Tuesday, June 21, 2016

Are sound-like bubbles whizzing around in DNA essential to life?

I got a link to a very interesting article about sound waves in DNA (see this). The article tells about THz de-localized modes claimed to propagate forth and back along DNA double strand somewhat like bullets. These modes involve collective motion of many atoms. These modes are interpreted as a change in the stiffness of the DNA double strand leading to the splitting of hydrogen bonds in turn leading to a splitting into single strands. The resulting gap is known as transcriptional bubble propagating along double strand is the outcome. I do not how sound the interpretation as sound wave is.

It has been proposed that sound waves along DNA give rise to the bubble. The local physical properties of DNA double strand such as helical structure and elasticity affect the propagation of the waves. Specific local sequences are proposed to favor a resonance with low frequency vibrational modes, promoting the temperary splitting of the DNA double strand. Inside the bubble the bases are exposed to the surrounding solvent, which has two effects.

Bubbles expose the nucleic acid to reactions of the bases with mutagens in the environment whereas so called molecular intercalators may insert themselves between the strands of DNA. On the other hand, bubbles allow proteins known as helicases to attach to DNA to stabilize the bubble, followed by the splitting the strands to start the transcription and replication process. The splitting would occur at certain portions of DNA double strand. For this reason, it is believed that DNA directs its own transcription.

The problem is that the strong interactions with the surrounding water are expected to damp the sound wave very rapidly. Authors study experimentally the situation and report that propagating bubbles indeed exist for frequencies in few THz region. Therefore the damping deo not seem to be effective. How this is possible? As an innocent layman I also wonder how this kind of mechanism can be selective: it would seem that the bullet like sound wave initiates transcription at many positions along DNA. The transcription should be localized to a region assignable to single gene. What could guarantee this?

Can TGD say anything interesting about the mechanism behind transcription and replication?

  1. In TGD magnetic body controls and coordinates the dynamics. The strongest hypothesis is that basic biochemical process are induced by those for dark variants of basic bio-molecules (dark variants of DNA, enzymes,...). The belief that DNA directs its own transcription translates to the statement that the dark DNA consisting most plausibly from sequences of dark proton triplets ppp at dark magnetic flux tubes controls the transcription: the transcription/replication at the level of dark DNA induces that at the level of ordinary DNA.

  2. If the dark DNA codons represented as dark proton triplets (ppp) are connected by 3 flux tube pairs, the reverse of the reconnection should occur and transform flux tube pairs to two U-shaped flux tubes assignable to the two dark DNA strands. Dark proton sequences have positive charge +3e per dark codon giving rise to a repulsive Coulomb force between them. There would be also an attractive force due to magnetic tension of the flux tubes. These two forces would compensate each other in equilibrium (there also the classical forces due to the negatively charged phosphates associated with nucleotides but these would not be so important).

    If the flux tube pairs are split, the stabilizing magnetic force however vanishes and the dark flux tubes repel each other and force the negatively charged DNA strands to follow so that also ordinary DNA strand splits and bubble is formed. The primary wave could therefore be the splitting of the flux tube pairs: whether one can call it as a sound wave is not clear to me. Perhaps the induced propagating splitting of ordinary DNA double strand could be regarded as an analog of sound wave.

    The splitting of flux tube pairs for a segment of DNA would induces a further splitting of flux tubes since repulsive Coulomb force tends to drive the flux tubes further away. The process could be restricted to DNA if the "upper" end of the split DNA region has some dark DNA codons which are not connected by flux tubes pairs. This model reason why for dark proton sequences.

  3. This model does not yet explain how the propagating splitting wave is initiated. Could a quantum phase transition increasing the value of heff associated with the flux tube pairs occur for some minimal portion of dark DNA "below the region associated with gene and lead to the propagating wave induced by the above classical mechanism? That the wave propagates in one direction only could be due to chirality of DNA double helix.

An interesting question is how the RNA world vision relates to this general picture.

  1. There are strong conditions on the predecessor of DNA and RNA satisfies many of them: reverse transcription to DNA making possible transition to DNA dominated era is possible. Double stranded RNA exists in cells and makes possible RNA genome: this would however suggest that cell membrane came first. RNA is a catalyst. RNA has ability to conjugate an amino-acid to the 3' end of RNA and RNA catalyzes peptide bond formation essential for translation. RNA can self-replicate but only relatively short sequences are produced.

  2. TGD picture allows to understand why only short sequences of RNA are obtained in replication. If the replication occurs at the level of dark ppn sequences as it would occur for DNA in TGD framework, long RNA sequences might be difficult to produce because of the stopping of the propagation of the primary wave splitting the flux tube pairs. This could be due to the neuron pairs to which there is associated no Coulomb repulsion essential for splitting.

  3. In TGD framework RNA need not be the predecessor of DNA since the evolution would occur at the level of dark nucleon strings and DNA as the dark proton string is the simpest dark nucleon string and might have emerged first. Dark nuclear strings would have served as templates and biomolecules would have emerged naturally via the transcription of their dark counterparts to corresponding bio-polymers.

An updated nuclear string variant is summarized and also its connection with the model of harmony is discussed in chapter Three new physics realizations of the genetic code and the role of dark matter in bio-systems and in the article About physical representations of genetic code in terms of dark nuclear strings

For a summary of earlier postings see Latest progress in TGD.

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