(CT)(CT)
(CT)(AC)
(CT)(TG)
(CT)(AG)
(CT)(TA)
(CT)(CG)

(AC)

(AC)(AC)
(AC)(TG)
(AC)(AG)
(AC)((TA)
(AC)(CG)

(TG)

(TG)(TG)
(GT)(AG)
(GT)(TA)
(GT)(CG)

(AG)

(AG)(AG)
(AG)(TA)
(AG)(CG)

(TA)
(TA)
(TA)
(TA)AA
(TA)GG
(TA)(CT)
(TA)(AC)
(TA)(GT)
(TA)(AG)
(TA)(TA)
(TA)(CG)

TT
CC

(CG)
(CG)
(CG)
(CG)AA
(CG)(GG)
(CG(CT)
(CG)(AC)
(CG)(TG)
(CG)(AG)
(CG)(TA)
(CG)(CG)

TT
CC

Only the upper half of the symmetric and independent coding (bold) and noncoding (lower font) elements of square symmetric matrix M (I, J) are shown. Under 4^thassumption, any combinations of (AT) NN and (CG) NN (where N is A, T, C, or G) in lower font are noncoding. The lower half of square symmetric matrix M (J, I) can be generated using M (J, I)=M (I, J) (where I=1, 2, 3 . . . 10, and J=1, 2, 3 . . . 10). The isocodon can be generated using these elements, as illustrated in rows 9 and 10 for columns 9 and 10, respectively.

The twenty bold independent protein-encoding codons from TABLE 2 (replacing T with U for mRNA) and the corresponding isocodons are shown in TABLE 3. In Table 4, the thirty-five unique, independent noncoding codons (retaining DNA bases) are shown in lower font.

TABLE 3

Twenty protein-encoding QED codons and their synonymous isocodons from

For protein synthesis, T in TABLE 2 has been replaced by U for mRNA.

Quadruplet Expanded DNA (QED) Codons
Hydrogen

Codons
Synonymous Isocodons, T(U)
Bond

1
UUUU
UUUU

8

2
CCCC
CCCC

12

3
AAAA
AAAA

8

4
GGGG
GGGG

12

5
(AA)(CC)
(CC)(AA)

10

6
(UC)CC
(CU)CC
CC(UC)
CC(CU)
11

7
(UG)UU
(GU)UU
UU(UG)
UU(GU)
9

8
(UG)GG
(GU)GG
GG(UG)
GG(GU)
11

9
(CA)CC
(AC)CC
CC(CA)
CC(AC)
11

10
(UU)(GG)
(GG)(UU)

10

11
(AC)(CA)
(AC)(AC)
(CA)(CA)
(CA)(AC)
10

12
(GA)(GA)
(GA)(AG)
(AG)(GA)
(AG)(AG)
10

13
(GU)(GU)
(GU)(UG)
(UG)(UG)
(UG)(GU)
10

14
(GA)(GG
GG(GA)
GG(AG)
(AG)GG
11

15
(CA)AA
(AC)AA
AA(CA)
AA(AC)
9

16
UU(UC)
UU(CU)
(UC)UU
(CU)UU
9

17
(AG)AA
AA(GA)
AA(AG)
(GA)AA
9

18
(AA)(GG)
(GG)(AA)

10

19
(CU)(CU)
(CU)(UC)
(UC)(UC)
(UC)(CU)
10

20
(UU)(CC)
(CC)(UU)

Bar graph 100 of FIG. 1 shows the number of hydrogen bonds in twenty QED protein-encoding codons from TABLE 3, above.

TABLE 4

Thirty-five noncoding regulatory QED codons from TABLE 2.

Noncoding

Codons
Iso-noncoding Codons
H. B.

1
(TA)(TA)
(TA)(AT)
(AT)(TA)
(AT)(AT)
8

2
(CG)(CG)
(GC)(GC)
(GC)(CG)
(GC)(GC)
12

3
(AT)GG
GG(TA)
GG(AT)
(TA)GG
10

4
(TG)(AC)
(AC)(TG)
(TG)(CA)
(AC)(GT)
10

5
(TG)(AG)
(GT)(AG)
(TG)(GA)
(GT)(AG)
10

6
(TG)AA
AA(TG)
(GT)AA
AA(GT)
9

7
(TA)(GT)
(GT)(TA)
(TA)(TG)
(GT)(AT)
9

8
(TA)(GA)
(AG)(TA)
(TA)(AG)
(GA)(AT)
9

9
(TA)(GC)
(TA)(CG)
(CG)(TA)
(CG)(AT)
10

10
(TA)AA
AA(TA)
(AT)AA

8

11
(TA)(AC)
(AC)((TA)
(TA)(CA)
(AC)((AT)
9

12
(TT)(AA)
(AA)(TT)

