Ahem...(j/k)

 Now, in answer to your prior question pertaining to gene conversion and chromosomal crossover and general recombinative repair, stripped to its bare essentials, this is my intro into general recombination. This introduction of mine was prepared for other purposes, so tell me if it sounds like gibberish. The following is a course on the bare essentials of recombination that I put together:

A serious problem occurs if the DNA breaks on both strands, which will stall the replication fork. If this occurs, there exist two mechanisms to fix the problem. The first is simple, and called non-homologous end joining, in which the two ends are simply rejoined after several nucleotides on both ends are degraded from the 5' ends. This causes a slight mutation and is a rough solution. A much more accurate solution is called homologous end joining, which, in diploid organisms, makes use of the fact that there are two chromosomes with homologous DNA sequences, by which one can be used as a template for the repair of the other.

-Suppose that a double strand break occurs in a DNA sequence. If this happens, then the 5' ends of both sides will be chewed back by an exonuclease, leaving protruding 3' ends.

-The initiation of this entails that the protruding 3' ends and their single strands search for  their homologous counterparts in the other chromosome. Whenthey find each other, they form a three-strand intermediate, and this is called DNA synapsis. In it, one of the protruding 3' ends of the DNA forms base pairs with the complementary s equence on the other strand on the homologous chromosome causing the base pairs normally associated with it to flip out which are then associated with the base pairs from the other protruding three ends. This stage is presumed to be long and difficult to accomplish. Because it entails that there is a portion of sequence where the bases from one strand from one chromosome are paired with those on the other, it forms a small heteroduplex joint. After this happens, an event called branch migration begins, in which an unpaired region extends to form bonds with the complementary homologous sequence. But in the absence of any other factors, the DNA will "walk back and forth" in the three strand intermediate, there is nothing to drive the unidirectional displacement of the DNA. A protein which in bacteria is called RecA, and has a human homolog called Rad51, serves as the solution. It is an ATP-dependant protein that binds tightly to the DNA, and drives the movement of the three-stranded intermediate in just one direction, forming a nucleoprotein filament in which the RecA "spins out" a recombined DNA strand, hence acting like a treadmill, driving the DNA branch migration in one direction.

There are two principle pathways. The first is meiotic recombination. The second is repair-based recombination, and the two pathways have different outcomes. In meiosis, the genome of a diploid organism  is duplicated, and then undergoes two rounds of division. The cells that result each have one complete set of chromosomes, or half the genetic content of the cell. These then fuse during fertilization to form the gametes. Homologous chromosomes will pair, or synpase, during meiosis. Homologous chromosomes are not the same thing as sister chromatids. Sister chromosomes are copies of the same chromosome caused by replication, whereas homologous chromosomes are different copies of the same chromosome which are inherited from each parent.

 Genetic recombination occurs when a strand of genetic  material from one chromosome is broken off and attached at the homologous site on the other. In meiosis, this occurs when a double strand break in one of the two homologous chromosomes is induced by the Spo11 protein. The 5' ends of the strands are then chewed back by exonucleases. This generates the free 3' ends which can then begin strand invasion and DNA synapsis on the complementary sites on the homologous chromosomes. The DNA synapsis is mediated by the RecA protein. The free 3' ends of the two strands bind to their complementary sequences as shown:

 

The Holliday Junction that forms as shown can be pulled along the DNA. After RecBCD helicase-exonuclease complex creates the free 3' ends, RecA proteins will bind to them forming nucleoprotein filaments which act as recombinases, catalyzing the invasion of the ssDNA into the homologous dsDNA.

 

Chromosomal recombination occurs before the double-cell division of meiosis, when the homologous chromosomes are held tightly together. This produces a unique blueprint for the gametes. Recombination hence explains something that hitherto puzzled scientists: Why is it that offspring of the same parents do not all look alike? The difference and variety of phenotype that can be generated by the recombination of genes is testimony to the advantageous nature of recombination, and hence of the principle upon which it is built: diploid genomes.

 

For recombinative repair, the 3' ends need to be created by the RecBCD complex, which is unique among the helicases in that it actually recognizes a specific sequence, called the Chi sequence, these being interspersed throughout the genome. The RecBCD acts as a helicase-exonuclease in the 5' to 3' direction, destroying DNA along ssDNA to create a protruding 5' end until it encounters the Chi sequence, at which point the DNA-binding causes a functionally induced change in the exonuclease function, also note that RecBCD is an ATP-dependant motor protein as it moves along the ssDNA. When this occurs, the RecBCD works on the other ssDNA strand, causing a protruding 3' end. RecBCD also serves to load the ATP-dependant RecA onto the protruding 3' end so that it can facilitate DNA invasive synapsis.



The DNA synapsis leads to branch migration, in which the Holliday junctions are pulled along the DNA:



The RuvABC complex can resolve the Holliday junction, as shown. The Holliday junction is the four strand intermediate that forms due to the pairing as shown above. After ligation, the junction can be pulled across the synapse by virtue of the RuvA/B complex (which also mounts a DNA helicase onto the strands to resolve any ssDNA structures). The branch migration is facilitated by ATP-dependant proteins, in humans called RAD51.

 RuvA and RuvB can pull the Holliday junctions along, whereas RuvC will resolve the strand by means of strand cutting:

 

 

The Holliday junction isomerizes by rotating, at which point the joints are resolved by strand cutting:



Hence two outcomes:



The two outcomes of meiotic recombination as shown. Gene conversion results from SDM after incorrect base pairing due to an overt difference in the two alleles. It is for this reason that gene-conversion represents non-Mendelian inheritance. Crossovers result from standard synapsis in which the Holliday junction is resolved by isomerization. If the Watson-Crick base pairing of the two alleles is not substantive enough, then the MutS-MutL complex will destroy one strand (the MutL as usual mounting a helicase onto the DNA and the MutS binding to the muTL dimer to loop out the DNA as an endonuclease trails behind). If this is the case, then the strand that was originally from the other parent will be used as a template for the mounting of DNA Polymerase onto the strand (to be then sealed by the ligase). If this is the case, then a chunk of information that was originally from the allele of one parent will be converted into that of another. This violates a fundamental law of genetics that both parents make a precisely equal contribution to the genome of the offspring and is hence non-Mendelian inheritance (this is contrast to ). (This is again constrast to recombinative repair, where one chromosome is not changed and the other is repaired by means of using the information of the  other as a template by which the synapsis does not alter the sequence of the donor chromosome, as opposed to meiotic recombination, which does. This constitutes roughly 99% of the recombination that occurs in meiotic cells).