[Effect of DNA local conformation on the affinity and binding specificity of bis-netropsins to DNA].
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'.
Surovaia
A N
AN
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia. annasur@eimb.ru
Grokhovskiĭ
S L
SL
Burkhardt
G
G
Fritzsche
H
H
Zimmer
C
C
Gurskiĭ
G V
GV
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
D000900:Anti-Bacterial Agents; D009429:Netropsin; D004247:DNA