TATA box DNA deformation with and without the TATA box-binding protein

Area of Science:

• Molecular Biology
• Biophysics
• Structural Biology

Background:

• The TATA box is a crucial DNA sequence in eukaryotic promoters, recognized by the TATA box-binding protein (TBP).
• Understanding the structural dynamics of TATA box DNA and its interaction with TBP is essential for deciphering transcription regulation.

Purpose of the Study:

• To investigate the intrinsic bending and flexibility of TATA box DNA.
• To determine how TATA box-binding protein (TBP) binding affects DNA structure.
• To explore the relationship between DNA structure, TBP recognition, and transcription regulation.

Main Methods:

• Utilized DNA ring closure kinetics to measure cyclization factors (J factors) for various DNA constructs.
• Assessed cyclization kinetics with and without TBP for wild-type and mutant TATA box DNA sequences.
• Analyzed TBP-DNA complexes to observe TBP-induced topoisomers, distinguishing unwinding from writhe.

Main Results:

• TATA box DNA exhibits significant intrinsic bending and anisotropic flexibility, opposing the bend induced by TBP.
• A mutant TACA box DNA sequence showed substantially reduced bending and flexibility compared to the wild-type TATA box.
• TBP binding induced dramatic DNA bending and unwinding, consistent with crystal structures, and generated unique topoisomers.

Conclusions:

• Intrinsic DNA bending and flexibility of the TATA box influence TBP recognition and may repress transcription in the absence of TBP.
• The TBP-DNA complex geometry is consistent with structural data, with TBP inducing significant DNA conformational changes.
• The minicircle approach can differentiate TBP-induced unwinding from writhe, suggesting supercoiling in small DNA domains controls TBP binding.