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Volumn 83, Issue 1, 2009, Pages 111-120

The design, synthesis and characterization of a novel acceptor for real time polymerase chain reaction using both computational and experimental approaches

Author keywords

DFT; Fluorescence quenching; Indocyanine; Nitro indocyanine; PCR pair; Time dependent DFT

Indexed keywords

DFT; FLUORESCENCE QUENCHING; INDOCYANINE; NITRO-INDOCYANINE; PCR PAIR; TIME-DEPENDENT DFT;

EID: 66049105891     PISSN: 01437208     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dyepig.2009.04.001     Document Type: Article
Times cited : (12)

References (49)
  • 1
    • 14744306436 scopus 로고
    • Simultaneous amplification and detection of specific DNA sequences
    • Higuchi R., Dollinger G., Walsh P.S., and Griffith R. Simultaneous amplification and detection of specific DNA sequences. Biotechnology 10 (1992) 413-417
    • (1992) Biotechnology , vol.10 , pp. 413-417
    • Higuchi, R.1    Dollinger, G.2    Walsh, P.S.3    Griffith, R.4
  • 2
    • 15744381713 scopus 로고
    • Kinetic PCR: real time monitoring of DNA amplification reactions
    • Higuchi R., Fockler C., Dollinger G., and Watson R. Kinetic PCR: real time monitoring of DNA amplification reactions. Biotechnology 11 (1993) 1026-1030
    • (1993) Biotechnology , vol.11 , pp. 1026-1030
    • Higuchi, R.1    Fockler, C.2    Dollinger, G.3    Watson, R.4
  • 4
    • 66049163844 scopus 로고    scopus 로고
    • Knobel R. Analytical method and instrument, WO2007071349, 2007.
    • Knobel R. Analytical method and instrument, WO2007071349, 2007.
  • 5
    • 49849099175 scopus 로고    scopus 로고
    • Mechanistic principles and applications of resonance energy transfer
    • Andrews D.L. Mechanistic principles and applications of resonance energy transfer. Canadian Journal of Chemistry 86 (2008) 855-870
    • (2008) Canadian Journal of Chemistry , vol.86 , pp. 855-870
    • Andrews, D.L.1
  • 6
    • 34250320825 scopus 로고    scopus 로고
    • Novel heptamethine cyanine dyes with large Stokes' shift for biological applications in the near infrared
    • Bertolino C.A., Caputo G., Barolo C., Viscardi G., and Coluccia S. Novel heptamethine cyanine dyes with large Stokes' shift for biological applications in the near infrared. Journal of Fluorescence 16 (2006) 221-225
    • (2006) Journal of Fluorescence , vol.16 , pp. 221-225
    • Bertolino, C.A.1    Caputo, G.2    Barolo, C.3    Viscardi, G.4    Coluccia, S.5
  • 9
    • 48249139029 scopus 로고    scopus 로고
    • The structure of cyanine5 terminally attached to double-stranded DNA: implications for FRET studies
    • Iqbal A., Wang L., Thompson K.C., Lilley D.M.J., and Norman D.G. The structure of cyanine5 terminally attached to double-stranded DNA: implications for FRET studies. Biochemistry 47 (2008) 7857-7862
    • (2008) Biochemistry , vol.47 , pp. 7857-7862
    • Iqbal, A.1    Wang, L.2    Thompson, K.C.3    Lilley, D.M.J.4    Norman, D.G.5
  • 11
    • 66049133978 scopus 로고    scopus 로고
    • Cyanine compounds and their application as quenching compounds. U.S. Pat. Appl. Publ
    • US 2005191643
    • Haugland R, Cheung C-Y, Yue S. Cyanine compounds and their application as quenching compounds. U.S. Pat. Appl. Publ.: US 2005191643, 2005.
    • (2005)
    • Haugland, R.1    Cheung, C.-Y.2    Yue, S.3
  • 12
    • 66049121226 scopus 로고    scopus 로고
    • Composition for optical film comprising a near-infrared absorbing dye and a quencher
    • Eur. Pat. Appl, EP 1496375
    • Miyako T, Moriwaki K. Composition for optical film comprising a near-infrared absorbing dye and a quencher. Eur. Pat. Appl.: EP 1496375, 2005.
    • (2005)
    • Miyako, T.1    Moriwaki, K.2
  • 14
    • 66049156860 scopus 로고    scopus 로고
    • Near IR-absorbing nonfluorescent cyanine dyes for probe labeling
    • PCT Int. Application: WO 2007005222
    • Peng XX, Xinshe D, Daniel R, Little GM, Chen J, Volcheck WM, Prescott, C. Near IR-absorbing nonfluorescent cyanine dyes for probe labeling. PCT Int. Application: WO 2007005222, 2007.
