Molecular Basis of Homologous Recombination

During homologous recombination two double-stranded DNA molecules recognize each other and form a crossover. This involves breaking one strand of each DNA duplex, exchanging strands and rejoining the ends (Fig. 14.03). This results in the formation of a Holliday junction, named after Robin Holliday who proposed this model in 1964. The Holliday junction contains two heteroduplex regions where single strands from the two separate DNA molecules have paired up. [A heteroduplex is any region of double-stranded nucleic acid, DNA or RNA, where the two strands come from two different original molecules.]

The Holliday junction can twist around and rearrange itself. The two interconvertible forms shown in Fig. 14.04 do not require any change in bonding or base pairing, they are simply alternative conformations. The important issue is that two heteroduplex A DNA double helix composed of single strands from two different DNA molecules

Holliday junction DNA structure formed during recombination and found at the crossover point where the two molecules of DNA are joined homologous recombination Recombination between two lengths of DNA that are identical, or nearly so, in sequence non-homologous recombination Recombination between two lengths of DNA that are largely unrelated. It involves specific proteins, that recognize particular sequences and form crossovers between them. Same as site-specific recombination

Homologous recombination

Non-homologous recombination

Crossing over

Crossing over

Recognition sequence

Recognition sequence

Crossing over

Crossing over

Rejoining

Rejoining

Rejoining

Rejoining

Recombination between un related DNA sequences can occur due to the involvement of specific recognition proteins.

Single-Strand Invasion and Chi Sites 371

FIGURE 14.03 Formation of a Crossover

Two homologous molecules of DNA align in regions of similar sequence. A single-stranded break occurs in the backbone of each molecule. The two ends switch with each other creating a crossover of single-stranded DNA. This crossover can rearrange itself via the intermediate chi form.

genuinely different products can be formed from the breakdown or resolution of the Holliday junction.Which product is obtained depends on which conformation the junction is in when it is resolved. One possible result is the regeneration of the two original DNA molecules. In fact they are not absolutely the same as before, and are sometimes known as "patch recombinants" as a short patch of heteroduplex remains in each molecule. The alternative is the formation of two hybrid DNA molecules by crossing-over. Resolution of the Holliday junction to give two separate DNA molecules requires an enzyme, known as a resolvase. In E. coli the RuvC and RecG protein both act as resolvases and can substitute for each other. Resolvases cut and rejoin the second (previously unbroken) strands at the junction, generating the complete, double-stranded crossover.

Another interesting property of the Holliday junction is that it can migrate along the DNA (Fig. 14.05), a process called "branch migration". This involves breaking and re-forming hydrogen bonds. This should, in theory, require no overall energy input, as an equal number of bonds are broken as re-formed. However, in practice, spontaneous migration is extremely slow and energy-dependent enzymes are needed to speed up the process. In E. coli, the RuvA protein binds to the junction and RuvB drives migration.

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