In Vitro DNA Binding Analysis of Bacillus subtilis DnaA at Single Nucleotide Resolution

269 binding regions for the bacterial replication initiator DnaA were identified using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). The dataset, produced by Janet L. Smith at MIT, provides single nucleotide resolution binding data for ATP-DnaA and ADP-DnaA, refining the consensus sequence of the DnaA binding site. It serves as a backdrop for interpreting in vivo binding and regulation of DnaA.

Use Cases

• Identifying DnaA binding motifs based on the refined consensus sequence mentioned in the description.
• Comparing relative binding affinities for ATP-DnaA versus ADP-DnaA across genomic regions.
• Benchmarking in vivo DNA binding experiments against the in vitro binding backdrop provided by this dataset.
• Developing models for cooperative DNA binding based on the identified 269 binding regions.

Strengths

• Data was generated at single nucleotide resolution using IDAP-Seq.
• Identifies 269 specific DnaA binding regions in the Bacillus subtilis genome.
• Compares binding affinities for two nucleotide states of the protein (ATP-DnaA and ADP-DnaA).

Limitations

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

Provenance

Source

Massachusetts Institute of Technology

Collection Method

In vitro DNA affinity purification and deep sequencing (IDAP-Seq) on Bacillus subtilis genomic DNA.