    • (2007)
    • Peng, X.X.1    Xinshe, D.2    Daniel, R.3    Little, G.M.4    Chen, J.5    Volcheck, W.M.6    Prescott, C.7
  • 15
    • 66049159999 scopus 로고    scopus 로고
    • Cyanine dyes and their applications as luminescence quenching compounds
    • US Patent Application: US 2006/0223076
    • Diwu Z, Zhang J, Tang, Y. Cyanine dyes and their applications as luminescence quenching compounds. US Patent Application: US 2006/0223076, 2006.
    • (2006)
    • Diwu, Z.1    Zhang, J.2    Tang, Y.3
  • 16
    • 66049147146 scopus 로고    scopus 로고
    • Nitro-substituted non-fluorescent asymmetric cyanine dye compounds
    • US Patent 7166715
    • Lee LG, Graham RJ, Mullah KB, Haxo FT. Nitro-substituted non-fluorescent asymmetric cyanine dye compounds. US Patent 7166715, 2005.
    • (2005)
    • Lee, L.G.1    Graham, R.J.2    Mullah, K.B.3    Haxo, F.T.4
  • 17
    • 66049103215 scopus 로고    scopus 로고
    • Della Ciana L, Grignani A, Cassullo M, Caputo G, Sulfobenz(e)indocyanine fluorescent dyes and their use. PCT Int. Appl. WO 9713810; 1997
    • Della Ciana L, Grignani A, Cassullo M, Caputo G, Sulfobenz(e)indocyanine fluorescent dyes and their use. PCT Int. Appl. WO 9713810; 1997.
  • 18
    • 0036835759 scopus 로고    scopus 로고
    • Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes
    • Marras S.A.E., Kramer F.R., and Tyagi S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acid Research 30 (2002) e122
    • (2002) Nucleic Acid Research , vol.30
    • Marras, S.A.E.1    Kramer, F.R.2    Tyagi, S.3
  • 20
    • 0030570285 scopus 로고    scopus 로고
    • Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory
    • Bauernshmitt R., and Ahlrichs R. Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory. Chemical Physics Letters 256 (1996) 454-464
    • (1996) Chemical Physics Letters , vol.256 , pp. 454-464
    • Bauernshmitt, R.1    Ahlrichs, R.2
  • 21
    • 0032533083 scopus 로고    scopus 로고
    • An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules
    • Stratmann R.E., Scuseria G.E., and Frisch M.J. An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules. Journal of Chemical Physics 109 (1998) 8218-8224
    • (1998) Journal of Chemical Physics , vol.109 , pp. 8218-8224
    • Stratmann, R.E.1    Scuseria, G.E.2    Frisch, M.J.3
  • 22
    • 31544460013 scopus 로고    scopus 로고
    • A theoretical study on the factors influencing cyanine photoisomerization: the case of thiacyanine in gas phase and in methanol
    • Improta R., and Santoro F. A theoretical study on the factors influencing cyanine photoisomerization: the case of thiacyanine in gas phase and in methanol. Journal of Chemical Theory and Computation 1 (2005) 215-229
    • (2005) Journal of Chemical Theory and Computation , vol.1 , pp. 215-229
    • Improta, R.1    Santoro, F.2
  • 23
    • 34247199000 scopus 로고    scopus 로고
    • Assessment of the efficiency of long-range corrected functionals for some properties of large compounds
    • Jacquemin D., Perpète E.A., Scalmani G., Frisch M.J., Kobayashi R., and Adamo C. Assessment of the efficiency of long-range corrected functionals for some properties of large compounds. Journal of Chemical Physics 126 (2007) 1441051-14410512
    • (2007) Journal of Chemical Physics , vol.126 , pp. 1441051-14410512
    • Jacquemin, D.1    Perpète, E.A.2    Scalmani, G.3    Frisch, M.J.4    Kobayashi, R.5    Adamo, C.6
  • 25
    • 33744991701 scopus 로고    scopus 로고
    • TDDFT investigation of the optical properties of cyanine dyes
    • Champagne B., Guillaume M., and Zutterman F. TDDFT investigation of the optical properties of cyanine dyes. Chemical Physics Letters 425 (2006) 105-109
    • (2006) Chemical Physics Letters , vol.425 , pp. 105-109
    • Champagne, B.1    Guillaume, M.2    Zutterman, F.3
  • 26
    • 34548501963 scopus 로고    scopus 로고
    • Time-dependent density functional theory investigation of the absorption and emission spectra of a cyanine dye
