Tuesday, January 29, 2008

Anomalous em charge and transposons

TGD based model of tqc relies on colored braids with the color of braid in one-one correspondence with nucleotides A,T,C,G and represented by 2 quarks and 2 anti-quarks. The basic prediction of the braid concept is anomalous em charge defined as the net quark charge assignable to DNA space-time sheets of DNA sequence. This notion makes sense also for more general molecules possessing braids. Transposons provide an especially simple manner to test the hypothesis that anomalous em charge is integer valued (quarks can form color singlet) or even vanishing (by stability).

Transposons (see this and the article of D. F. Voytas (2008), Fighting fire with fire, Nature vol 451, January) are moving and copying genes. Moving genes cut from initial position and past to another position of double strand. Copying genes copy themselves first to RNA and them to a full DNA sequence which is then glued to the double strand by cut and paste procedure. They were earlier regarded as mere parasites but now it is known that their transcription is activated under stress situations so that they help DNA to evolve. In tqc picture their function would be to modify tqc hardware. For copying transposons the cutting of DNA strand occurs usually at different points for DNA and cDNA so that "sticky ends" result ("overhang" and its complement) (see ). Often the overhang has four nucleotides. The copied transposon have ends which are reversed conjugates of each other so that transposons are palindromes as are also DNA hairpins. This is suggestive of the origin of transposons./p>

In order to avoid boring repetitions let us denote by "satisfy P" for having having integer valued (or even vanishing) Qa. The predictions are following:

  1. The double strand parts associated with the segments of DNA produced by cutting should satisfy P.
  2. The cutting of DNA should take place only at positions separated by segments satisfying P.
  3. The overhangs should satisfy P.
  4. Transposons should satisfy P.
In the example mentioned here, the overhang is CTAG and has vanishing Qa.

It is known that transposons - repeating regions itself - tend to attach to the repeating regions of DNA.

  1. There are several kinds of repeating regions. 6-10 base pair long sequences can be repeated in untranslated regions up to 105 times and whole genes can repeat themselves 50-104 times.
  2. Repeats are classified into tandems (say TTAGGG associated with telomeres), interspersed repetitive DNA (nuclear elements), and transposable repeat elements. Interspersed nuclear elements (INEs) are classified LINEs (long), SINEs (short), TLTRs (Transposable elements with Long Terminal Repeats), and DNA transposons themselves.
  3. LINEs contain AT rich regions. SINEs known as alus (about 280 bps) contain GC rich regions whereas mariner elements (about 80 bps) are flanked by TA pairs. LTRs have length 300-1000 bps. DNA transposons are flanked with two short inverted repeat sequences flanking the reading frame: "inverted" refers to the palindrome property already mentioned.

AT and CG have vanishing Qa so that their presence in LINEs and SINEs would make the cutting and pasting easy allowing to understand why transposons favor these regions. Viruses are known to contain long repeating terminal sequences (LTR). One could also check whether DNA decomposes to regions satisfying P and surrounded by repeating sequences which satisfy P separately or as whole as in the case DNA transposons.

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

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