by Jean-Claude PEREZ, August 2000
|
Highlights
|
“The principle of Jean-Claude Perez’s discovery appeals to me. Indeed, it is quite possible, that, beyond the sequences, there is a kind of “supra-code” of the DNA .
That could particularly explain these sequences within the DNA which do not code, which are not used for the synthesis of the proteins and of which one says that they are not used for nothing”
PASTEUR Institute – Paris
In “Sciences et Avenir”,
“la musique des gènes” April 1995 (4)
|
Abstract
|
If we must define what is TRANS-GENOMICS, we would say two things :
- TRANS-GENOMICS approaches the study of GENOMICS and PROTEOMICS using new theoretical concepts and basic research laws.
- TRANS-GENOMICS solutions are characterized by a MORE GLOBAL and UNIFYING approach of Genetics.
We have voluntarily selected a first example of illustration which complies with these two rules which will define from now on this term “TRANS-GENOMICS”.
For this example, we chose the “JUNK-DNA” that the too reductionistic Molecular Biology approaches are unaware of or, at best, regard as a curiosity.
Technology used here will be principally the oldest (improved since 1990!) and the least powerful of our two new technologies : DNA SUPRA-CODE. Meanwhile, we prove also a LINE1 high level structure using the other powerfull “GUGC” technology.
We want to thus bring Genetics researchers who will consult the geNum.com’s WEB site to be discovered, suddenly, that the TRANS-GENOMICS world is already a to-day’s reality…
About DNA SUPRA-CODE…
The Supra-code of DNA measures STABILITY, therefore the solidity of the DNA molecule. This high level of organization is checked everywhere, in all points of the genomes : the genes, well on, but also junk DNA…
About GENOMICS / PROTEOMICS UNIFICATION…
The “GUGC” (Global Unified Genetic Code) discovery unifies globally GENOMICS and PROTEOMICS worlds. This law comes from the bio-atoms weights low level to the long-range level of wholes genomes. The “GUGC” based technology UNIFIES the three Genetics worlds : DNA, RNA and Proteins.
Now, we will show here how LINE1 (usually also named “L1”), the most frequent retrotransposon of the human genome has a superstructure as well on the level of the relative TCAG bases proportions distribution as on the level of the BALANCE of its ATOMIC WEIGHTS
|
Introduction
|
Genomic mobile elements, called RETROTRANSPOSONS, make up about 40% of the mammalian genome (1)… Their “copy-process” is based on reverse-transcritase process similar with retroviruses as HIV. Then the RNA intermediary stage is a major step of this copy-process.
Precisely, we introduce with “GUGC” and “ATGC” basic research discoveries particular rules where we prove that the role of G an T(U) nucleotides is major in the RNA world.
In other hand, DNA SUPRA-CODE discovery contributes to measure the mechanical stability of the DNA and/or RNA strands (2).
The major retrotransposon is the “LINE1” sequence of 6045bp lenght. There are roughly 500000 truncated LINE1 sequences and 5000 full-length dispersed throughout the human genome, accounting for 15% to 17% of its mass!!!
In this analysis, we work from a particular case of mutation where a retrotransposon within the Betaglobin gene intron 2 causes the BETA-THALASSEMIA blood human disease (3).
The goal of our short report is to demonstrate the very high organisation level of the “major human genome JUNK component” : the LINE1 sequence.
Then we do both analysis using our two different technologies “GUGC : Global Unified Genetic Code” and, more particularly, “the DNA SUPRA-CODE”.
|
Genomics / Proteomics Global Unification proves that “Junk Line1”
is a perfect life jewellery junk |
The LINE1 sequence includes various functional sub-areas, particularly, a reverse transcriptase (within ORF2) and two proteins : ORF1 encodes a nucleic acid binding protein, than ORF2 encodes various sub-functions and, particularly, a zinc finger-like motif.
