Open AccessFluorescence Properties of Pyrimidopyrimidoindole Nucleoside dCPPI Incorporated into Oligodeoxynucleotides
Author(s) -
Masahiro Mizuta,
Kohji Seio,
Akihiro Ohkubo,
Mitsuo Sekine
Publication year - 2009
Publication title -
the journal of physical chemistry. b
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.864
H-Index - 392
eISSN - 1520-6106
pISSN - 1520-5207
DOI - 10.1021/jp807562c
Subject(s) - guanine , oligonucleotide , phosphoramidite , chemistry , fluorescence , quenching (fluorescence) , nucleoside , cytosine , dna , base pair , photochemistry , stereochemistry , combinatorial chemistry , nucleotide , biochemistry , physics , quantum mechanics , gene
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. The fluorescence of oligonucleotides incorporating dC(PPI) derivatives increased upon binding to the counter strands, except when dC(PPI) and guanine formed a base pair. It was revealed that dGMP quenched the fluorescence of the cyano derivative 3a most effectively, whereas it affected that of the methoxy derivative 2a least effectively. The involvement of the electron transfer from guanine to the dC(PPI) derivatives in the fluorescence quenching was supported by energy considerations.