernthaler, A.1    Amann, R.2
  • 19
    • 27644555223 scopus 로고    scopus 로고
    • Simultaneous fluorescence in situ hybridization of mRNA and rRNA for the detection of gene expression in environmental microbes
    • Pernthaler, A., and Pernthaler, J. (2005) Simultaneous fluorescence in situ hybridization of mRNA and rRNA for the detection of gene expression in environmental microbes. Methods Enzymol 397: 351-371.
    • (2005) Methods Enzymol , vol.397 , pp. 351-371
    • Pernthaler, A.1    Pernthaler, J.2
  • 20
    • 0036276618 scopus 로고    scopus 로고
    • Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria
    • Pernthaler, A., Pernthaler, J., and Amann, R. (2002a) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68: 3094-3101.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 3094-3101
    • Pernthaler, A.1    Pernthaler, J.2    Amann, R.3
  • 21
    • 0036151819 scopus 로고    scopus 로고
    • Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine Bacteria and Archaea
    • Pernthaler, A., Preston, C.M., Pernthaler, J., DeLong, E.F., and Amann, R. (2002b) Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine Bacteria and Archaea. Appl Environ Microbiol 68: 661-667.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 661-667
    • Pernthaler, A.1    Preston, C.M.2    Pernthaler, J.3    Delong, E.F.4    Amann, R.5
  • 22
    • 21244484895 scopus 로고    scopus 로고
    • Sensitive multi-color fluorescence in situ hybridization for the identification of environmental microorganisms
    • Akkermans, A.D.L., de Bruijn, F.J., and van Elsas, J.D. (eds). Dordrecht, the Netherlands: Kluwer Academic Publishers
    • Pernthaler, A., Pernthaler, J., and Amann, R. (2004) Sensitive multi-color fluorescence in situ hybridization for the identification of environmental microorganisms. In Molecular Microbial Ecology Manual. Akkermans, A.D.L., de Bruijn, F.J., and van Elsas, J.D. (eds). Dordrecht, the Netherlands: Kluwer Academic Publishers, pp. 711-726.
    • (2004) Molecular Microbial Ecology Manual , pp. 711-726
    • Pernthaler, A.1    Pernthaler, J.2    Amann, R.3
  • 23
    • 0022586762 scopus 로고
    • Denaturation, renaturation, and loss of DNA during in situ hybridization procedures
    • Raap, A.K., Marijnen, J.G.J., Vrolijk, J., and Ploeg, M.v.d. (1986) Denaturation, renaturation, and loss of DNA during in situ hybridization procedures. Cytometry 7: 235-242.
    • (1986) Cytometry , vol.7 , pp. 235-242
    • Raap, A.K.1    Marijnen, J.G.J.2    Vrolijk, J.3    Ploeg, M.V.D.4
  • 24
    • 0013822867 scopus 로고
    • Dependence of the melting temperature of DNA on salt concentration
    • Schildkraut, C., and Lifson, S. (1965) Dependence of the melting temperature of DNA on salt concentration. Biopolymers 3: 195-208.
    • (1965) Biopolymers , vol.3 , pp. 195-208
    • Schildkraut, C.1    Lifson, S.2
  • 25
    • 0026636186 scopus 로고
    • Calculation of sequence divergence from the thermal stability of DNA heteroduplexes
    • Springer, M.S., Davidson, E.H., and Britten, R.J. (1992) Calculation of sequence divergence from the thermal stability of DNA heteroduplexes. J Mol Evol 34: 379-382.
    • (1992) J Mol Evol , vol.34 , pp. 379-382
    • Springer, M.S.1    Davidson, E.H.2    Britten, R.J.3
  • 26
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 27
    • 0027931265 scopus 로고
    • Identification of whole fixed bacterial cells with nonradioactive 23S rRNA-targeted polynucleotide probes
    • Trebesius, K., Amann, R., Ludwig, W., Muhlegger, K., and Schleifer, K.-H. (1994) Identification of whole fixed bacterial cells with nonradioactive 23S rRNA-targeted polynucleotide probes. Appl Environ Microbiol 60: 3228-3235.
    • (1994) Appl Environ Microbiol , vol.60 , pp. 3228-3235
    • Trebesius, K.1    Amann, R.2    Ludwig, W.3    Muhlegger, K.4    Schleifer, K.-H.5
  • 29
    • 0002459355 scopus 로고
    • Thermal denaturation of DNA molecules: A comparison of theory with experiment
    • Wartell, R.M., and Benight, A.S. (1985) Thermal denaturation of DNA molecules: a comparison of theory with experiment. Phys Rep 126: 67-107.
    • (1985) Phys Rep , vol.126 , pp. 67-107
    • Wartell, R.M.1    Benight, A.S.2
  • 30
    • 0025944267 scopus 로고
    • DNA probes: Applications of the principles of nucleic acid hybridization
    • Wetmur, J.G. (1991) DNA probes: applications of the principles of nucleic acid hybridization. Crit Rev Biochem Mol Biol 26: 227-259.
    • (1991) Crit Rev Biochem Mol Biol , vol.26 , pp. 227-259
    • Wetmur, J.G.1
  • 31
    • 0014413352 scopus 로고
    • Kinetics of renaturation of DNA
    • Wetmur, J.G., and Davidson, N. (1968) Kinetics of renaturation of DNA. J Mol Biol 31: 349-370.
    • (1968) J Mol Biol , vol.31 , pp. 349-370
    • Wetmur, J.G.1    Davidson, N.2
  • 32
    • 0034909188 scopus 로고    scopus 로고
    • DNA polynucleotide probes generated from representatives of the genus Acinetobacter and their application in fluorescence in situ hybridization of environmental samples
    • Zimmermann, J., Ludwig, W., and Schleifer, K.H. (2001) DNA polynucleotide probes generated from representatives of the genus Acinetobacter and their application in fluorescence in situ hybridization of environmental samples. Syst Appl Microbiol 24: 238-244.
    • (2001) Syst Appl Microbiol , vol.24 , pp. 238-244
    • Zimmermann, J.1    Ludwig, W.2    Schleifer, K.H.3
  • 33
    • 19444375339 scopus 로고    scopus 로고
    • Fluorescence in situ hybridisation (FISH): The next generation
    • Zwirglmaier, K. (2005) Fluorescence in situ hybridisation (FISH): the next generation. FEMS Microbiol Lett 246: 151-158.
    • (2005) FEMS Microbiol Lett , vol.246 , pp. 151-158
    • Zwirglmaier, K.1
  • 34
    • 0346964274 scopus 로고    scopus 로고
    • Recognition of individual genes in a single bacterial cell by fluorescence in situ hybridization - RING-FISH
    • Zwirglmaier, K., Ludwig, W., and Schleifer, K.H. (2004) Recognition of individual genes in a single bacterial cell by fluorescence in situ hybridization - RING-FISH. Mol Microbiol 51: 89-96.
    • (2004) Mol Microbiol , vol.51 , pp. 89-96
    • Zwirglmaier, K.1    Ludwig, W.2    Schleifer, K.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.