title: [Effect of DNA local conformation on the affinity and binding specificity of bis-netropsins to DNA].
abstract: The interaction of short nucleotide duplexes with bis-netropsins, in which netropsin fragments are linked in the tail-to-tail orientation via cis-diammineplatinum group (<--Nt-Pt(NH3)-Nt-->) or aliphatic pentamethylene chain (<--Nt-(CH2)5-Nt-->), has been studied. Both the bis-netropsins have been shown to bind to DNA oligomer 5'-CCTATATCC-3' (I) as a hairpin with parallel orientation of netropsin fragments in 1:1 stoichiometry. Monodentate binding has been detected upon binding of bis-netropsins to other duplexes of sequences 5'-CCXCC-3'--where X = TTATT (II), TTAAT (III), TTTTT (IV), and AATTT (V)--along with the binding of bis-netropsins as a hairpin. The formation of dimeric antiparallel motif between the halves of two bound bis-netropsin molecules has been observed in the complexes of <--Nt-(CH2)5-Nt--> with DNA oligomers IV and V. The ratio of binding constant of bis-netropsin as a hairpin (K2) to monodentate binding constant (K1) has been shown to correlate with the width and/or conformational lability of DNA in the binding site. The share of bis-netropsin bound as a hairpin decreases in the order: TATAT > TTATT > TTAAT > TTTTT > AATTT, whereas the contribution of monodentate binding rises. The minimal strong binding site for <--Nt-Pt(NH3)-Nt--> and <--Nt-(CH2)5-Nt--> binding as a hairpin has been found to be DNA duplex 5'-CGTATACG-3'.
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia. annasur@eimb.ru
authors.forename: A N
authors.initials: AN
authors.lastname: Surovaia
authors.forename: S L
authors.initials: SL
authors.lastname: Grokhovskiĭ
authors.forename: G
authors.initials: G
authors.lastname: Burkhardt
authors.forename: H
authors.initials: H
authors.lastname: Fritzsche
authors.forename: C
authors.initials: C
authors.lastname: Zimmer
authors.forename: G V
authors.initials: GV
authors.lastname: Gurskiĭ
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D020180:Heteroduplex Analysis; D009429:Netropsin / Q000737:chemistry / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D016385:TATA Box
chemical_list: D000900:Anti-Bacterial Agents; D009429:Netropsin; D004247:DNA