Thursday, January 31, 2008

Possible symmetries of DNA implied by the model of topological quantum computation

The following gives a list of possible symmetries of DNA inspired by the identification of braid color as mapping of A,T,C,G to u,d and their antiquarks in the TGD based model for DNA as topological quantum computer (see the earlier postings and also the latest ones).

1. Color confinement in strong form

The states of quarks and anti-quarks associated with DNA both wormhole wormhole throats of braided (living) DNA strand can be color singlets and have thus integer valued anomalous em charge. The resulting prediction depends on the assignment of quarks and antiquarks to A,T,C,G which in principle should be determined by the minimization of em interaction energy between quark and nucleotide. For instance 2(A-T)-(G-C) mod 3=0 for a piece of living DNA which could make possible color singletness. As a matter fact, color singletness conditions are equivalent for all possible for braid color assignments. This hypothesis might be weakened. For instance, it could hold true only for braided parts of DNA and this braiding are dynamical. It could also hold for entire braid with both ends included only: in this case it does not pose any conditions on DNA. Questions: Do all living DNA strands satisfy this rule? Are only the double stranded parts of DNA braided and satisfy the rule. What about loops of hairpins?

2. Matter antimatter asymmetry at quark level

A←→ T and G←→ C corresponds to charge conjugation at the level of quarks (quark ←→ antiquark). Chargaff's rules states A≈ T and C≈ G for long DNA strands and mean matter-antimatter symmetry in the scale of DNA strand. Double strand as a whole is matter anti-matter symmetric. Matter-antimatter asymmetry is realized functionally at the level of DNA double strand in the sense that only DNA strand is transcribed. The study of some examples shows that genes defined as transcribed parts of DNA do not satisfy Chargaff's rule. This inspires the hypothesis about the breaking of matter antimatter symmetry. Genes have non-vanishing net A-T and C-G and therefore also net Qa with sign opposite to that in control regions. Just as the Universe is matter-antimatter asymmetric, also genes would be matter-antimatter asymmetric.

3. Isospin symmetry at quark level

A←→ G and T←→ A correspond change of anomalous em charge by 1 unit and these operations respect color confinement condition. Local modifications of DNA inducing these changes should be preferred. The identification for the symmetries A←→ G and T←→ A for the third nucleotide of code is as isospin symmetries. For the vertebrate mitochondrial code the symmetry exact and for nuclear code slightly broken.

4. Matter antimatter asymmetry and isospin symmetries for the first two nucleotides

The first two nucleotides of the codon dictate to a high degree which amino-acid is coded. This inspires the idea that 3-code has emerged as fusion of 1- and 2-codes in some sense. There are two kinds of 2-codons. The codons of type A have fractional em charge and net quark number (consisting of either matter or antimatter at quark level) and are not able to form color singlets. The codons of type B have integer em charge and vanishing quark number (consisting of matter and antimatter) and are able to form color singlets. The 2-codons of type A (resp. B) are related by isospin rotations and there should be some property distinguishing between types A and B. There indeed is: if 2-codon is matter-antimatter symmetric, 1-codon is not and vice versa.

  1. For almost all type A codons the amino-acid coded by the codon does not depend on the last nucleotide. There are two exceptions in the case of the nuclear code: (leu,leu,phe,phe) and (ile,ile,ile,met). For human mitochondrial code one has (ile,ile,ile,ile) and thus only one exception to the rule. The breaking of matter-antimatter symmetry for the third nucleotide is thus very small.

  2. For codons of type B the 4-columns code always for two doublets in the case of vertebrate mitochondrial code so that for codons with vanishing net quark number the breaking of matter-antimatter symmetry for the third nucleotide is always present.

5. Em stability

Anomalous em charge Qa vanishes for DNA and perhaps also mRNA strand containing also the G cap and poly-A tail which could compensate for the Qa of the transcribed region so that

2(A-T)-(G-C)≈ 0

or some variant of it holds true. Chargaff's rules for long DNA strands imply the smallness of Qa.

6. Summary of testable working hypothesis

Following gives a summary of testable working hypothesis related to the isospin symmetry and color singletness. The property of having integer valued/vanishing Qa is referred to as property P.

  1. Gene plus control region and also DNA repeats should have property P. Transcribed and control regions of gene have Qa with opposite signs.

  2. Transposons, repeating regions, the overhangs associated with the cut and paste of transposon, and the DNA strands resulting in cutting should have property P. This could explain why transposons can paste themselves to AT and GC (Qa=0) rich repeating regions of DNA. The points at which DNA can be cut should differ by a DNA section having property P. This gives precise predictions for the points at which transposons and pieces of viral DNA can join and could have implications for genetic engineering.

  3. If also mRNA is braided, it has property P. This can be only true if the poly-A tail compensates for the non-vanishing Qa associated with the translated region.

  4. Living hairpins should have property P. If only double helix parts of hairpins are braided, the prediction is trivially true by the palindrome property. tRNA or at least parts of it could be braided. Braids could end to the nuclear membrane or mRNA or to the amino-acid attachable to tRNA. For stem regions Qa is integer valued. The fact that the nucleotide of the anticodon corresponding to the third nucleotide of codon can base pair with several nucleotides of mRNA suggests that I(nositol) can have Qa opposite to that of A,T,C and U opposite to that of A,G. For 2-anticodon the pairing would be unique. This would give a lot of freedom to achieve property P in weak sense for tRNA. Braid structure for tRNA + amino-acid could be different that for tRNA alone and also in the translation the braid structure could change.

  5. Also aminoacids could be braided. Qa could vary and correspond to Qa for one of the codons coding for it. The aminoacid sequences of catalysts attaching to DNA strand should have opposite Qa for each codon-aminoacid pair so that aminoacid would attach only to the codons coding for it.

For a more detailed exposition and background see the chapter DNA as Topological Quantum Computer of "Genes and Memes".

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