B-DNA Structure and Supercoiling Overview

B-DNA Structure and Dimensions

• B-DNA double helix has a diameter of approximately 20 Å (angstroms).
• The distance between the 1’ carbons of opposite strands is around 11 Å, but the larger diameter is due to the presence of deoxyribose and phosphate groups.
• The helix has an additional width due to its structural characteristics, resulting in a "hole" in the center.

DNA Supercoiling Overview

• DNA can be likened to a coiled string and can undergo supercoiling when twisted either over or under its natural helical turns.
• Supercoiling can be demonstrated with a phone cord, illustrating how coiling can transition into supercoiling.

Types of Supercoiling

• Positive supercoiling occurs when DNA is overwound in the same direction as the helical turns, resulting in increased tightness of the coil.
• Negative supercoiling occurs when DNA is underwound in the opposite direction to the helical turns, resulting in a loosening effect.

Characteristics of Circular DNA and Supercoiling

• Circular relaxed DNA manifests no supercoiling, featuring one helical turn per 10.5 base pairs (bp).
• Overwound circular DNA leads to positive supercoiling, while underwound circular DNA results in negative supercoiling.
• Supercoiling is contingent upon the integrity of both DNA strands; any breaks can lead to uncoiling instead of supercoiling.

Linear vs. Circular Chromosomes

• Bacteria and Archaea typically possess supercoiled circular chromosomes.
• Eukaryotic genomes are composed of linear DNA chromosomes, which can form supercoils between anchored points.
• Linear DNA can become relaxed or supercoiled based on twisting conditions around its constrained anchors.

Linking Number and Supercoil Calculation

• Linking number (Lk) indicates how many times one DNA strand winds around another.
• The relaxed linking number (Lko) for relaxed DNA is calculated by dividing the total number of base pairs by 10.5.
• Supercoils (S) are determined by S = Lk - Lko; a negative S indicates the presence of positive supercoils, while a positive S indicates negative supercoils.

Typical Cellular DNA State

• In most cells, DNA is naturally negatively supercoiled, enhancing strand separation and facilitating DNA replication and transcription processes.
• Negatively supercoiled DNA exhibits a tendency to accommodate structural strain, either through supercoiling or strand separation.

Supercoiling during Replication and Transcription

• DNA strand separation during replication creates tension, leading to overwinding and the formation of positive supercoils in front of the separation fork.
• Conversely, negative supercoils form behind the moving fork, resulting from underwinding.
• The supercoiling dynamics are essential for efficient DNA replication and transcription, as they help relieve tension in the DNA strands.