DNA circles go into our chromosomes. Conventional theory states that they when they enter, they fuse with the main chromosome and become a linear segment of it. DNA circles also come out of our chromosomes. Conventional theory says this means they have to reform circles prior to exiting the chromosome. The laws of thermodynamics make the likelihood of regenerating a circle from a fused linear segment more improbable as the size of the DNA circle increases. A quick google search indicates that a broken chromosome from a bacterium like E. coli has a linear length of about 1,200 microns, similar to lengths found in double minute circular chromosomes released from chromosomes like our own when they are damaged by radiation or drugs. Our own cells are in the range of 10 microns in diameter, so a linear chromosome that is 120 times the length of the cell must somehow come together within the cell to form a circular chromosome. When you really think about it, how can this make any sense? Isn’t it more probable that the circular chromosome pre-existed in the main chromosome and was simple plucked away from an attachment site like a cassette from a tape recorder or a memory chip from a computer?
The main crux of my blog and my original work has been the idea that circular DNA exists within the eukaryotic chromosome (our chromosomes). Conventional theory states this is not the case, that any circular DNA that enters the chromosome is simply fused together with the rest of the linear DNA. The idea of a linear chromosome containing simple linear DNA has been around for a long time; so long, in fact, that data is cherry picked to support this idea. Scientists who perform recombinant DNA studies cut up foreign DNA into linear fragments so it can be inserted into the host genome. However, they splice this DNA into a circular plasmid or virus prior to introducing it into the foreign cell. The reason is simple enough: It works. Circular DNA cannot be destroyed by the foreign cell’s exonucleases, giving it time to enter into the chromosome. The efficiency of integration drops dramatically if the plasmid is linearized. So the next question is how this circular DNA integrates into the main chromosomal DNA; by simple fusion as all the texbooks suggest, or perhaps by another means? In my opinion, nature takes the simplest route in solving a problem, just like electricity looks for the path of least resistance in which to travel or water always flows down hill. It is natural law. In this case, it is natural selection. Natural selection favors cells that can outcompete other cells using a minimum amount of resources and energy. Scientists talk about DNA cassettes, chunks of DNA that get plugged into the genome, much like a cassette tape gets plugged into a tape player. These cassettes are always circular in nature. Audio cassettes were created to make playing tapes faster and easier to do. Back in the day, tape recorders were reel to reel, which meant that the user had to thread the tape through the machine and onto the other reel before it could be played. Cutting a circular piece of DNA and also the main chromosome and splicing them together may be simple enough to do, but once the circular DNA is linearized how do you reverse the process? The laws of thermodynamics indicate this would be almost irreversible, yet somehow these cassettes pop in and out of chromosomes as easily as plucking grapes off a vine. My model suggests that instead of linearizing the DNA, it binds to specific attachment sites on the chromosome and maintains its circular structure. Once attached, it can be easily deleted, amplified, or permanently fused to the genome through a process known as illegimate recombination. You can learn more about how this might be done by visiting the models page. You can also learn more about it by accessing the video link located on the home page.