Multiple non-B-DNA conformations of polypurine.polypyrimidine sequences in plasmids

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• Polypurine.polypyrimidine (Pur.Pyr) sequences are known to form non-B-DNA structures.
• The conformational flexibility of these sequences is influenced by environmental conditions.
• Understanding these alternative DNA structures is crucial for comprehending DNA function and regulation.

Purpose of the Study:

• To investigate the multiple non-B-DNA conformations adopted by Pur.Pyr sequences with central interruptions in plasmids.
• To elucidate the influence of pH, supercoiling, and sequence variations on DNA structure.
• To describe novel folded DNA geometries arising from these sequences.

Main Methods:

• Utilized specific chemical probes (OsO4, diethyl pyrocarbonate, dimethyl sulfate) to detect DNA conformations.
• Employed two-dimensional gel electrophoresis to analyze DNA structures.
• Cloned and studied a family of related Pur.Pyr sequences with varying characteristics.

Main Results:

• Mirror repeat Pur.Pyr sequences formed single intramolecular triplexes at pH 7.0-6.0.
• Lowering pH and increasing supercoiling induced novel conformational changes in mirror repeat sequences.
• Non-mirror repeat sequences and sequences with longer interruptions exhibited distinct non-B-DNA conformations and structural behaviors.

Conclusions:

• Pur.Pyr sequences with central interruptions display remarkable conformational plasticity in plasmids.
• DNA structural transitions are sensitive to pH, supercoiling, and sequence composition.
• Novel folded DNA geometries are proposed to explain the observed structural diversity.