8

13
(CC)(GG)
(GG)(CC)

12

14
TT(TA)
(TA)TT
(AT)TT

8

15
TT(AC)
(AC)TT
(CA)TT

9

16
TT(AG)
(GA)TT
(AG)TT

9

17
TT(CG)
(CG)TT
TT(GC)

10

18
CC(TA)
(TA)CC
(AT)CC

10

19
CC(TG)
(TG)CC
(GT)CC

11

20
CC(AG)
(AG)CC
(GA)CC

11

21
CC(CG)
(CG)CC
(GC)CC

12

22
AA(CT)
(CT)AA
(TC)AA

9

23
AA(CG)
(GC)AA
(CG)AA

10

24
GG(CT)
(CT)GG
(TC)GG

10

25
GG(CG)
(CG)GG
(GC)GG

12

26
GG(AC)
(AC)GG
(CA)GG

11

27
(AC)(CG)
(CA)(CG)
(CA)(GC)
(AC)(GC)
11

28
(AC)(AG)
(AC)(GA)
(CA)(GA)
(CA)(AG)
10

29
(AG)(CG)
(GA)(CG)
(AG)(GC)
(GA)(GC)
11

30
(CT)(TA)
(TC)(TA)
(CT)(AT)
(TC)(AT)
9

31
(CT)(CG)
(TC)(CG)
(CT)(GC)
(TC)(CG)
11

32
(CT)(AC)
(TC)(AC)
(CT)(CA)
(CT)(AC)
10

33
(CT)(AG)
(TC)(AG)
(CT)(GA)
(TC)(GA)
10

34
(CT)(TG)
(TC)(TG)
(CT)(GT)
(TC)(GT)
10

35
(GT)(CG)
(TG)(CG)
(GT)(GC)
(TG)(GC)
11

Bar graph 200 of FIG. 2 shows the number of hydrogen bonds in thirty-five noncoding QED codons from TABLE 4, above.

QED Codon Assignment

In some embodiments, the QED codons are applicable for protein synthesis and regulatory functions in both eukaryotes and prokaryotes. Since the protein-coding process is similar in prokaryotic and eukaryotic cells, the tentative QED protein-coding codon assignment could use the already verified triplet code based on at least the first two bases, ignoring the degeneracy due to a wobbly third base. For this purpose, the triplet codon table was rearranged with amino acids, degenerate codons, and corresponding tRNA by imposing the above four QED codon constraints. The final result is TABLE 5, where disallowed triplet codons are stricken.

TABLE 5

Amino acids, triplet mRNA codons and tRNA anticodons with the 4th QED

rule.

Triplet mRNA Codons under QED Constraint and tRNA Anticodons

Amino Acids
Triplet Codon/QED
Compressed Form
tRNA-Anticodon(38, 39)

Ala/A
[Image Omitted]

, GCA?
UGC

Arg/R
[Image Omitted]

AGR
CCG, ACG

AGA, AGG

Asn/N
[Image Omitted]

, AAC
AAC
GUU

Asp/D
[Image Omitted]

, GAC?
GUC

Cys/C
UGU, [Image Omitted]

UGU
GCA

Gln/Q
CAA, [Image Omitted]

CAA
UUG

Glu/E
GAA, GAG
GAR
YUC

Gly/G
GGU, [Image Omitted]

, GGA, GGG
GGD
NCC

His/H
[Image Omitted]

, CAC
CAC
GUG

Ile/I
[Image Omitted]

, AUC?
GAU

Leu/L
[Image Omitted]

, UUG, CUU, CUC,
UUG, CUY
YAA

[Image Omitted]

Lys/K
AAA, AAG
AAR
YUU

Met/M
[Image Omitted]

, AUG?
CAU

Phe/F
UUU, UUC
UUY
RAA

Pro/P
CCU, CCC, CCA, [Image Omitted]

CCH
KGG

Ser/S
UCU, UCC, [Image Omitted]

UCY
GGA

Thr/T

, ACC, ACA, [Image Omitted]

ACM
NGU

Trp/W
UGG
UGG
CCA

Tyr/Y
[Image Omitted]

, UAC?
GUA

Val/V
GUU, [Image Omitted]

, GUG
GUK
NAC

START
AUG
AUG

STOP
UAA, UAG, UGA
UAR, UGA

N: Any U, C, A, or G; Purine: R; Pyrimidine: Y; D: Not C; H: Not G; K G or U; M: A or C QED protein-coding codons are assigned using TABLE 3 and TABLE 5.

