Symmetries have not been completely determined and explained from the discovery of the DNA structure in 1953 and the genetic code in 1961. We show, during 10 years of investigation and research, our ...discovery of the Supersymmetry Genetic Code table in the form of 2 × 8 codon boxes, quadruplet DNA symmetries, and the classification of trinucleotides/codons, all built with the same physiochemical double mirror symmetry and Watson-Crick pairing. We also show that single-stranded RNA had the complete code of life in the form of the Supersymmetry Genetic Code table simultaneously with instructions of codons' relationship as to how to develop the DNA molecule on the principle of Watson-Crick pairing. We show that the same symmetries between the genetic code and DNA quadruplet are highly conserved during the whole evolution even between phylogenetically distant organisms. In this way, decreasing disorder and entropy enabled the evolution of living beings up to sophisticated species with cognitive features. Our hypothesis that all twenty amino acids are necessary for the origin of life on the Earth, which entirely changes our view on evolution, confirms the evidence of organic natural amino acids from the extra-terrestrial asteroid Ryugu, which is nearly as old as our solar system.
The Supersymmetry Genetic code (SSyGC) table is based on five physicochemical symmetries: (1) double mirror symmetry on the principle of the horizontal and vertical mirror symmetry axis between all ...bases (purines A, G) and pyrimidines (U, C) and (2) of bases in the form of codons; (3) direct-complement like codon/anticodon symmetry in the sixteen alternating boxes of the genetic code columns; (4) A + T-rich and C + G-rich alternate codons in the same row between both columns of the genetic code; (5) the same position between divided and undivided codon boxes in relation to horizontal mirror symmetry axis. The SSyGC table has a unique physicochemical purine-pyrimidine symmetry net which is as the core symmetry common for all, with more than thirty different nuclear and mitochondrial genetic codes. This net is present in the SSyGC table of all RNA and DNA living species. None of these symmetries are present in the Standard Genetic Code (SGC) table which is constructed on the alphabetic horizontal and vertical U-C-A-G order of bases. Here, we show that the free energy value of each codon incorporated as fundamentally mapping the "energy code" in the SSyGC table is compatible with mirror symmetry. On the other hand, in the SGC table, the same free energy values of codons are dispersed and a mirror symmetry between them is not recognizable. At the same time, the mirror symmetry of the SSyGC table and the DNA quadruplets together with our classification of codons/trinucleotides are perfectly imbedded in the mirror symmetry energy mapping of codons/trinucleotides and point out in favor of maintaining the integrity of the genetic code and DNA genome. We also argue that physicochemical symmetries of the SSyGC table in the manner of the purine-pyrimidine symmetry net, the quadruplet symmetry of DNA molecule, and the free energy of codons have remined unchanged during all of evolution. The unchangeable and universal symmetry properties of the genetic code, DNA molecules, and the energy code are decreasing disorder between codons/trinucleotides and shed a new light on evolution. Diversity in all living species on Earth is broad, but the symmetries of the Supersymmetry Genetic Code as the code of life and the DNA quadruplets related to the "energy code" are unique, unchangeable, and have the power of natural laws.
It is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs ...(Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo et al., comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga et al., identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.
From the recent genome assembly NHGRI_mPonAbe1-v2.0_NCBI (GCF_028885655.2) of orangutan chromosome 13, we computed the precise alpha satellite higher-order repeat (HOR) structure using the novel ...high-precision GRM2023 algorithm with Global Repeat Map (GRM) and Monomer Distance (MD) diagrams. This study rigorously identified alpha satellite HORs in the centromere of orangutan chromosome 13, discovering a novel 59mer HOR—the longest HOR unit identified in any primate to date. Additionally, it revealed the first intertwined sequence of three HORs, 18mer/27mer/45mer HORs, with a common aligned “backbone” across all HOR copies. The major 7mer HOR exhibits a Willard’s-type canonical copy, although some segments of the array display significant irregularities. In contrast, the 14mer HOR forms a regular Willard’s-type HOR array. Surprisingly, the GRM2023 high-precision analysis of chromosome 13 of human genome assembly T2T-CHM13v2.0 reveals the presence of only a 7mer HOR, despite both the orangutan and human genome assemblies being derived from whole genome shotgun sequences.
