nitrogen bases in DNA

[kmpoulin]

What determines which nitrogen bases form pairs in DNA?

[pioneer]

The base pairing is defined by the number of hydrogen bonding hydrogen available and the number of hydrogen bonds that can form between the base pairs. Adenine and Thymine have three hydrogen bonding hydrogen but only can use two, while Guanine and Cytosine have five but only use three. The extra hydrogen bonding hydrogen get connected to the oxygen of water. These pairs uses the least amount of water. All the others pair use more water and are at higher energy with the water trying to minimize this.

 

The water also combines with all the nitrogen that don't participate in the hydrogen bonding between base pairs, with the water providing the hydrogen. The result is a double helix of water, with slight bulges depending on the base pairing. This double helix becomes extended even further since the water also forms hydrogen bonding with the sugars and the phosphate. The surface water of the DNA reflects the amount of water throughout the entire system and tags the surface to differentiate which base pairing as well as the exact defects in the base pairing. The enzymes read the water and can see inside the double helix.

 

 

 

[pioneer]

Methylation of DNA

 

The one thing that water, DNA, RNA and protein have in common is hydrogen bonding. What that means is the hydrogen bondable areas of DNA, RNA and protein, are interchangeable with water. By this I mean, under the right circumstances water can take the place. But with organic molecules creating some level of surface tension with water (adds energy to water), there is usually a phase separation with most of the water squeezed out, such as in the DNA double helix. But there are often other places designed in these molecules where the water is still able to bind.

 

Relative to the DNA we end up with a double helix of water, plus more if the base pairing is wrong. If we were to separate the double helix of DNA, water will flow in and try to hydrogen bond to whatever is open. But once the DNA reforms, this extra water is squeezed back out. We still have the double helix of water. The result is the continuity of DNA's water, with the exterior bulk water is never broken.

 

This ebb and flow of the external water plays a role in which enzyme is best for which water, since that water reflects the real time state of the DNA. The enzymes have their own continuity with water. Each hydrogen bond you need to break in the water is about 1/10 the strength of a covalent bond. If the enzyme needs to break 10 hydrogen bonds to get to the DNA, the enzyme has just lost advantage. But if its own water can add to the local or real time water, it can use the water to gain some energy. They need to plow through water to get to the DNA since water is everywhere. Those that can do this with the least expenditure of energy have an advantage.

 

Let me change directions and talk about the methylation of the DNA. The methylation of DNA, or the addition of a methyl group -CH3 to the #5 carbon of cytosine, typically inhibits genes. Where it adds is near the #4 position N which has two hydrogen, one which is occupied by water. The resonance in cytosine help to keep the molecule sort of flat.

 

This next part is speculation, with logic. I would tend to think the methyl group impacts the water double helix. If the O of water shares the NH its hydrogen are pointing up and sort of repelled by the methyl H. This is the worse arrangement to lower the surface tension between water and this little bead of methyl oil. One possible affect, if this was true, is the methyl group is like a little resistor placed in the water double helix. It is a hot spot for the water, which tags the surface.