In TABLE 5, Nirenberg showed (References 9, 10) that polyU, polyA, and polyC encode the amino acids Phe, Lys, and Pro, respectively. The assignments directly linked mRNAs, tRNAs, amino acids, codons, and anticodons in ribosome protein synthesis. Additionally, in References 9, 10, oligo chain lengths of 3 and 4: (oU)₃and (oU)₄showed nearly the same activities. Therefore, it is reasonable to assume that if triplet UUU can encode Phe, quadruplet UUUU could also encode Phe. Following this reasoning, LLLL-Lys and CCCC-Pro have been assigned. Since GGG in TABLE 5 encodes Gly, GGGG-Gly has also been assigned. Thus, four QED codons have been assigned as follows:

QED: UUUU-Phe; AAAA-Lys; CCCC-Pro; and GGGG-Gly are listed in TABLE 6.

Next, sixteen QED codons are assigned following the TABLE 5 triplet codon assignments. In Crick's original proposal, only two bases of codons could encode only sixteen amino acids. Hence, he added a third base, creating codon degeneracy and allowing the third base to form a dangling bond with the first base of the tRNA anticodon. For QED codon assignments, the first two bases of the triplet codon of each amino acid in TABLE 5 are compared with the first two bases of the QED protein-coding codons in TABLE 3. The matching QED codon is assigned to that amino acid when a match occurs. Following this method, the QED codons are assigned as follows:

TABLE 5, Arg/R-AGA, AGG: If G is added to AGA and A is added to AGGA, then under QED assumptions 2 and 3, (AG)(GA) will represent both. In TABLE 3, element #12 (AG)(GA) matches this outcome. Thus, in TABLE 6, QED (AG)(GA)-Arg/R is assigned.

TABLE 5, Asn/N-AAC: Under QED assumption-4, only C can be added at the fourth position, resulting in AA (CC). Element #5 of TABLE 3 matches this outcome. Thus, in TABLE 6, AA (CC)-Asn/N is assigned.

TABLE 5, Cys/C-UGU: Under the QED constraint, only U can be added, resulting in UGUU. Element #7 of TABLE 3 matches this outcome. Thus, in TABLE 6, (UG) UU-Cys/C is assigned.

TABLE 5, Gln/Q-CAA: U and G are not allowed under the QED rules. Only A can be added, resulting in (CA) AA. Element #15 of TABLE 3 matches this outcome, and (CA) AA-Gln/Q is assigned in TABLE 6.

TABLE 5, Glu/E-GAA, GAG: Here, either A or G can be added to either codon, but adding A to GAA will result in a lower preferred bonding energy. Thus, GAAA is preferred. Isoform element #17 of TABLE 3 matches this outcome and is assigned (GA) AA-Gln/Q in TABLE 6.

TABLE 5, His/H-CAC: Under the QED rules, only C can be added in the fourth position, resulting in CACC. Element #9 of TABLE 3, (CA) CC matches this outcome and is assigned (CA)CC-His/H in TABLE 6.

TABLE 5, Leu/L-UUG, CUU, and CUC: Here, at the third position, there are one purine and two pyrimidines. Thus, a pyrimidine (U or C) will be preferred. Since U will require a lower bonding energy than C, U is selected for the fourth position, leading to (CU) (CU). In TABLE 3, element #19, (CU) (CU) matches this and is assigned (CU) (CU)-Leu/L in TABLE 6.

TABLE 5, Ser/S-UCU, UCC: As in the previous case, either U or C can be added at the fourth potion. Adding U to UCU will result in a lower energy (UC) UU. Element #16 of TABLE 3 matches this outcome and is assigned (UC) UU-Ser/S in TABLE 6.

TABLE 5, Thr/T-ACC, ACA: Following the previous reasoning, A is added to ACC and C to ACA, transforming these two codons into the same codon ((AC) (CA)). Element #11 of TABLE 3 matches this outcome. Therefore, (AC) (CA)-Thr/T is assigned in TABLE 6.

TABLE 5, Trp/W-UGG: Adding G at the fourth position is safe, resulting in UGGG. Element #8 of TABLE 3, (UG) GG, matches this outcome and is assigned as (UG) GG-Trp/W in TABLE 6.