Unraveling the intricate centromere structure of human chromosomes holds profound implications, illuminating fundamental genetic mechanisms and potentially advancing our comprehension of genetic ...disorders and therapeutic interventions. This study rigorously identified and structurally analyzed alpha satellite higher-order repeats (HORs) within the centromere of human chromosome 15 in the complete T2T-CHM13 assembly using the high-precision GRM2023 algorithm. The most extensive alpha satellite HOR array in chromosome 15 reveals a novel cascading HOR, housing 429 15mer HOR copies, containing 4-, 7- and 11-monomer subfragments. Within each row of cascading HORs, all alpha satellite monomers are of distinct types, as in regular Willard's HORs. However, different HOR copies within the same cascading 15mer HOR contain more than one monomer of the same type. Each canonical 15mer HOR copy comprises 15 monomers belonging to only 9 different monomer types. Notably, 65% of the 429 15mer cascading HOR copies exhibit canonical structures, while 35% display variant configurations. Identified as the second most extensive alpha satellite HOR, another novel cascading HOR within human chromosome 15 encompasses 164 20mer HOR copies, each featuring two subfragments. Moreover, a distinct pattern emerges as interspersed 25mer/26mer structures differing from regular Willard's HORs and giving rise to a 34-monomer subfragment. Only a minor 18mer HOR array of 12 HOR copies is of the regular Willard's type. These revelations highlight the complexity within the chromosome 15 centromeric region, accentuating deviations from anticipated highly regular patterns and hinting at profound information encoding and functional potential within the human centromere.
In this article, we show that mono/oligonucleotide quadruplets, as basic structures of DNA, along with our classification of trinucleotides, disclose an organization of genomes based on ...purine–pyrimidine symmetry. Moreover, the structure and stability of DNA are influenced by the Watson–Crick pairing and the natural law of DNA creation and conservation, according to which the same mono- or oligonucleotide insertion must be inserted simultaneously into both strands of DNA. Taken together, they lead to quadruplets with central mirror symmetry and bidirectional DNA strand orientation and are incorporated into Chargaff’s second parity rule (CSPR). Performing our quadruplet frequency analysis of all human chromosomes and of Neuroblastoma BreakPoint Family (NBPF) genes, which code Olduvai protein domains in the human genome, we show that the coding part of DNA violates CSPR. This may shed new light and give rise to a novel hypothesis on DNA creation and its evolution. In this framework, the logarithmic relationship between oligonucleotide order and minimal DNA sequence length, to establish the validity of CSPR, automatically follows from the quadruplet structure of the genomic sequence. The problem of the violation of CSPR in rare symbionts is discussed.
Tandem repeats (TRs) are important components of eukaryotic genomes; they have both structural and functional roles: (i) they form essential chromosome structures such as centromeres and telomeres; ...(ii) they modify chromatin structure and affect transcription, resulting in altered gene expression and protein abundance. There are established links between variations in TRs and incompatibilities between species, evolutionary development, chromosome mis-segregation, aging, cancer outcomes and different diseases. Given the importance of TRs, it seemed essential to develop an efficient, sensitive and automated application for the identification of all kinds of TRs in various genomic sequences. Here, we present our new GRM application for identifying TRs, which is designed to overcome all the limitations of the currently existing algorithms. Our GRM algorithm provides a straightforward identification of TRs using the frequency domain but avoiding the mapping of the symbolic DNA sequence into numerical sequence, and using key string matching, but avoiding the statistical methods of locally optimizing individual key strings. Using the GRM application, we analyzed human, chimpanzee and mouse chromosome 19 genome sequences (RefSeqs), and showed that our application was very fast, efficient and simple, with a powerful graphical user interface. It can identify all types of TRs, from the smallest (2 bp) to the very large, as large as tens of kilobasepairs. It does not require any prior knowledge of sequence structure and does not require any user-defined parameters or thresholds. In this way, it ensures that a full spectrum of TRs can be detected in just one step. Furthermore, it is robust to all types of mutations in repeat copies and can identify TRs with various complexities in the sequence pattern. From this perspective, we can conclude that the GRM application is an efficient, sensitive and automated method for the identification of all kinds of TRs.
•Our novel ISyGC purine -pyrimidine symmetry net is common for all known genetic codes.•it is therefore common for all nuclear and mitochondrial genetic codes.•It contains physical–chemical ...properties as opposed to the standard genetic code.•It decreases disorder between codons and preserves the integrity of the system.•ISyGC symmetry net represents an evolutionary common “frozen accident”
Ever since Nirenberg’s discovery in 1961 in which codons code individual amino acids, numerous scientists searched for symmetries within the genetic code. The standard genetic code (SGC) table is an alphabetic artificial construct based on the U-C-A-G ordering of nucleotides without natural symmetries. Up to the present, complete symmetry in the genetic code has not been found, leaving doubt as to whether the symmetrical nature as the protector of order even exists. Our novel Ideal Symmetry Genetic Code (ISyGC) table reflects a unique fundamental physicochemical purine-pyrimidine symmetry net for all more than thirty known variations of nuclear and mitochondrial genetic codes. The nuclear genetic code for RNA and DNA viruses also contains the same purine-pyrimidine symmetry net. We show that the ISyGC table leads to automatic transformation into a DNA sequence akin to the 5′3 codon and 3′5 anticodon patterns. As a result of purine-pyrimidine symmetries between codons in the ISyGC table, algorithms of the first two bases as well of the third base of codons show how tRNA cognate anticodons can recognize synonymous codons during mRNA decoding. We show that the ISyGC purine-pyrimidine net with its physicochemical properties represents an evolutionary common “frozen accident” at the onset of each genetic code creation and RNA to DNA evolution. As such, during all of evolution the unique fundamental purine-pyrimidine symmetry net of all genetic codes remains unchangeable. In this way, evolution is a road paved with symmetries.
