Hi,
Thank you bngenoh for the website, it was a good refresher and opens up possibilities.
First of all, let me say the guy certainly has some points. I like his way of describing the concepts and his willingness to accept the limitations of his model. To continue with the claims:
-While non-helical DNA structure is convincing in the presence of protamine, this typical setting is limited to sperms since protamine is only used in sperms(at least to the current knowledge of science) for packing DNA. He also claims this topology is also seen in circular DNA which is the characteristic of viral and some bacterial genomes, this also makes sense, however it is not the genome structure of humans and higher organisms except for our mitochondrial DNA.
http://en.wikipedia.org/wiki/Protamine
-What was interesting most was how different DNA strands come together to form 4 or more DNA strands with the help of protamine. Maybe this is similar to the mechanism of 12 stranded DNA C's talk about? But as I said, protamine seems to be limited to sperms, so we lack data on that regard.
-For other cells, we have histones as the guy mentions. He doesn't want to model histone-DNA interaction which makes perfect sense since it is much more complicated and impossible for him to do by himself. However, he has something to say about the crystal structure of histone-DNA interaction about distances and impossibility of ionic bonds. This I have checked and he seems to be right. Check this 3D model to see for yourself:
http://www.rcsb.org/pdb/explore/jmol.do?structureId=1AOI&opt=3&bionumber=1
At the display options below the image, Change the Style to Backbone and Color to Amino Acid. Double click on two points that are close to each other, one on the histone the other on DNA to measure the distance between them.
-Non-helical model is also useful for histone binding of DNA, but the difference between histone and protamine is as the guy differentiates, histone is globular protein and protamine is a beta sheet. What this means is protamine is like a fibril adjacent to DNA, but histone is like a cylinder and DNA is the coil that wraps around it. So even though DNA is non-helical and the strands do not turn around each other, double stranded DNA turns around the histone.
http://www.mun.ca/biology/scarr/Histone_Protein_Structure.html
-It is entirely possible for the structure of DNA to be changed due to crystallographic preparation and give different results under different conditions. From that perspective, Watson-Crick model may indeed be wrong. Also unzipping of DNA to start transcription or replication requires unwinding of the helix which requires special enzymes(at least this is what scientists claim) and is a huge field of study for theoretical biologists. Who knows, maybe they are chasing ghosts with their thermodynamic calculations and models.
-If we come to question of what is the implication as Buddy asks, there are proteins that bind to DNA. These proteins recognize the grooves in the helix structure and hold on to there. Imagine it as cracks in a rock that climbers utilize to hold on to. If DNA is not helical and there are no grooves, holding onto DNA would be much harder to initiate RNA or DNA production. On the other hand, if there are no helix structure, it may be easier to initiate RNA production from genes. What effect would this have is impossible to predict, or so I think. Maybe less control causes chaos, or on the contrary, it opens up possibilities and leads to order.
Overall, with my current knowledge, I think it is a great idea and entirely possible in the specific settings this guy mentions such as sperm and circular DNA(there is a circular DNA inside mitochodria of every higher organism, so it is applicable to us to some extent) but as for the nuclear genome, I am not so sure, because I can not imagine what would be like if there is no helix in there. That doesn't mean there couldn't be, I just don't know what may be the cause and the implications of it.
My two cents, fwiw.