TABLE 5, Val/V-GUU, GUG: As in the two previous cases, G is added to GUU, and U is added to GUG, resulting in the same codon ((GU) (UG)). Element #13 of TABLE 3 matches this and is assigned as (GU) (UG)-Val/V in TABLE 6.

TABLE 6

QED Codon Assignments

Amino

Acids
mRNA under QED
QED codons
Ref./comm.

Arg/R
AGA, AGG
(GA)(GA)
38

Asn/N
AAC
(AA)(CC)
38

Cys/C
UGU
(UG)UU
38

Gln/Q
CAA
(CA)AA
38

Glu/E
GAA, GAG
(AG)AA
38

Gly/G
GGU, GGA, GGG
GGGG
9, 10

His/H
CAC
(CA)CC
38

Leu/L
UUG, CUU, CUC
(CU)(CU)
38

Lys/K
AAA, AAG
AAAA
9, 10

Phe/F
UUU, UUC
UUUU
9, 10

Pro/P
CCU, CCC, CCA
CCCC
9, 10

Ser/S
UCU, UCC
(UC)UU
38

Thr/T
ACC, ACA
(AC)(CA)
38

Trp/W
UGG
(UG)GG
38

Val/V
GUU, GUG
(GU)(GU)
38

Ala/A
[Image Omitted]

(GG)(AA)*

Asp/D
[Image Omitted]

(GA)(GG)*

Ile/I
[Image Omitted]

UU(GG)*

Met/M
[Image Omitted]

(UC)CC*

Tyr/Y
[Image Omitted]

(UU)(CC)*

START
AUG
noncoding
Regulatory

STOP
UAA, UAG, UGA
noncoding
Regulatory

•To be assigned

Since five amino acids in TABLES 5 and 6 (Ala, Asp, Ile, Met, and Tyr) did not meet the QED codon requirements, they are listed with a question mark (?) and must be determined. Similarly, the remaining five QED codons: (GG)(AA), (GA)(GG), UU(GG), (UC)CC, and UU(CC) are also not assigned.

Consider the following amino acids: Ala, Asp, Ile, Met, and Tyr. Applying additional constraints, their QED coding assignment is predicted.

Multiple codons code the same amino acid in triplet coding, but one tRNA decodes many amino acids. However, AUG encodes both START and Met. The cause of this dual role additionally needs to be clarified. Further, Met is not the first amino acid in every protein. When Met is the first amino acid and is then removed, what is the mechanism?

It has been reported (Reference 40) that GUG and UUG encode Met. Thus, according to the prior procedure, if U is added to GUG and G to UUG, then in QED, the codon (UU) (GG) will cover both codons. Element #10 of TABLE 3 matches this outcome, and (UU) (GG)-Met is assigned. Since AUG has been assigned the noncoding START codon in QED, the double role dilemma will not arise.

TABLE 5. Ala, the triplet code GCN, N being U, C, A or G encodes Ala. Under QED, adjacent GC are not allowed. Since C has triple bond, replace C by G as GGN. Now replace GGN by GGA. Under QED, C and U are not allowed but G and A are allowed at fourth position making GGAG acceptable. Thus, (GG)(GA), number 14 of TABLE 3 matches encoding Ala shown in TABLE 6.

TABLE 5. Asp, the triplet GA(U/C) encodes. This could be GA(UC) but U and C are not allowed. But A replacing U and G replacing C will maintain the Hydrogen Bonds. Thus,

- GA(AG) or synonymous (GG)(AA) meets the requirement and number 18 matches is assigned for Asp.

TABLE 5. Tyr, the triplet UA(UC) encode Tyr. Under QED, A and G are not allowed. A combination of (UU)(CC) meets the requirement and number 20 matches. Thus, (UU)(CC) is assigned.

TABLE 5. Ile, the triplet AUH (H being U or C or A) encode Ile. Adjacent AU are not allowed but UU or AA is ok. Thus, UC (U or C) or (UC)(CC) will satisfy. The number 6 of TABLE 3 matches and is assigned to encode Ile under QED.

TABLE 7

QED protein-coding codon assignment based on TABLE 6 with the

corresponding numbers of hydrogen bonds.

