The 5' to 3' path of DNA replication why is that?

DNA replication this is the propeller for very existence of many organism whose genetic material is DNA,for eon,epochs,periods and eras this is been going on except during the RNA world or what is commonly called as RNA world hypothesis.

Is there any reason  all organisms evolved to go from 5' to 3'?Is it energetic or something else?

Possible question arise regarding the pros and cons of replication from 5' to 3' direction?

1. is it thermodynamically favorable of  using 5' to 3'? 
2. whether  3'-OH of the existing strand to attach the phosphate of the free nucleotide more energetically favorable than using the 3'-OH of the free nucleotide to attach the phosphate of the existing strand? 
3. Is 3' to 5' polymerase activity impossible??

DNA replication goes in the 5' to 3' direction because DNA polymerase acts on the 3'-OH of the existing strand for adding free nucleotides. This is how this is being happening.

The phosphodiester bond is the major bond that is responsible  for holding the nucleic acid.The energy needed for the formation of the phosphodiester bond comes from the dNTP, which has to be added. 

dNTP is a nucleotide which has two additional phosphates attached to its 5' end. To form bond with 3'OH group with the phosphate of the next nucleotide, a oxygen need to be removed from this phosphate group. This oxygen is also attaches to two extra phosphates, which are also attached to a Mg++. Mg++ divalent ions  pulls up the electrons of the oxygen, which weakens this bond and the so called nucleophilic attack of the oxygen from the 3'OH succeeds, thus forming the phospodiester bond.

So most important thing is the nucleophilic attack to happen.

Therefore if a  dNTP's 3'OH group is tried  to  bond with the 5' phosphate of the adjacent  nucleotide, there won't be feasible  energy  required  to weaken the bond between the oxygen connected to the 5' phosphorous the other two phosphates of the dNTP are on the 5' end, which are present at  the 3' end, which makes the nucleophilic attack harder.There for by course of evolution the DNA replication might have evolved from 5' to 3' way.

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Unknown Tuesday, February 25, 2014  No comment

What are the consequences to replication of having a replication machinery with no 5’->3’ exonuclease activity?

The exonuclease activity can be also described as ---5'-to-3' exonuclease (Nick translation activity)

This enzymatic activity that is 5'-to-3' exonuclease activity plays an essential role by removing RNA primers during replication. This process is similar to nick translation , the simultaneous polymerization in the 5'-to-3' direction from a nick with concurrent removal of nucleotides ahead by the 5'-to-3' exonuclease activity.

So this helps in making the extension in a smoother way with less error incorporation

5'-3' exonuclease activity is an repair strategy used DNA polymerase I. the polymerase would move in the forwards direction and excise the miss-matched nucleotides at any position . This mechanism is used in case of UV-mutation where the strand gets mutated due to UV and in turn the strand is deformed.

One example I would give which I used in my lab is this ---T7 Exonuclease enzyme

This T7 Exonuclease acts in the 5' to 3' direction, catalyzing the removal of 5' mononucleotides from duplex DNA. T7 Exonuclease is able to initiate nucleotide removal from the 5' termini or at gaps and nicks of double-stranded DNA

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Unknown Monday, December 23, 2013  No comment