The following map shows a good level of organization of the GLOBAL LINE1 sequence, of 6045 nucleotides length.
|
|
The “GENOMICS / PROTEOMICS coupling” and “Functional sites” concepts will be specified in other sections of this site. Meanwhile, we can already affirm the high level of global and homogeneous organization of LINE1. For example :
|
|
DNA Supra-Code proves that “Junk Line1”
is a perfect stable DNA-Double Strand |
Now, we will show that these thousands of JUNK LINE1 sequences are very highly organized and form coherent entities probably very STABLE.
Another study, such as those which we carry out on the TRANSGENES and G.M crops DNA sequences, would show how the “random” insertion of LINE1 sequences within the genome contributes probably, to increase and reinforce the global genomic stability…
Let us recall that the SUPRA-CODE of ADN seeks contiguous sequences of bases which are split, exactly, according to FIBONACCI’s and LUCAS’s Numbers (which one knows that they control morphogenesis and the proportions of eggs, nautilus, apple-pines, cactus, sunflowers etc…). The DNA SUPRA-CODE discovery is described in the following book “L’ADN décrypté” (as “DNA deciphered”, see reference 2).
We recall both series :
FIBONACCI’s serie :
1 1 2 3 5 8 13 21 34 55 89 144 233 377 610 987 1597 2584 4181 etc…
LUCAS’s serie :
1 3 4 7 11 18 29 47 76 123 199 322 521 843 1364 2207 3571 etc…
Each term is obtained there by making the sum of the 2 precedents.
The ratio of two consecutive terms (Exp. 89/55) approach very quickly the famous proportion PHI known as “of the Golden section” : PHI=1.618033989…
People of Antiquity considered Golden section to the same fundamental level as PI=3.14…
We demonstrate in (2) that “Golden section” of natural structures reinforces the mechanical and physical STABILITY and SOLIDITY.
Please, see “EGGS” SOLIDITY due to PHI shapes proportions, see also the “NAUTILUS” shell SOLIDITY (and AESTHETICS) resulting, also, from PHI based proportions (FIBONACCI’s numbers controlling growth and shape)…
One introduces the concept of resonance of a DNA section :
If, for example, 89 bases TCAG are divided into 34 bases T and 55 bases ACG, we will say that this partition ( 34 T + 55 ACG = 89 TCAG ) constitutes a resonance.
One discovers thousands of “resonances” within DNA strands, of which some are very long.
In addition, we discovered, in GUGC (Total Unified Genetic Code), the major part played by sub-clusters of bases G and T (or U), in opposition to two other remaining bases A and C.
We thus will seek here possible “resonances” between :
T+G <==> A+C,
and, consequently, between T+G <==> T+C+A+G, on the one hand,
and between A+C <==> T+C+A+G on the other hand.
Here the table showing very long resonances TG/AC structuring “LINE1” retrotransposon :
| LINE1: 6045nt |
Resonances
Length/number |
Resonances
Length/number |
Resonances
Length/number |
Resonances
Length/number |
Total
|
| Fibonacci’s resonances FFF: lenght |
—
|
1597
|
2584
|
4181
|
—
|
| FFF: number |
46
|
56
|
41
|
16
|
159
|
| Lucas’s resonances LLL: lenght |
843
|
1364
|
2207
|
3571
|
—
|
| LLL: number |
—
|
53
|
27
|
67
|
201
|
| Total |
—
|
—
|
—
|
83
|
360
|
Note: “FFF” is related to “Fibonacci/Fibonacci/Fibonacci” resonances, where the three components of the resonance are three consecutive Fibonacci’s numbers.
“LLL” is related to “Lucas/Lucas/Lucas” resonances, where the three components of the resonance are three consecutive Lucas’s numbers.
We remark that 360 resonances of more than 843 bases length for a long DNA segment of just 6000 bases, it is considerable… These resonances constitute a virtual ARCHITECTURE of the LINE1 retrotransposon DNA molecule.
