Why only RNA act as primer in DNA replication?

[asaroj27]

please give me some idea that why only RNA primer used in DNA replication ?

[MedGen]

If you mean instead of a DNA primer, then the reason is that the DNA polymerases that catalyse second strand synthesis simply cannot start working from scratch, they require a primer to do this. RNA polymerases however do not, thus you get a primer for a DNA polymerase made of RNA. It may also have evolved as a part of the proofreading mechanisms inherent in DNA replication, not to mention all those endonucleases floating around could quite easily just come along and degrade a DNA primer, then you wouldn't get any replication!

 

I'm sure there's more to it than that, maybe one of our resident experts can fill in the rest.

[CharonY]

Sounds about right. Normal textbook answer is that primases (which synthesize the RNA primer) do not require a primer themselves.

[pioneer]

If you compare RNA to DNA (as single helixes) DNA creates slightly more surface tension in water. The sugar on RNA has an extra polar OH group and one of the bases of DNA has an extra -CH3 group. Pound for pound DNA is more non polar. The DNA double helix reflects this, sort of beads up into the double helix. RNA does not bead as much and will form a single helix.

 

What the slightly lower surface tension of the RNA primer does is lower the hydrogen bonding potential in the water near the RNA primer. This appears to create the proper configurational equilibrium for DNA polymerase. If you started with a DNA primer, the equilibrium enzyme configuration in that local water would need to have a higher hydrogen bonding potential. This will form a better equilibrium with the endonuclease.

 

If you look at either enzyme, the total affect is more than an enzyme. Both have hydrated water forming an enzyme-water composite. This water has to match the primer's water for the enzyme to become optimize for its specific task. Physical chemists have demonstrated enzyme reactions do not form a proper energy balance unless you include the energetic of this local water. The matching water enzyme-primer, also prevents traffic jams but causing the proper enzyme to be in the right place, most of the time, so proper enzyme fires bulls eye, with minimum wrong enzyme duds.

[MedGen]

If you compare RNA to DNA (as single helixes) DNA creates slightly more surface tension in water. The sugar on RNA has an extra polar OH group and one of the bases of DNA has an extra -CH3 group. Pound for pound DNA is more non polar. The DNA double helix reflects this, sort of beads up into the double helix. RNA does not bead as much and will form a single helix.

 

What the slightly lower surface tension of the RNA primer does is lower the hydrogen bonding potential in the water near the RNA primer. This appears to create the proper configurational equilibrium for DNA polymerase. If you started with a DNA primer, the equilibrium enzyme configuration in that local water would need to have a higher hydrogen bonding potential. This will form a better equilibrium with the endonuclease.

 

If you look at either enzyme, the total affect is more than an enzyme. Both have hydrated water forming an enzyme-water composite. This water has to match the primer's water for the enzyme to become optimize for its specific task. Physical chemists have demonstrated enzyme reactions do not form a proper energy balance unless you include the energetic of this local water. The matching water enzyme-primer, also prevents traffic jams but causing the proper enzyme to be in the right place, most of the time, so proper enzyme fires bulls eye, with minimum wrong enzyme duds.

 

What? Water is very important for enzyme catalysed reactions, but mostly where water molecules in the enzyme active site help to stabilise the other non-covalent interactions that allow for the ES complex to exist for long enough for the enzyme to reduce the activation energy for the ES complex state.

The hydration shell around the polymerases doesn't seem to play an important part in the enzymes activity, but is essential for it to remain in solution, particularly in high salt/sugar environments (see halophiles).

[pioneer]

Enzymes will not work properly, if at all, in any solvent but water. With any other solvent the energetic don't add up. Enzymes will also not work in air, or without a solvent, especially water. When we tweak the water we are altering the local solvent properties, although it it more complicated than that.

 

With RNA and DNA primers the extended water structure will look different. Particular enzymes are optimized to each of these micro-solvents. The energetics are due to hydrogen bonding which has about the same energy as the ATP molecule, more or less.

[MedGen]

Sorry, my "what" was in reference to your word salad. It made no sense whatsoever, and in fact I would go so far as to call it pseudoscience.

 

Not to mention such spurious claims as this:

The energetics are due to hydrogen bonding which has about the same energy as the ATP molecule, more or less.

 

No, quite simply, the energy released by the hydrolysis of the high energy bonds between the phosphate groups in ATP is nowhere the same as that of a typical hydrogen bond, different bond energies altogether.

[iNow]

Don't worry, MedGen... That's just Pioneer. You can safely ignore most of his posts.

[MedGen]

Oh okay, got that impression from a previous thread, I just didn't want the OP to think that it was a valid answer and go away with some utter bunkum filling his head. Thanks for the pointer, I'll remember it for the future.

[pioneer]

Hydrogen bonding is cooperative. What that means is if we form a chain of hydrogen bonds, such as in water, the bond strength gets stronger and stronger as the chain lengthens. When you get water added to an extended structure of water, the energy given off is higher that the typical dimer of one hydrogen bond.

 

One simple model proposed due to observation data, is liquid water exists in high and low density domains. The low density is hydrogen bonded while the high density are much less so, allowing the hydrogen to get closer where the bonds are not optimized. Snapping back and forth between domains gives or releases energy.

 

Back to the original question, which was RNA primers, the existing wisdom doesn't have any. The reason it doesn't, is it leaves out a variable. The rest of the stuff doesn't add up. We know how but why is mysterious almost like magic when you leave out variables.