title: Actinomycin D binds strongly and dissociates slowly at the dGpdC site with flanking T/T mismatches.
abstract: Comparative electrophoretic, thermal denaturation, and spectroscopic studies with dodecamers of the form d(ATTA-XGCX-TAAT) and their self-complementary counterparts suggest that actinomycin D (ACTD) binds strongly to a 5'GC3' site with flanking T/T mismatches and moderately to that with C/C mismatches but weakly to those with other G/G or A/A mismatches. The relative binding order is found to be T/T > C/C > G/G > A/A. The ACTD binding affinity for the GC site with T/T mismatches is comparable to the strong binding of self-complementary-XGCY-sequences. Both the ACTD association and dissociation kinetics at the GC site with flanking T/T mismatches require two-exponential fits. The slow component of the association rates is slower than those of the self-complementary sequences, whereas that of the dissociation is only slightly faster than that of the -TGCA- sequence. Interestingly, the slow component of dissociation is decidedly slower than those of -AGCT- and -CGCG- sites and is more than an order of magnitude slower than those with C/C, G/G, and A/A mismatches. These kinetic results are further corroborated by fluorescence measurements using 7-amino-ACTD, a fluorescent analog of ACTD. In addition, fluorescence and absorbance spectral characteristics indicate that the binding mode at the GC site with flanking T/T mismatches resembles those of strong-binding self-complementary -XGCY- sites which are known to be intercalative in nature. The observed slow ACTD dissociation at the T/T-mismatched site suggests that the minor-groove environment near the T/T-mismatched pairs provides favorable interactions with the pentapeptide rings of the drug, whereas the others, especially those of bulkier purine/purine mismatches, result in less favorable interactions.
authors.affiliation: Department of Chemistry, Tennessee State University, Nashville 37209-1561, USA.
authors.forename: C
authors.initials: C
authors.lastname: Liu
authors.forename: F M
authors.initials: FM
authors.lastname: Chen
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D002942:Circular Dichroism; D003609:Dactinomycin / Q000737:chemistry*; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013941:Thymine
chemical_list: D009838:Oligodeoxyribonucleotides; D003609:Dactinomycin; D013941:Thymine