Amino Acids
QED Codons
HB Bonds
QED Codons
Amino Acids

Arg
(GA)(GA)
10
(CU)(CU)
Leu

Asn
(AA)(CC)
10
(UU)(GG)
*Met

Cys
(UG)UU
9
(CA)AA
Gln

Glu
(GA)AA
9
(CU)UU
Ser

Gly
GGGG
12
CCCC
Pro

His
(CA)CC
11
(UG)GG
Trp

Lys
AAAA
8
UUUU
Phe

Thr
(AC)(CA)
10
(GU)(GU)
Val

Try
(UU)(CC)
10
(GG)(AA)
Asp

Ile
(UC)CC
11
(GA)GG
Ala

QED codons encoding amino acids in TABLE 7 have an exciting feature.

In some embodiments, the anticodon of the QED codon encoding an amino acid is the encoding QED codon of the other amino acid. For example, UUUU encodes Phe, and its anticodon AAAA encodes Lys. (UG)UU encodes Cys, and its anticodon is (AC)AA which is synonymous with (CA)AA, see TABLE 3 number 9. The same trait is valid for the remaining codons.

Based on the QED codon-anticodon relation, a possibility exists that only ten tRNA may be needed to synthesize proteins using canonical amino acids.

TABLE 8

QED regulatory noncoding codon assignments.

Triplet Codons
Noncoding QED Codons
QED Regulatory & Control

1
Absent
(TA)(TA)
TATA Box-Transcription start

2
Absent
(CG)(CG)
(CG)(CG), Exon/Intron Interface

3
START-AUG
(AU)GG
START
Comments

4
STOP-UGA (OPAL)
(UG)(AG)
STOP

5
STOP-UAG(AMBER)
(UA)(GA)
STOP

6
STOP-UAA(OCHER)
(UA)AA
STOP

7

(UG)(AC)
Regulatory
*
STOP

8

(UG)AA
Regulatory
*
STOP

9

(UA)(GC)
Regulatory
*
STOP

10

(UA)(GU)
Regulatory
*
STOP

11

(UA)(AC)
Regulatory
*
STOP

12

(TT)(AA)
Regulatory
*

13

(CC)(GG)
Regulatory
*

14

TT(TA)
Regulatory
*

15

TT(AC)
Regulatory
*

16

TT(AG)
Regulatory
*

17

TT(CG)
Regulatory
*

18

CC(TA)
Regulatory
*

19

CC(TG)
Regulatory
*

20

CC(AG)
Regulatory
*

21

CC(CG)
Regulatory
*

22

AA(CT)
Regulatory
*

23

AA(CG)
Regulatory
*

24

GG(CT)
Regulatory
*

25

GG(CG)
Regulatory
*

26

GG(AC)
Regulatory
*

27

(AC)(CG)
Regulatory
*

28

(AC)(AG)
Regulatory
*

29

(AG)(CG)
Regulatory
*

30

(CT)(TA)
Regulatory
*

31

(CT)(CG)
Regulatory
*

32

(CT)(AC)
Regulatory
*

33

(CT)(AG)
Regulatory
*

34

(GT)(CG)
Regulatory
*

35

(GT)(AG)
Regulatory
*To be assigned

Digital Representation

Bioinformatics and NGS analyses of DNA use digital techniques for the sequencing, analysis and interpretation of the results extensively. In some embodiments, for the future application of such techniques, QED codons are digitally represented. In some embodiments, four bases can be represented by two bits: 0 and 1, as follows: T: 11, A: 10, C: 01, and G: 00. Thus, each quadruplet QED codon will be represented by 8 digits consisting of 0 and 1 or one byte.

For example:

- TTTT: 11111111; CCCC: 01010101, AAAA: 10101010; GGGG: 00000000

Accordingly, each of the twenty protein-coding codons and thirty-five regulatory codons can be expressed by 8 bits (one byte). This will allow the development of compatible applications that easily capitalize on the usage of bioinformatics and cybersecurity tools.

In some embodiments, since HIPAA limits access to eHealth data, digitally encrypted codons and security codes will be employed to overcome this limitation. Furthermore, this capability will make it easy to develop and certify the diagnostic tools used at the point of care (POC) and provide a clear path for developing personalized medicine.

Incurable Rare Monogenic Diseases, Multigenic Cancers and Vaccines

The currently accepted disease model is that a dysfunctional protein causes disease. Gene mutations, errors in transcription and splicing are responsible for producing dysfunctional proteins. At present, more than 7,000 rare monogenic diseases are listed on the NIH website. To date, no cure for these diseases beyond the management of symptoms has been found.

