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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