    • Guillaume M., Liégois V., Champagne B., and Zutterman F. Time-dependent density functional theory investigation of the absorption and emission spectra of a cyanine dye. Chemical Physics Letters 446 (2007) 165-169
    • (2007) Chemical Physics Letters , vol.446 , pp. 165-169
    • Guillaume, M.1    Liégois, V.2    Champagne, B.3    Zutterman, F.4
  • 28
    • 0037443885 scopus 로고    scopus 로고
    • Solvent influence on absorption and fluorescence spectra of merocyanine dyes: a theoretical and experimental study
    • Baraldi I., Brancolini G., Momicchioli F., Ponterini G., and Vanossi D. Solvent influence on absorption and fluorescence spectra of merocyanine dyes: a theoretical and experimental study. Chemical Physics 288 (2003) 309-325
    • (2003) Chemical Physics , vol.288 , pp. 309-325
    • Baraldi, I.1    Brancolini, G.2    Momicchioli, F.3    Ponterini, G.4    Vanossi, D.5
  • 30
    • 0000189651 scopus 로고
    • Density-functional thermochemistry. III. The role of exact exchange
    • Becke A.D. Density-functional thermochemistry. III. The role of exact exchange. Journal of Chemical Physics 98 (1993) 5648-5652
    • (1993) Journal of Chemical Physics , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 31
    • 0001475454 scopus 로고    scopus 로고
    • Toward reliable density functional methods without adjustable parameters: the PBE0 model
    • Adamo C., and Barone V. Toward reliable density functional methods without adjustable parameters: the PBE0 model. Journal of Chemical Physics 110 (1999) 6158
    • (1999) Journal of Chemical Physics , vol.110 , pp. 6158
    • Adamo, C.1    Barone, V.2
  • 32
    • 11744305193 scopus 로고
    • Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations
    • Wolinski K., Hilton J.F., and Pulay P. Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations. Journal of the American Chemical Society 112 (1990) 8251-8260
    • (1990) Journal of the American Chemical Society , vol.112 , pp. 8251-8260
    • Wolinski, K.1    Hilton, J.F.2    Pulay, P.3
  • 33
    • 0000197433 scopus 로고
    • Calculation of magnetic response properties using a continuous set of gauge transformations
    • Keith T.A., and Bader R.F.W. Calculation of magnetic response properties using a continuous set of gauge transformations. Chemical Physics Letters 210 (1993) 223-231
    • (1993) Chemical Physics Letters , vol.210 , pp. 223-231
    • Keith, T.A.1    Bader, R.F.W.2
  • 34
    • 84946893847 scopus 로고
    • Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects
    • Miertus S., Scrocco E., and Tomasi J. Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chemical Physics 55 (1981) 117
    • (1981) Chemical Physics , vol.55 , pp. 117
    • Miertus, S.1    Scrocco, E.2    Tomasi, J.3
  • 36
    • 66049157286 scopus 로고    scopus 로고
    • TURBOMOLE, Program package for ab initio electronic structure calculations, University of Karlsruhe, Germany, ver 5.71
    • TURBOMOLE, Program package for ab initio electronic structure calculations, University of Karlsruhe, Germany, ver 5.71.
  • 37
    • 0042208571 scopus 로고
    • The synthesis of nitro- and aminoindoles analogous to serotonin
    • Shaw E., and Woolley D.W. The synthesis of nitro- and aminoindoles analogous to serotonin. Journal of the American Chemical Society 75 (1953) 1877-1881
    • (1953) Journal of the American Chemical Society , vol.75 , pp. 1877-1881
    • Shaw, E.1    Woolley, D.W.2
  • 38
    • 0000734918 scopus 로고
    • Cyanine borate salts that form penetrated ion pairs in benzene solution: synthesis, properties, and structure
    • Murphy S., Yang X., and Schuster G.B. Cyanine borate salts that form penetrated ion pairs in benzene solution: synthesis, properties, and structure. Journal of Organic Chemistry 60 (1995) 2411-2422
    • (1995) Journal of Organic Chemistry , vol.60 , pp. 2411-2422
    • Murphy, S.1    Yang, X.2    Schuster, G.B.3
  • 39
    • 84980127075 scopus 로고
    • Preparation of organic iodides from the corresponding bromides and chlorides
