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L-Form Chirality of DNA Nucleotides

Author: Danut Dragoi, PhD

In a paper titled “Chiral purity of nucleotides as a necessary condition of complementarity”, see link in here, the question about the role of chiral purity (homochirality) of nucleotides in the formation of complementary replicas is been discussed. A qualitative answer to this question can be obtained from molecular models constructed to simulate the chiral defect in the polynucleotidic chain. It shows the necessity of homochirality of nucleotides for the complementarity preservation.

As we know living cells have  the natural amino acids in  the L (levogir) form, but not D form (dextrogir). Synthetic procedure to make amino acids produces both L and D forms, so they coexist in a mixture 50/50 percents, called racemic state. Within the living cells the situation is different, some special synthesis is occurring with high precision. For example DNA double helix strands, A-DNA and B-DNA have D chirality, see link in here. The rare form Z-DNA has the opposite chirality and for this reason is not included in this posting.

It s interesting to note that the sugar structure in each DNA strand has D chirality.  The sugar within the DNA strand is optical active that gives the chirality character of the DNA.

The twisted structure of the DNA suggests to make a mechanical  model that uses the effect of torsion of both DNA strands in equilibrium with a Left twist in each nucleotide. For this reason I considered a  mechanical model, see picture below, where the white vertical bands are two light ribbons of paper connected with small strands of paper whose ends are Left twisted at 180 degrees. After assembling, the system was freed of any mechanical constraints, so that the entire system took shape of the D (right) double helix as expected.

Image SOURCE: Danut Dragoi, the author of this Post

Since the nucleotides that are the four codons, A, T, C, and G, are related with the production of the 20 natural amino acids, we can say that the two letters association, AT, and GC (the nucleotides), preserve the chirality L. The picture below shows schematically an example  Arginine amino acid produced by Adenine, Guanine, and Adenine.

Image SOURCE: http://reasonandscience.heavenforum.org/t2057-origin-of-translation-of-the-4-nucleic-acid-bases-and-the-20-amino-acids-and-the-universal-assignment-of-codons-to-amino-acids

Summary

We can derive the chirality  of a complex ensemble of molecules by knowing the chirality of the components. The rare case of Z-DNA, in which the two DNA strands have a wavy configuration, requires a separate analysis.

REFERENCES

http://onlinelibrary.wiley.com/store/10.1016/0014-5793(86)80036-9/asset/feb20014579386800369.pdf;jsessionid=F631F1ABFD1BAFF62C11D3ECEC9EEBB4.f04t02?v=1&t=iltzzvnl&s=674d6afafa94dc4226d0dd005dc50f9839126e66&systemMessage=Wiley+Online+Library+will+be+unavailable+for+up+to+3+hours+on+Saturday+19th+March+2016+from++11%3A00-14%3A00+GMT+%2F+07%3A00-10%3A00+EDT+%2F+19%3A00-22%3A00+SGT+for+essential+maintenance.++Apologies+for+the+inconvenience.

https://books.google.com/books?id=ahvA1IWjIGIC&pg=PA114&lpg=PA114&dq=DNA+double+helix+strands+has+D+chirality&source=bl&ots=DTFNLdBpAO&sig=qVHxI_W6xISF3n8v57TF2VAJv40&hl=en&sa=X&ved=0ahUKEwiZxZWkyMLLAhXEKWMKHa2JBzMQ6AEIQjAE#v=onepage&q=DNA%20double%20helix%20strands%20has%20D%20chirality&f=false

SOURCES

http://onlinelibrary.wiley.com/doi/10.1016/0014-5793(86)80036-9/pdf

http://www.encyclopedia.com/topic/amino_acid.aspx

http://www.phschool.com/science/biology_place/biocoach/bioprop/landd.html

http://reasonandscience.heavenforum.org/t2057-origin-of-translation-of-the-4-nucleic-acid-bases-and-the-20-amino-acids-and-the-universal-assignment-of-codons-to-amino-acids