But we now will show that this balance is not only mathematical, abstracted, virtual and symbolic… This balance subtle is even REAL at the MOST CONCRETE level which can be imagined : the BALANCE OF the ATOMIC MASSES of the DNA molecule.
|
Harmonic Balancing of the DNA Atomic Masses in the Junk world
|
We could compute the exact atomic weights of the five fundamental nucleotides C,U,T,A,G :
- C = 110.095859
- U = 111.080595
- T = 125.107589
- A = 134.121023
- G = 150.120453
This precise values results from the chemical composition of nucleotides and from the atomic weights of the five bio-atoms constituting nucleotides :
- C = 12.0111
- H = 1.007947
- O = 15.99943
- N = 14.006747
- P = 30.9737624
One then can, for each resonance, to calculate and analyze the balance of the masses.
Thus, if one considers the first of 360 long found resonances, it starts at base 264 and extends over a length from 3571 bases :
It includes 650 bases T and 714 bases G, therefore: 1364 bases T or G.
It includes also 1399 bases A and 808 bases C, therefore: 2207 bases A or C.
1364, 2207 and 3571 are three consecutive LUCAS’s numbers.
Then the ratios between numbers of bases are:
TCAG / AC = 1.61803353 = Phi.
TCAG / TG = 2.618035191 = Phi*2.
AG / TG = 1.618035191 = Phi.
Then, if we replace, in each DNA strand, each symbolic base by its atomic mass, then we obtain :
TaCgAtGc / AtCg = 1.618403547 = Phi.
TaCgAtGc / TaGc = 2.618403547 = Phi*2.
AtCg / TaGc = 1.61706705 = Phi.
In this notation, we noted in capital letter the bases of the principal DNA strand and in small letters the facing bases on the complementary DNA strand (Crick/Watson bases pairs).
If we do the same computations for DNA/RNA strands (RNA transcripts from DNA double strand), we obtain also good atomic weights balances but however worse (example : 1.602489256 for ratio UaCgAtGc / AtCg (in this hybrid double strand, one stand contains UCAG bases and the other strand contain TCAG bases).
The long list below will demonstrate, for 83 very long resonances :
- their origin,
- their length,
- their ratio DNA nucleotides proportions TCAG / AC,
- and their ratio DNA atomic weights TaCgAtGc / AtCg.
Origin | Length | Ratio bases | Ratio weights
_______ resonances 1 to 20 __________
264 3571 1.618033 1.618403
265 3571 1.618033 1.618401
266 3571 1.618033 1.618400
267 3571 1.618033 1.618400
268 3571 1.618033 1.618400
270 3571 1.618033 1.618400
271 3571 1.618033 1.618401
277 3571 1.618033 1.618401
279 3571 1.618033 1.618402
339 3571 1.618033 1.618404
386 3571 1.618033 1.618411
388 3571 1.618033 1.618412
393 3571 1.618033 1.618414
400 3571 1.618033 1.618413
402 3571 1.618033 1.618413
403 3571 1.618033 1.618411
404 3571 1.618033 1.618410
405 3571 1.618033 1.618408
406 3571 1.618033 1.618407
410 3571 1.618033 1.618408
Origin | Length | Ratio bases | Ratio weights
_______ resonances 21 to 40 _________
411 3571 1.618033 1.618407
413 3571 1.618033 1.618407
415 3571 1.618033 1.618405
416 3571 1.618033 1.618405
419 3571 1.618033 1.618400
420 3571 1.618033 1.618401
426 3571 1.618033 1.618401
427 3571 1.618033 1.618399
434 3571 1.618033 1.618398
435 3571 1.618033 1.618398
436 3571 1.618033 1.618397
437 3571 1.618033 1.618395
438 3571 1.618033 1.618394
439 4181 1.618034 1.618376
439 3571 1.618033 1.618392
440 4181 1.618034 1.618375
440 3571 1.618033 1.618392
441 3571 1.618033 1.618392
446 3571 1.618033 1.618393
448 3571 1.618033 1.618393
Origin | Length | Ratio bases | Ratio weights
_______ resonances 41 to 60 _________
449 3571 1.618033 1.618394
450 3571 1.618033 1.618395
452 3571 1.618033 1.618394
455 3571 1.618033 1.618397
456 3571 1.618033 1.618397
457 3571 1.618033 1.618398
460 3571 1.618033 1.618398
462 3571 1.618033 1.618401
465 3571 1.618033 1.618404
476 3571 1.618033 1.618406
477 3571 1.618033 1.618406
