The design of a novel, fluorescence acceptor for use in real time polymerase chain reaction analysis was carried out with the help of in-depth computational analysis of structure/property relationships. A functionalized indocyanine dye was synthesized in order to quench a fluorescent cyanine dye. The pentamethine indocyanine dye was functionalized with nitro groups so as to enhance its quenching abilities; ad hoc substituents were used to enable conjugation with DNA strands. The visible absorption and photoemission of the indocyanine dye as well as that of an unsubstituted indodicarbocyanine dye, employed as a reference model chromogenic system, were addressed both theoretically and experimentally. A Forster resonance energy transfer analysis was simulated experimentally to evaluate the quenching efficiency of the donor/acceptor couple.

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

BENZI, Caterina;BERTOLINO, Chiara Alessandra;MILETTO, IVANA;BAROLO, CLAUDIA;VISCARDI, Guido;COLUCCIA, Salvatore;CAPUTO, Giuseppe
2009

Abstract

The design of a novel, fluorescence acceptor for use in real time polymerase chain reaction analysis was carried out with the help of in-depth computational analysis of structure/property relationships. A functionalized indocyanine dye was synthesized in order to quench a fluorescent cyanine dye. The pentamethine indocyanine dye was functionalized with nitro groups so as to enhance its quenching abilities; ad hoc substituents were used to enable conjugation with DNA strands. The visible absorption and photoemission of the indocyanine dye as well as that of an unsubstituted indodicarbocyanine dye, employed as a reference model chromogenic system, were addressed both theoretically and experimentally. A Forster resonance energy transfer analysis was simulated experimentally to evaluate the quenching efficiency of the donor/acceptor couple.
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http://www.journals.elsevier.com/dyes-and-pigments
Indocyanine; DFT; Time-dependent DFT; Fluorescence quenching; PCR pair; Nitro-indocyanine
Benzi C.; Bertolino C.A.; Miletto I.; Ponzio P.; Barolo C.; Viscardi G.; Coluccia S.; Caputo G.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2318/73985
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