utorak, 19. listopada 2010.

Correlation of the methylation of BRCA1 and RASSF1A in EOC tissues (6)

Arithmetic progression

We shall now give some mathematical evidences that will prove that in the biochemistry of BRCA1 and RASSF1A in EOC tissues there really is programmatic and cybernetic algorithm in which it is „recorded“, in the language of mathematics, how the molecule will be built and what will be the quantitative characteristics of the given genetic information.

Primer sequences





Progression of atomic numbers



5’

G

G

T

T

A

A

T

T

T

A

G



156

222

288



494

560


696

774















1696

1618

1552



1346

1280


1148

1078

5’

T

C

A

A

C

A

A

A

C

T

C



124

194

264



462

532


656

714















1552

1494

1424



1226

1156


1028

962

5’

G

G

T

T

A

A

T

T

T

A

G



156

222

288



494

560


696

774















1680

1602

1536



1330

1264


1132

1062

5’

T

C

A

A

C

G

A

A

C

T

C



124

194

264



470

540


664

722















1592

1534

1464



1258

1188


1060

994















7080

7080

7080



7080

7080


7080

7080






Progression of atomic numbers




5’

……

A

G

A

G

T

T

T

T

G

A

G

A




774


922





1264


1412



















1078


930





588


440


5’

……

T

C

A

C

A

C

C

A

C

A

C

A




714


842





1156


1284



















962


834





520


392


5’

……

A

G

A

G

T

T

T

C

G

A

G

A




774


922





1256


1404



















1062


914





580


432


5’

……
















5364


5364





5364


5364

















Figure 5. Progression of atomic numbers of BRCA1 and RASSF1A in EOC tissues

Notes: By using chemical-information procedures, we calculated the arithmetic progression for the information content of aforementioned nucleotides.

We would particularly like to stress here that the genetic, as well as biochemical information in a broader sense of the word, is determined and characterized by very complex cybernetic and information principles. The constantans in those principles are: the number of atoms and molecules, atomic numbers, atomic weight, physical and chemical parameters, even and odd values, codes and analogue codes, standard deviations, frequencies, primary and secondary values, and many other things.

DISCUSSION

The results of our research show that the processes of sequencing the molecules are conditioned and arranged not only with chemical and biochemical lawfulness, but also with program, cybernetic and informational lawfulness too. At the first stage of our research we replaced nucleotides from the Amino Acid Code Matrix with numbers of the atoms and atomic numbers in those nucleotides. Translation of the biochemical language of these amino acids into a digital language may be very useful for developing new methods of predicting protein sub-cellular localization, membrane protein type, protein structure secondary prediction or any other protein attributes. Since the concept of Chou's pseudo amino acid composition was proposed 1,2, there have been many efforts to try to use various digital numbers to represent the 20 native amino acids in order to better reflect the sequence-order effects through the vehicle of pseudo amino acid composition. Some investigators used complexity measure factor 3, some used the values derived from the cellular automata 4-7, some used hydrophobic and/or hydrophilic values 8-16, some were through Fourier transform 17,18, and some used the physicochemical distance 19. The author [34-42] is devoted to provide a digital code for each of 20 native amino acids. These digital codes should more complete and better reflect the essence of each of the 20 amino acids. Therefore, it might stimulate a series of future work by using the author’s digital codes to formulate the pseudo amino acid composition for predicting protein structure class [20-22], subcellular location [23, 24], membrane protein type [9, 25], enzyme family class [26, 27], GPCR type [28, 29], protease type [30], protein-protein interaction [31], metabolic pathways [32], protein quaternary structure [33], and other protein attributes. It is going to be possible to use a completely new strategy of research in genetics in the future. However, close observation of all these relationships, which are the outcomes of periodic laws (more specifically the law of binary coding), stereo-chemical and digital structure of proteins.

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