482 3571 1.618033 1.618403
490 3571 1.618033 1.618402
491 3571 1.618033 1.618403
492 3571 1.618033 1.618404
493 3571 1.618033 1.618406
494 3571 1.618033 1.618406
500 3571 1.618033 1.618406
511 3571 1.618033 1.618401
556 3571 1.618033 1.618399
Origin | Length | Ratio bases | Ratio weights
_______ resonances 60 to 83 _________
577 3571 1.618033 1.618388
596 3571 1.618033 1.618390
597 3571 1.618033 1.618390
608 3571 1.618033 1.618388
1741 4181 1.618034 1.618325
1743 4181 1.618034 1.618325
1744 4181 1.618034 1.618324
1745 4181 1.618034 1.618324
1752 4181 1.618034 1.618326
1753 4181 1.618034 1.618327
1825 4181 1.618034 1.618322
1828 4181 1.618034 1.618322
1829 4181 1.618034 1.618322
1845 4181 1.618034 1.618329
1846 4181 1.618034 1.618329
1847 4181 1.618034 1.618329
1848 4181 1.618034 1.618329
1849 4181 1.618034 1.618329
2324 3571 1.618033 1.618306
2330 3571 1.618033 1.618308
2331 3571 1.618033 1.618310
2333 3571 1.618033 1.618311
2334 3571 1.618033 1.618311
It is noted that these very long resonances overlaps the quasi full 6045bp LINE1 sequence. (from base 264 to base 6029=1848+4181). Particularly, we note the fact that the 200 first bases are not overlapped by long-range resonances. Perhaps this fact reinforces the poorly characterized 5′ internal promoter reported by researchers (1).
In other hand, the ideal PHI ratio is strongly approached throughout this sequence. We recall the ideal PHI value : PHI=1.618033989.
It is particularly interesting to analyse the “ratio weights” :
- An absolute error varying between 0.000272 and 0.000374.
- A relative error varying between 16/100000 and 23/100000.
More precisely, these ratios mean that the ratio between the total mass of the double helix overlapped by the resonance and accumulate T and G weights of the principal strand and their complements A or C of the complementary strand reaches this ideal balance of PHI…
A hidden reason of this ideal balance results from the quasi equality between the sums of masses T+A and C+G. One will note finally this UNIFICATION of the laws since our interest for the sets of bases T(U) and G comes from RNA world laws whereas physical balance that we reveal here operates in the double helix DNA world.
|
Conclusions
|
We have just introduced here a new technology which is able to discover an unsuspected order in mediums, that the specialists had baptized “JUNK DNA”, because, precisely, they did not see null structure… there
The Genetics universe is organized according to mathematical laws which take their source as of the fundamental level of the atomic masses of the bio-atoms…
We here have just shown how these new laws “structure” and organize overall most banal, but also most frequent, of the sequences of the human genome : retrotransposon “LINE1” …
We show that LINE1 has a GLOBAL BALANCE constituting a true subtle ARCHITECTURE which is propagated up to the level of the BALANCE of the masses of its DNA molecule…
It is by controlling such laws that geNum can, for example, to analyze the STABILITY of the TRANSGENES and to propose scientifically founded strategies of G.M. (Genetically Manipulated) and TRANSGENICS CROPS…
But, it is also why geNum’s TECHNOLOGY controls these same laws, as geNum can inform RISKS of the G.M. “arranged” such as one them are built presently…
Now, you are welcome in the new TRANS-GENOMICS technology world.
BIBLIOGRAPHY :
(1) – Haig H. Kazazian jr., SCIENCE 289 1152-1153 18 august 2000.
(2) – Jean-claude Pérez, “L’ADN décrypté”, Ed Marco Pietteur 39 av. du centenaire – 4053 Embourg Belgium (1997) – ISBN 2-87211-017-8.
(3) – Kimberland, M.L. et al, ” Full-length human L1 insertions retain the capacity for high frequency retrotransposition in cultured cells”, submitted (10 May 1999) journal Genetics, see GENBANK AF149422.