Crossing Over

At present, you have a DNA repair theory of crossing over. I would like to propose a new theory of crossing over. This theory can be called the "DNA Structure Theory of Crossing Over". In this theory, eukaryotic DNA has 3 structures, the fact that eukaryotic DNA has 3 structures is evident in the fact that when eukaryotic DNA is heated and becomes single stranded, and then cooled slowly, the strands realign at 3 different temperatures. The highly repetitive DNA, which aligns at the highest temperature, and the moderately repetitive DNA, which aligns at the in-between temperature are both resonance structures. The highly repetitive DNA is aligning such that the first base pair of a sequence aligns with other first base pairs. The second base pair of a sequence, aligns with other base pairs, and so on and so forth, until the last base pair of the repetition sequence. Thus, the first base pairs would be, A's and T's (or a very high proportion of them A's and T's), or G's and C's (or a very high proportion of them G's and C's). The resonance structure is planar and perpendicular to the length of the chromosome. The moderately repetitive DNA resonance structure runs along the length of the chromosome where the base pairs slip up and down with the length of the chromosome.

Because the highly repetitive DNA is a resonance structure that is perpendicular to the length of the chromosome, it is possible for the same sequence on an adjacent chromosome to align and become part of the resonance structure. Thus, two adjoining resonance structures become one larger resonance structure.

The bases are rotating in the plane, thus is it possible and probable that any 1 strand is matched to a number of other strands. When a strand breaks, the repair mechanism may match it to one of the adjacent strands.

The last step is for the protein mechanisms to copy the chromosomes and match up the strands such that they go with 1 chromatid or the other.

Thus, because the structure of DNA varies in different parts of the chromosome at some locations, it is possible for the DNA to align, and be matched to the opposite chromatid. The copying mechanism itself ensures connection to one chromatid or the opposite chromatid.

This not only explains how crossing over works, but also why crossover distances do not correspond to chromosomal length.

The highly repetitive sequences have purpose inasmuch as they facilitate the lignin up of chromosomes, as well as crossing over. The entire sequence is part of the resonance structure and conserved. Because the highly repetitive sequences have purpose, they can be/are being selected for. The evolution of the organism correlates to the evolution of the highly repetitive sequences. The highly repetitive sequences evolve quickly in species which are evolving quickly. The single copy DNA evolves at a slow rate that does not correlate with speciation. The moderately repetitive DNA evolves rapidly in organisms evolving rapidly, and slowly in organisms which are evolving slowly.