    • Finkelstein H. Preparation of organic iodides from the corresponding bromides and chlorides. Berichte der Deutschen Chemischen Gesellschaft 43 (1910) 1528-1532
    • (1910) Berichte der Deutschen Chemischen Gesellschaft , vol.43 , pp. 1528-1532
    • Finkelstein, H.1
  • 40
    • 66049092906 scopus 로고    scopus 로고
    • Jelinek CF, Kleinschmidt RF. Preparation of malonaldehyde dianils. US 2549097 19510417; 1951
    • Jelinek CF, Kleinschmidt RF. Preparation of malonaldehyde dianils. US 2549097 19510417; 1951.
  • 41
    • 66049107050 scopus 로고    scopus 로고
    • New fluorescent cyanine labels containing a sulfonamido linker arm. Eur
    • Pat Appl. EP 1065250;
    • Caputo G, Della Ciana L. New fluorescent cyanine labels containing a sulfonamido linker arm. Eur Pat Appl. EP 1065250; 2001;
    • (2001)
    • Caputo, G.1    Della Ciana, L.2
  • 42
    • 66049143288 scopus 로고    scopus 로고
    • Cyanine-type compounds having an alkynyl linker arm
    • WO 2005014723, 2005
    • Caputo G. Cyanine-type compounds having an alkynyl linker arm. PCT Int Appl (2005) WO 2005014723, 2005
    • (2005) PCT Int Appl
    • Caputo, G.1
  • 43
    • 66049133564 scopus 로고    scopus 로고
    • Improved process and method for the preparation of asymmetric monofunctionalized indocyanine labelling reagents and obtained compounds,
    • Patent Application EP1209205A1
    • Caputo G, Della Ciana L, Improved process and method for the preparation of asymmetric monofunctionalized indocyanine labelling reagents and obtained compounds, Patent Application EP1209205A1, 2002.
    • (2002)
    • Caputo, G.1    Della Ciana, L.2
  • 44
    • 0007243914 scopus 로고
    • Merocyanine dyes, derivatives of rhodanine. V. Some tetra- and hexamethinemerocyanines, derivatives of 3-ethylrhodanine
    • Deichmeister M.V., Levkoev I.I., and Lifshits E.B. Merocyanine dyes, derivatives of rhodanine. V. Some tetra- and hexamethinemerocyanines, derivatives of 3-ethylrhodanine. Zhurnal Obshchei Khimii 23 (1953) 1529-1535
    • (1953) Zhurnal Obshchei Khimii , vol.23 , pp. 1529-1535
    • Deichmeister, M.V.1    Levkoev, I.I.2    Lifshits, E.B.3
  • 46
    • 0242593999 scopus 로고    scopus 로고
    • Dynamics of radiationless transitions in large molecular systems: a Franck-Condon-based method accounting for displacements and rotations of all normal coordinates
    • Borrelli R., and Peluso A. Dynamics of radiationless transitions in large molecular systems: a Franck-Condon-based method accounting for displacements and rotations of all normal coordinates. Journal of Chemical Physics 119 (2003) 8437-8448
    • (2003) Journal of Chemical Physics , vol.119 , pp. 8437-8448
    • Borrelli, R.1    Peluso, A.2
  • 47
    • 12344331148 scopus 로고    scopus 로고
    • Reliable NMR chemical shifts for molecules of biological interest in condensed phases by methods rooted in the density functional theory
    • Benzi C., Crescenzi O., Pavone M., and Barone V. Reliable NMR chemical shifts for molecules of biological interest in condensed phases by methods rooted in the density functional theory. Magnetic Resonance in Chemistry 42 (2004) S57-S67
    • (2004) Magnetic Resonance in Chemistry , vol.42
    • Benzi, C.1    Crescenzi, O.2    Pavone, M.3    Barone, V.4
  • 48
    • 0030820621 scopus 로고    scopus 로고
    • Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes
    • Randolph J.B., and Waggoner A.S. Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes. Nucleic Acids Research 25 (1997) 2923-2929
    • (1997) Nucleic Acids Research , vol.25 , pp. 2923-2929
    • Randolph, J.B.1    Waggoner, A.S.2
  • 49
    • 0018278640 scopus 로고
    • Surface density determination in membranes by fluorescence energy transfer
    • Fung B.K.K., and Stryer L. Surface density determination in membranes by fluorescence energy transfer. Biochemistry 17 (1978) 5241-5248
    • (1978) Biochemistry , vol.17 , pp. 5241-5248
    • Fung, B.K.K.1    Stryer, L.2


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