The fundamental role of symmetry in the genetic code is to decrease disorder between codons and to preserve the integrity of system. The Standard Genetic Code (SGC) table is structured alphabetically ...in a horizontal and vertical array of U–C-A-G bases only with aesthetic symmetry.
We postulate “the symmetry theory of genetic code” which is based on the unique physicochemical purine – pyrimidine symmetry net between codons of our Supersymmetry genetic code (SSyGC) table. The common purine – pyrimidine symmetry net as “the golden rule” and a core of the SSyGC table is universal, remaining unchanged during all of evolution. It is identical for more than 30 known genetic codes including those that will be discovered in the future, as well as for all RNA and DNA species. The unique SSyGC table has five physicochemical symmetries between bases, codons, and amino acids: 1) purine – pyrimidine symmetry on the principle of the Watson – Crick pairing (A↔U, C↔G), 2) direct – complement symmetry between codons, 3) mirror symmetry between bases and codons, 4) A + T rich and C + G rich symmetry between codons, and 5) symmetry between position of amino acids. Opposite to the SGC table where the third base is inactive, in the SSyGC table the role of the third base in codons is dominant in creation of symmetries. There are also present for the first time the symmetric positions of all boxes with amino acids. Opposite of the SGC table, the SSyGC code table contains three sextets for Serine, Arginine, and Leucine, each with six codons, positioned in continuity. Multi – facet symmetries of the SSyGC table as a natural law exclude the individual random creation of amino acids even in primitive life form. Accordingly, we hypothesize that the contemporary life arose due to common activity of all natural amino acids. With discovery of the unique physicochemical Supersymmetry genetic code table, the new light is shed on the symmetry of the genetic code.
•60 years remain a search for symmetries in relation to decrease of disorder in genetic code.•The Standard genetic code table is alphabetically structured without any physicochemical symmetry.•Our unique Supersymmetry genetic code table has 5 symmetries between bases, codons, and amino acids.•Core symmetry is physicochemical purine–pyrimidine symmetry net common for RNA&DNA species and unchangeable during evolution.•The unique and common physicochemical symmetry net is “the golden rule” of all nuclear and mitochondrial genetic codes.
Identification of approximate tandem repeats is an important task of broad significance and still remains a challenging problem of computational genomics. Often there is no single best approach to ...periodicity detection and a combination of different methods may improve the prediction accuracy. Discrete Fourier transform (DFT) has been extensively used to study primary periodicities in DNA sequences. Here we investigate the application of DFT method to identify and study alphoid higher order repeats.
We used method based on DFT with mapping of symbolic into numerical sequence to identify and study alphoid higher order repeats (HOR). For HORs the power spectrum shows equidistant frequency pattern, with characteristic two-level hierarchical organization as signature of HOR. Our case study was the 16 mer HOR tandem in AC017075.8 from human chromosome 7. Very long array of equidistant peaks at multiple frequencies (more than a thousand higher harmonics) is based on fundamental frequency of 16 mer HOR. Pronounced subset of equidistant peaks is based on multiples of the fundamental HOR frequency (multiplication factor n for nmer) and higher harmonics. In general, nmer HOR-pattern contains equidistant secondary periodicity peaks, having a pronounced subset of equidistant primary periodicity peaks. This hierarchical pattern as signature for HOR detection is robust with respect to monomer insertions and deletions, random sequence insertions etc. For a monomeric alphoid sequence only primary periodicity peaks are present. The 1/fbeta- noise and periodicity three pattern are missing from power spectra in alphoid regions, in accordance with expectations.
DFT provides a robust detection method for higher order periodicity. Easily recognizable HOR power spectrum is characterized by hierarchical two-level equidistant pattern: higher harmonics of the fundamental HOR-frequency (secondary periodicity) and a subset of pronounced peaks corresponding to constituent monomers (primary periodicity). The number of lower frequency peaks (secondary periodicity) below the frequency of the first primary periodicity peak reveals the size of nmer HOR, i.e., the number n of monomers contained in consensus HOR.
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