A similar situation is observed for multigenic cancers. Over the last five decades since the establishment of the NCI (1970), cancer treatments have not changed considerably. Once a cancer is detected and shown not to have metastasized, treatment is initiated with surgery, followed by radiation and chemotherapy, with the goal of extending life by 5 years. Once metastasis or remission occurs, no further treatment is available. Thus, even if cancer is detected early, there is no cure, only life extension.

In rare diseases, dysfunctional proteins can be corrected at the protein level or the DNA level. At the protein level, this requires the replacement of incorrect amino acids with the correct ones. However, the currently accepted triplet codon is degenerate, with multiple codons encoding the same amino acid. This is a major hurdle in selecting a unique codon among the degenerate ones. The nondegenerate protein-coding QED codons are subject to no such limitation. At the DNA level, mutated genes can be corrected with CRISPR gene editing tools. When genes are correctly edited, normal proteins are generated to replace dysfunctional proteins.

In cancers, the lack of any biological technique for selectively accessing cancerous cells is the major hurdle that must be overcome. The fact that the triplet code does not apply to eukaryotes might have prevented the development of such a technique. Since the QED codon code is applicable to eukaryotes, it presents potential for the development of such a technique. Thus, the combination of this code, dysfunctional protein correction techniques, and the availability of the Human Cell Atlas (Reference 41) and direct cell RNA sequencing (Reference 42) are anticipated to provide the possibility of finding cures for the multigenic disease cancer.

Vaccines and antibiotics are the best preventive tools for controlling some diseases. Antibiotics kill bacteria (prokaryotes) by disrupting their protein production ability. On the other hand, viruses take over the cell's (eukaryote) protein production machinery and speed up cellular protein production, leading to cell death. One way to prevent cell death is to produce antibody proteins that can destroy the virus proteins and virus itself. Once the virus genome is known, antibody synthesis will become easier. This was recently demonstrated the successful production of an effective COVID-19 virus vaccine by generating antibody proteins using viral mRNA. Since the QED codons were developed for eukaryotes, universal vaccine development and the production of targeted antibiotics are distinct possibilities.

Protein Synthesis to Correct Dysfunctional Proteins and Cure Diseases

In some embodiments, QED codons translate the genetic information carried in mRNA into proteins at the ribosome. The translation process is the same in eukaryotes, prokaryotes and viruses, but the starting and intervening steps differ. The different roles of the QED codons in control and translation are shown in bold.

Protein synthesis pathway diagram 300 of FIG. 3 shows the synthesis of proteins in eukaryotic cells with noncoding QED codons, with the various noncoding QED codons including various cis-regulatory elements.

More specifically, protein synthesis pathway diagram 300 shows the synthesis of eukaryotic proteins with noncoding codons, such as TATA, AT-rich, CG-rich, CAAT, and ATCG, in the upstream promotor area, such as ACTIVATOR, ENHANCER, REPRESSOR, and SENSOR.

Eukaryotic protein synthesis is not a binary process and is triggered by cell-cell communication and the needs of specific cells. The noncoding QED eukaryotic code contains nearly all the cis-regulatory elements shown in protein synthesis pathway diagram 300.

In some embodiments, there are common bases between cis-regulatory elements and the noncoding eukaryotic QED code, and all cis-regulatory elements should be noncoding.

The protein-encoding processes in the QED code and triplet code are similar. Since the triple code has only two translational control elements, START and STOP, the prediction of QED START and STOP noncoding codons was done using the triplet START and STOP codes as a guide.

In some embodiments, cis-regulatory elements and eukaryotic noncoding QED codon bases have a high degree of coincidence in eukaryotic transcription and splicing.

The cis-regulatory elements in the eukaryotic promoter region have been observed to start, activate, enhance, sense and/or moderate to control transactions and splicing processes in the nucleus; this process transports mRNA to the cytoplasm for protein synthesis at the ribosome. Whether these cis-regularity bases are noncoding has yet to be established. However, the eukaryotic noncoding QED code model meets the necessary conditions.

In some embodiments, a protein production pathway in eukaryotes is provided, in which transcription and splicing are additional critical mRNA preprocessing steps not found in prokaryotes. These steps include the generation of rRNA, tRNA and pre-RNA. In some embodiments, noncoding QED codons control and regulate transcription and pre-RNA splicing to obtain exons, as shown. Alternative splicing control allows multiple proteins to be generated from one gene. In some embodiments, QED codons translate the mRNA code to synthesize a protein.

DNA transcription pathway diagram 400a of