DNA replication is one of the main processes underlying biological evolution and the very origin of life. It must be simple enough to occur in the early stages of biochemical evolution. On the other hand, we now see a surprisingly complex system of enzymes, and it is not clear how it was possible to do without it before. Therefore, it can be assumed that some generally accepted ideas are erroneous.
In my opinion, the first mistake is the wrong model of the DNA molecule in the form of a double helix. I have proposed another model called the ribbon helix, in which the two chains are not intertwined, but run in parallel.
https://www.researchgate.net/project/A-new-model-of-DNA
It is clear that the replication process in the case of such a model is radically simplified. And yet, difficulties remain -- due to the fact that, according to conventional wisdom, the two strands are anti-parallel. So, the need for Okazaki fragments remains.
That's why I want to ask: Maybe the two chains are actually pointing in the same direction?
Yes it is absolutely certain that the two DNA strands are antiparallel. There are innumerable experiments that require this to be the case which would otherwise have failed. As an example, PCR amplification would never work with the selected primer pairs if they were not antiparallel. There are also numerous solved X-ray structures of DNA that show the two strands in molecular detail. There are also some cases where overlapping genes found on both strands have mutations with functions that would only be predicted by antiparallel strands.
I also don't think you can have the appropriate hydrogen bonding between strands on the model you propose.
I would question the assumption that the generally accepted ideas must be erroneous. Just because over evolutionary time the systems have become more complex and require more enzymes does not mean something is wrong, but is more parsimonious to consider it simply is the result of requiring improved efficiency, fidelity and mechanisms for control and regulation.
Thank you Dr Michael J. Benedik
>>There are innumerable experiments that require this to be the case which would otherwise have failed. As an example, PCR amplification would never work with the selected primer pairs if they were not antiparallel.
Maybe you're right. I have not analyzed these things. I'm only afraid that anti-parallelism is accepted as an axiom and no other option is considered.
>> There are also numerous solved X-ray structures of DNA that show the two strands in molecular detail.
No, these are oligonucleotides, not native DNA.
>>I also don't think you can have the appropriate hydrogen bonding between strands on the model you propose.
To judge, you need to perform a conformational analysis.
There are x-ray structures of DNA molecules that are not oligo's (although also many are oligos). In fact the Watson and Crick model is based on that and numerous others since then.
There are undoubtedly many forms of DNA, (A-form, B-form, Z-form), triplexes etc. which are found in the laboratory and in nature, so I would never say your model is not possible under some circumstances, but the experimental evidence for B-form being the norm is overwhelming.
>>There are undoubtedly many forms of DNA, (A-form, B-form, Z-form), triplexes etc. which are found in the laboratory and in nature,
There are no single crystals of long DNA, only short fragments. Therefore, all these forms cannot be attributed with full confidence to native DNA.
>> I would never say your model is not possible under some circumstances, but the experimental evidence for B-form being the norm is overwhelming.
You will laugh: it was this phrase that I heard 42 years ago when I introduced my idea to DNA specialists. I didn't agree with them then and I don't agree with you now.
- There was an interesting essay (1997) on this topic by Prof. Robert Root-Bernstein
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