DNA Topology and Its Importance

Introduction

• Double-stranded DNA: Forms a double helix structure.
• DNA topology: Involves the twisting and turning of the double helix into different conformations.
• Significance: Understanding DNA shape changes is crucial for cellular functions.

Key Concepts

DNA Structure

• Relaxed DNA structure: 10.4 base pairs per turn of the helix.
• Twist and Writhe:
  • Twist: Number of helical turns of one strand around the other.
  • Writhe: Describes how the double helix crosses over itself, can be positive or negative.
  • Linking number: Sum of twist and writhe.

DNA Conformations

• Circular DNA: Topologically constrained, linking number changes require strand breaking.
• Overwound DNA:
  • Fewer than 10.4 base pairs per turn.
  • Positively supercoiled, higher linking number.
  • Strands are difficult to separate.
• Underwound DNA:
  • Greater than 10.4 base pairs per turn.
  • Negatively supercoiled, lower linking number.
  • Strands separate more easily.

Enzymes Modifying DNA Topology

Topoisomerases

• Function: Restore DNA to a relaxed state by altering linking number.
• Types:
  • Type I Topoisomerase:
    • Breaks one DNA strand, changes linking number by 1.
    • Does not require additional energy.
  • Type II Topoisomerase:
    • Breaks both strands, changes linking number by 2.
    • Requires energy (ATP or NADH).

Special Topoisomerases

• Gyrase: Type II enzyme in bacteria, negatively supercoils DNA.
• Reverse Gyrase: In thermophiles, positively supercoils DNA to stabilize under high temperatures.

Biological Importance

Thermophiles

• Positive supercoiling: Adds twists to stabilize DNA at high temperatures.

Most Organisms

• Negative supercoiling:
  • Stores free energy.
  • Aids in processes requiring strand separation, such as replication and transcription.
  • Facilitates strand separation without introducing strain.

Conclusion

• DNA topology: Extends beyond basic structure, critical for cellular processes.
• Understanding enzyme roles: Essential for modeling and manipulating DNA conformations.
• Practical applications: Efficient replication and transcription via controlled topology.