Rolling circle replication

In E. coli, the parental DNA strand remains circular.
- This is true for many, but not all, circular DNA.
During replication, the circular DNA molecules exhibit a theta-like (θ) shape due to replicating bubbles initiating at the origin (ori).
As the two DNA strands untwist, positive supercoils form elsewhere in the molecule.

Supercoiling refers to the coiling of a coil.
- DNA is naturally coiled in the form of a double helix.
- Further coiling of this axis produces DNA supercoiling, which is a manifestation of structural strain.
When there is no net bending of the DNA axis, it is called a relaxed state.

Supercoiling occurs through the winding and twisting of the DNA around itself.
- Overtwisting leads to positive supercoiling.
- Undertwisting results in negative supercoiling.
If DNA is circular, or its ends are rigidly held (forming a loop), over twirling or under twirling can lead to supercoiling.

During processes like replication and transcription, DNA strands must separate.
Twisting reduces the twist number, creating tension which leads to writhe formation.
Enzymes like topoisomerase relieve the stress and reduce the linking number to ease supercoiling.

DNA topoisomerase regulates supercoiling by catalyzing the winding and unwinding of DNA strands.
They make incisions that break the DNA backbone, allowing DNA strands to pass through each other, swiveling, and resealing the breaks.
Two groups:
- Class I DNA Topoisomerase: Breaks one strand of the DNA helix; ATP independent; rotates the broken strand around the intact strand.
- Class II DNA Topoisomerase: Breaks two strands of DNA helix; ATP dependent; passes an intact helix through the gap made by the broken helix.

Essential for packaging DNA within cells as DNA length can be thousands of times longer than the cell.
- Reduces space needed for DNA packaging.
Required for DNA and RNA synthesis.
Involves histones which form 10 nm fibers; these fibers coil into 30 nm structures and form chromosomes.

Fits DNA into cell:
- Stretched DNA in a cell is 2 nm long.
- Must be highly organized to fit into the cell.
Provides stability for cellular functions.
Prevents unnecessary enzymatic reactions.
Controls and maintains the gene expression profile.
Forms chromatin, chromatids, and chromosomes.

Applies to replication of several viral DNAs (e.g., bacteriophages φX174 and λ).
Starts with a circular double-stranded DNA molecule.
In φX174, a complementary strand is synthesized using circular single-stranded genomic DNA as a template.
In λ, circular molecules result from pairing of short complementary single-stranded ends of linear double-stranded DNA after bacterial infection.

Replication in eukaryotes is bidirectional; rolling circle type is unidirectional.
Ideal examples include circular plasmid replication in bacteria.
Initiation occurs through helicase and topoisomerases leading to the separation of DNA strands.

Elongation proceeds as the DNA polymerase moves in a circular path, displacing the end of the broken strand and allowing for continuous elongation.

At termination, linear DNA is cleaved from the circle, resulting in a double-stranded circular DNA molecule and a single-stranded linear DNA molecule.
The linear molecule is then circularized by ligase to form a double-stranded circular plasmid.

Conjugation between F+ and F- bacteria occurs, illustrating the transfer of genetic material.