Proton NMR studies of [N-MeCys3,N-MeCys7]TANDEM binding to DNA oligonucleotides: sequence-specific binding at the TpA site.
[N-MeCys3,N-MeCys7]TANDEM, an undermethylated analogue of Triostin A, contains two N-methyl groups on the cysteine residues only. Footprinting results showed that [N-MeCys3,N-MeCys7]TANDEM binds strongly to DNA rich in A.T residues [Low, C. M. L., Fox, K. R., Olsen, R. K., & Waring, M. J. (1986) Nucleic Acids Res. 14, 2015-2033]. However, it was not known whether specific binding of [N-MeCys3,N-MeCys7]TANDEM requires a TpA step or an ApT step. In 1:1 saturated complexes with the octamers [d(GGATATCC)]2 and [d(GGTTAACC)]2, [N-MeCys3,N-MeCys7]TANDEM binds to each octamer as a bis-intercalator bracketing the TpA step. The octadepsipeptide ring binds in the minor groove of the DNA. Analysis of sugar coupling constants from the phase-sensitive COSY data indicates that the sugar of the thymine in the TpA binding site adopts predominantly an N-type sugar conformation, while the remaining sugars on the DNA adopt an S-type conformation, as has been observed in other Triostin A and echinomycin complexes. The drug does not bind to the octamer [d(GGAATTCC)]2 as a bis-intercalator. Only weak nonintercalative binding is observed to this DNA octamer. These results show unambiguously that [N-MeCys3,N-MeCys7]TANDEM binds sequence specifically at TpA sites in DNA. The factors underlying the sequence specificity of [N-MeCys3,N-MeCys7]TANDEM binding to DNA are discussed.
Addess
K J
KJ
Department of Chemistry and Biochemistry, University of California, Los Angeles 90024.
Gilbert
D E
DE
Olsen
R K
RK
Feigon
J
J
D000227:Adenine Nucleotides / Q000737:chemistry; D000900:Anti-Bacterial Agents / Q000138:chemical synthesis / Q000378:metabolism*; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D003855:Deoxyribose / Q000737:chemistry; D007364:Intercalating Agents / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008745:Methylation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry* / Q000235:genetics; D011810:Quinoxalines / Q000138:chemical synthesis / Q000737:chemistry; D013942:Thymine Nucleotides / Q000737:chemistry; D014961:X-Ray Diffraction
D000227:Adenine Nucleotides; D000900:Anti-Bacterial Agents; D007364:Intercalating Agents; D009841:Oligonucleotides; D011810:Quinoxalines; D013942:Thymine Nucleotides; D003855:Deoxyribose; C017738:TANDEM (quinoxaline); D004247:DNA