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A classical question: "Why does 3'-5' polarity of DNA strand acts as template?"
#1
Have you ever wondered as to why does 3'-5' strand acts as the template and not 5'-3' strand?

Looking forward to your answers. I am actually looking forward to the best answer (one which is amazingly explained, so that anyone can understand the reason without much a do).

P.S. I'm thinking of awarding the author of best answer (in my own personal judgement) with a little award (A book titled "Science Lessons: What the business of biotech taught me about management", by Gordon Binder (former CEO of Amgen Inc)...this book is amongst Top 10 best books to read in Biotechnology field...so I hope who so ever wins, will love this little present from me...I am doing this personal contest sort of activity first time ever on this forum, if it turns out nice, will post more of these mini contests in future (as and when my wallet has some extra bucks to go for these activities ).

Looking forward..
Sunil Nagpal
MS(Research) Scholar, IIT Delhi (Alumnus)
Advisor for the Biotech Students portal (BiotechStudents.com)
Computational Researcher in BioSciences at a leading MNC


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#2
The two complementary strands of double-stranded DNA (dsDNA) are usually differentiated as the "sense" strand and the "antisense" strand. The DNA sense strand looks like the messenger RNA (mRNA) and can be used to read the expected protein code; for example, ATG in the sense DNA may correspond to an AUG codon in the mRNA, encoding the amino acid methionine. However, the DNA sense strand itself is not used to make protein by the cell. It is the DNA antisense strand which serves as the source for the protein code, because, with bases complementary to the DNA sense strand, it is used as a template for the mRNA. Since transcription results in an RNA product complementary to the DNA template strand, the mRNA is complementary to the DNA antisense strand. The mRNA is what is used for translation (protein synthesis).
Hence, a base triplet 3'-TAC-5' in the DNA antisense strand can be used as a template which will result in an 5'-AUG-3' base triplet in mRNA (AUG is the codon for methionine, the start codon). The DNA sense strand will have the triplet ATG, which looks just like AUG but will not be used to make methionine because it will not be used to make mRNA. The DNA sense strand is called a "sense" strand not because it will be used to make protein (it won't be), but because it has a sequence that looks like the protein codon sequence.
Regards ,
Lavkesh Sharma

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#3
(02-18-2017, 11:35 PM)SunilNagpal Wrote: Have you ever wondered as to why does 3'-5' strand acts as the template and not 5'-3' strand?

Looking forward to your answers. I am actually looking forward to the best answer (one which is amazingly explained, so that anyone can understand the reason without much a do).

P.S. I'm thinking of awarding the author of best answer (in my own personal judgement) with a little award (A book titled "Science Lessons: What the business of biotech taught me about management", by Gordon Binder (former CEO of Amgen Inc)...this book is amongst Top 10 best books to read in Biotechnology field...so I hope who so ever wins, will love this little present from me...I am doing this personal contest sort of activity first time ever on this forum, if it turns out nice, will post more of these mini contests in future (as and when my wallet has some extra bucks to go for these activities  ).

Looking forward..
Chemically/Energitically -

Nucleic acid polymerization - Transcription/Replication is a SN2 nucleophilic reaction. 3'OH  oxygen is a good attacking group and so the leaving group(pyrophosphate - also very good leaving group) does not require additional energy source(ATP) for the removal oxygen. 

This energetic constraint leads to
evolutionary Selectivity-

i.e - Protein synthesis(Translation), also occurs from 5' - 3'.(Ref 1 - Rna Based evolution)
Ref -1
http://fire.biol.wwu.edu/cmoyer/zztemp_f...rld_02.pdf

So the regulatory/initiation sequences(Eg - Shine-Dalgarano Sequence) also lie on 5' end of the transcript. 

In addition other machinery(repair) also evolved in a similar fashion. (Ref 2)They show that organisms with 5' - 3' polymerase  activity have better survival rates(mutations - Repair machinery require 5'-3' activity).
Ref -2
http://journals.plos.org/plosone/article...ne.0018881.


BTW - 3'-5' synthesis is also possible both, in vivo/in vitro - Thg1 superfamily proteins(Ref -3).

Ref - 3
https://www.ncbi.nlm.nih.gov/pubmed/22456265
Ref - 4
http://onlinelibrary.wiley.com/doi/10.10...201203859/
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A classical question: "Why does 3'-5' polarity of DNA strand acts as template?"00