title: NMR solution structure of a DNA-actinomycin D complex containing a non-hydrogen-bonding pair in the binding site.
abstract: The solution structures of two different DNA duplexes (one containing a G-T mismatched base pair and the other a non-hydrogen-bonding G-F pair, where F is difluorotoluene) in complex with the peptide antibiotic actinomycin D (ActD) are presented. Using (1)H, (19)F NMR, and molecular dynamics simulations, we show that there are three major differences between the complexes: (1) ActD binds to the GF duplex in an orientation that is flipped 180° relative to its position in the GT duplex; (2) whereas the difluorotoluene moiety takes the typical anti glycosidic conformation in the "free" (uncomplexed) GF duplex, it takes the syn conformation in the GF:ActD complex; and (3) in GF:ActD, the difluorotoluene moiety is completely unstacked in the helix; however, the guanine of the G-F pair is stacked quite well with the ActD intercalator and the flanking base on the 5' side. In GT:ActD, the G-T base pair (although pushed into the major groove from the non-Watson-Crick hydrogen-bonding pattern) stacks favorably with the ActD intercalator and the flanking base pair on the 5' side. The results described here indicate that a sequence-specific DNA binding ligand such as actinomycin D will, indeed, recognize and bind with high affinity to a DNA incorporating a non-natural, non-hydrogen-bonding nucleoside mimic despite the presentation of modified functionality in the binding site.
authors.affiliation: Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, USA.
authors.forename: Shannen L
authors.initials: SL
authors.lastname: Cravens
authors.forename: Alyssa C
authors.initials: AC
authors.lastname: Navapanich
authors.forename: Bernhard H
authors.initials: BH
authors.lastname: Geierstanger
authors.forename: Deborah C
authors.initials: DC
authors.lastname: Tahmassebi
authors.forename: Tammy J
authors.initials: TJ
authors.lastname: Dwyer
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism*; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D003609:Dactinomycin / Q000737:chemistry / Q000378:metabolism*; D006860:Hydrogen Bonding; D007364:Intercalating Agents / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation
chemical_list: D000900:Anti-Bacterial Agents; D007364:Intercalating Agents; D003609:Dactinomycin; D004247:DNA