Diverse modes of 5'-[4-(aminoiminomethyl)phenyl]-[2,2'-bifuran]-5-carboximidamide (DB832) interaction with multi-stranded DNA structures.
The modes of binding of 5'-[4-(aminoiminomethyl)phenyl]-[2,2'-Bifuran]-5-carboximidamide (DB832) to multi-stranded DNAs: human telomere quadruplex, monomolecular R-triplex, pyr/pur/pyr triplex consisting of 12 T*(T x A) triplets, and DNA double helical hairpin were studied. The optical adsorption of the ligand was used for monitoring the binding and for determination of the association constants and the numbers of binding sites. CD spectra of DB832 complexes with the oligonucleotides and the data on the energy transfer from DNA bases to the bound DB832 assisted in elucidating the binding modes. The affinity of DB832 to the studied multi-stranded DNAs was found to be greater (K(ass) approximately 10(7)M(-1)) than to the duplex DNA (K(ass) approximately 2 x 10(5)M(-1)). A considerable stabilizing effect of DB832 binding on R-triplex conformation was detected. The nature of the ligand tight binding differed for the studied multi-stranded DNA depending on their specific conformational features: recombination-type R-triplex demonstrated the highest affinity for DB832 groove binding, while pyr/pur/pyr TTA triplex favored DB832 intercalation at the end stacking contacts and the human telomere quadruplex d[AG(3)(T(2)AG(3))(3)] accommodated the ligand in a capping mode. Additionally, the pyr/pur/pyr TTA triplex and d[AG(3)(T(2)AG(3))(3)] quadruplex bound DB832 into their grooves, though with a markedly lesser affinity. DB832 may be useful for discrimination of the multi-sranded DNA conformations and for R-triplex stabilization.
Kaluzhny
Dmitry N
DN
Engelhardt Institute of Molecular Biology RASc, Moscow 119991, Russia.
Borisova
Olga F
OF
Shchyolkina
Anna K
AK
D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D005663:Furans / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008024:Ligands; D008969:Molecular Sequence Data; D016615:Telomere / Q000737:chemistry / Q000378:metabolism
C547691:5'-(4-(aminoiminomethyl)phenyl)-(2,2'-bifuran)-5-carboximidamide; D005663:Furans; D008024:Ligands; D004247:DNA