A new fluorescent deoxycytidine analog, 10-(2-deoxy-beta -D-ribofuranosyl)-pyrimido[4',5' :4,5]-pyrimido[1,6-a]indole-6,9(7H)-dione (dC(PPI)) was synthesized. Its fluorescent properties were studied in detail. It was found that this fluorescent nucleoside dC(PPI) could be used as a fluorescent label for DNA probes with minimal disturbance of their overall structure.
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Fluorescence properties of pyrimidopyrimidoindole nucleoside dC(PPI) incorporated into oligodeoxynucleotides.
J Phys Chem B
July 2009
Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
A series of oligodeoxynucleotides labeled by a pyrimidopyrimidoindole deoxynucleoside (1a: dC(PPI)) and its derivatives 2a and 3a substituted with electron-donating and -withdrawing groups, respectively, were synthesized according to the phosphoramidite approach. The photophysical properties and quenching efficiencies of oligonucleotides incorporating dC(PPI) derivatives were studied in detail. The thermal denaturation experiments and molecular dynamics simulation of DNA duplexes incorporating dC(PPI) suggested that a modified base of dC(PPI) could form base pairs with guanine and adenine in canonical Watson-Crick and reverse-wobble geometries, respectively.
View Article and Find Full Text PDFA pyrimidopyrimidoindole nucleoside (dC PPI): photophysical properties and thermal stability of the modified DNA duplexes.
Nucleosides Nucleotides Nucleic Acids
March 2008
CREST, Japan Science and Technology Agency, Yokohama, Japan.
A new fluorescent deoxycytidine analog, 10-(2-deoxy-beta -D-ribofuranosyl)-pyrimido[4',5' :4,5]-pyrimido[1,6-a]indole-6,9(7H)-dione (dC(PPI)) was synthesized. Its fluorescent properties were studied in detail. It was found that this fluorescent nucleoside dC(PPI) could be used as a fluorescent label for DNA probes with minimal disturbance of their overall structure.
View Article and Find Full Text PDFFluorescent pyrimidopyrimidoindole nucleosides: control of photophysical characterizations by substituent effects.
J Org Chem
July 2007
Department of Life Science, Frontier Collaborative Research Center, Tokyo Institute of Technology, and CREST of JST, 4259 Nagatsuta, Midori-ku Yokohama, Japan.
10-(2-Deoxy-beta-D-ribofuranosyl)pyrimido[4',5':4,5]pyrimido[1,6-a]indole-6,9(7H)-dione (dCPPI) and its derivatives were synthesized via the Suzuki-Miyaura coupling reaction of 5-iododeoxycytidine with 5-substituted N-Boc-indole-2-borates and characterized by UV-vis and fluorescence spectroscopy. The new fluorescent nucleosides showed rather large Stokes shifts (116-139 nm) in an aqueous buffer. The fluorescent intensities were dependent on the nature of the substituents on the indole rings.
View Article and Find Full Text PDFSynthesis of fluorescent cyclic cytosine nucleosides and their fluorescent properties upon incorporation into oligonucleotides.
Nucleic Acids Symp Ser (Oxf)
August 2007
Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
We report here the synthesis and spectroscopic characterization of a new fluorescent pyrimidopyrimidoindole nucleoside derivative (dC(PPI)) modified at the cytosine base. The photophysical properties of dC(PPI) were examined by fluorescent spectroscopy and quantum chemical calculations. It was found that dC(PPI)-labeled oligonucleotides gave almost the same thermal stability as that of the corresponding unmodified sequences.
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