Article

Spectroscopic study on the binding of a cationic porphyrin to DNA G-quadruplex under different K+ concentrations.

School of Life Science and Technology, Beijing Institute of Technology, Beijing, 100081, China.
Photochemical and Photobiological Sciences (impact factor: 2.58). 09/2008; 7(8):948-55. DOI:10.1039/b809322a pp.948-55
Source: PubMed

ABSTRACT We have performed systematic spectroscopic titrations to characterize the binding reaction of cationic meso-tetrakis(4-(N-methylpyridiumyl))porphyrin (TMPyP4) with the G-quadruplex (G4) of human telomeric single-strand oligonucleotide d[TAGGG(TTAGGG)3T] (S24), for which special effort was made to examine the TMPyP4-G4 binding stoichiometry, the binding modes, and the conformational conversion of the G4 structure under different potassium ion (K+) concentration. It is found that, in the presence of 0, 10 mM, and 100 mM K+, TMPyP4 forms a complex with the anti-parallel G4 in a TMPyP4-to-G4 molar ratio of 5, 5 and 3, respectively, and the increase of K+ concentration would reduce the binding affinity of TMPyP4 to G4. For the TMPyP4-G4 complex, the end-stacking mode and groove binding mode were presumed mainly by the results of time-resolved fluorescence spectroscopy in the three cases. Most importantly, it is found that TMPyP4 can directly induce the formation of the anti-parallel G4 structure from the single-strand oligonucleotide S24 in the absence of K+, and that it can preferentially induce the conformational conversion of the G4 structure from the hybrid-type to the anti-parallel one in the presence of K+.

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Keywords

anti-parallel
 
anti-parallel G4
 
anti-parallel G4 structure
 
binding reaction
 
cationic meso-tetrakis(4-(N-methylpyridiumyl))porphyrin
 
conformational conversion
 
different potassium ion
 
G-quadruplex
 
G4 structure
 
human telomeric single-strand oligonucleotide d[TAGGG(TTAGGG)3T]
 
K+ concentration
 
single-strand oligonucleotide S24
 
special effort
 
systematic spectroscopic titrations
 
three cases
 
time-resolved fluorescence spectroscopy
 
TMPyP4-G4 binding stoichiometry
 
TMPyP4-G4 complex
 
TMPyP4-to-G4 molar ratio