NMR Study of DNA Duplexes Complexed with Actinomycin D: Minimized Average Structures

Nuclear magnetic resonance (NMR) data on the three-dimensional structure of self-complementary DNA octamers complexed with the anticancer drug actinomycin D. The dataset, from a study by Chenyang Lian at the University of Illinois Urbana-Champaign, contains minimized average structures derived from NOE-restrained refinement. The analysis reveals how drug binding affinity and structural perturbations, such as kinks and methyl group interactions, are influenced by flanking DNA sequences.

Use Cases

• Modeling the structural basis of actinomycin D's sequence preference based on described interactions at GpC, ApG, and TpG steps.
• Training machine learning models to predict drug-induced DNA kinks from sequence context, as described for the -(AGCT)2- complex.
• Analyzing how mismatched base pairs, like the T:T pair in d(GATGCTTC)2, influence drug binding stability as mentioned in the description.
• Benchmarking molecular dynamics simulations against high-resolution structural information for -XGCY- tetranucleotide motifs.

Strengths

• Data is derived from NOE-restrained refinement, a high-resolution structural biology technique.
• Analysis includes specific, named DNA sequences (d(GAAGCTTC)2, d(GATGCTTC)2, d(GAAGCATC)2) with described binding outcomes.
• Provides structural insights into sequence-dependent drug binding, a key factor in anticancer drug design.

Limitations

• Row count and dataset size are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

University of Illinois Urbana-Champaign

Collection Method

NOE-restrained refinement of NMR data