Unitary structure of palindromes in DNA

Tibatan, Mehmet Ali; Sarisaman, Mustafa

doi:10.1016/j.biosystems.2021.104565

Cited by 3 publications

(9 citation statements)

References 46 publications

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“…It seems obvious, as in the article by Tibatan and Sarisaman [ 9 ], that symmetry properties, insufficiently exploited to date, play a more important role in the exploration of biological sequences, both at the molecular and sub-molecular levels. The new palindromic descriptors presented in this work should contribute in a non-negligible way and should be widely applied in the study of biological sequences.…”

Section: Discussionmentioning

confidence: 99%

“…The palindromic analysis of discrete sequences has partly revolutionized molecular biology and is widely used as shown by the following work [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 ], to name a few. Very recently, the study of quantum behavior [ 9 ], encountered in palindromes within the DNA structure, revealed that the symmetry properties of the unitary structure, other than those present in classical palindromes, play an important role in the origin and cause of mutations.…”

Section: Introductionmentioning

confidence: 99%

“…In the continuity of the work carried out by Tibatan and Sarisaman [ 9 ], our article aims to highlight the symmetry links between the concept of frieze and the concept of palindrome, which have been insufficiently exploited until now in the analysis of binary data.…”

Section: Introductionmentioning

confidence: 99%

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Palindromic Vectors, Symmetropy and Symmentropy as Symmetry Descriptors of Binary Data

Girault

Ménigot

2022

Entropy

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Today, the palindromic analysis of biological sequences, based exclusively on the study of “mirror” symmetry properties, is almost unavoidable. However, other types of symmetry, such as those present in friezes, could allow us to analyze binary sequences from another point of view. New tools, such as symmetropy and symmentropy, based on new types of palindromes allow us to discriminate binarized 1/f noise sequences better than Lempel–Ziv complexity. These new palindromes with new types of symmetry also allow for better discrimination of binarized DNA sequences. A relative error of 6% of symmetropy is obtained from the HUMHBB and YEAST1 DNA sequences. A factor of 4 between the slopes obtained from the linear fits of the local symmentropies for the two DNA sequences shows the discriminative capacity of the local symmentropy. Moreover, it is highlighted that a certain number of these new palindromes of sizes greater than 30 bits are more discriminating than those of smaller sizes assimilated to those from an independent and identically distributed random variable.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Palindromic Vectors, Symmetropy and Symmentropy as Symmetry Descriptors of Binary Data

Girault

Ménigot

2022

Entropy

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“…where σx and σz are the celebrated Pauli sigma matrices and I k×k is k-dimensional unit matrix, see [2] for details of these conventions. In principle, we can admit |E⟩ R = |E⟩.…”

Section: Construction Of the Formalism: Regular Dna Structurementioning

confidence: 99%

“…This motivation firstly provided us with a basis for understanding the quantum features in DNA, and in this way, it was possible to reveal various symmetrical structures related to DNA that are not yet known. In this way, the unitary character of DNA was studied and its extraordinary aspects were deciphered in [2], see also Refs. [3,4,5,6,7,8,9,10] for the literature on some symmetrical features found in DNA.…”

Section: Introductionmentioning

confidence: 99%

Mutation Mechanism In DNA: Non-Hermitian Approach

Sarısaman,

Tibatan,

Uzunal

2023

Preprint

Self Cite

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We propose a novel mutation mechanism for points and ordinary or palindromic sequences of DNA and RNA. We adopted non-Hermitian approaches based on quantum mechanics. Hermiticity is in the limelight of any physical structure with quantum character, like DNA, or RNA, as it creates quantum stability in that it yields real eigenvalues and orthonormal states. We show that, through the mutation mechanism we constructed based on non-Hermitian physics, the deterioration of the Hermitian character of the original DNA states, nucleotides, does not create a stability problem. We show that Weyl’s perturbation theory helps us determine the stability of mutated DNA or RNA. We prove that mutations made in the laboratory with conventional nucleotides using non-Hermitian physics methods are not different from mutations that occur spontaneously in nature. This result may help to reveal the quantum nature of genetic diseases in the near future and may shape the molecular approaches.

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The complete mitochondrial genome of Echinolaelaps fukienensis provide insights into phylogeny and rearrangement in the superfamily Dermanyssoidea

He,

Li,

Yuan

et al. 2023

PLoS ONE

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Background Echinolaelaps fukienensis is the dominant mite species parasitic on the body surface of the genus Niviventer. The mitochondrial genome (mitogenome) has its own independent genetic material and genetic system, and is now widely used in population genetics, genealogical biogeography, phylogeny and molecular evolution studies. Species diversity of the superfamily Dermanyssoidea is very rich, but its mitogenomes AT content is high, and it is difficult to amplify the complete mitogenome by routine PCR. To date, we have only obtained the mitogenomes of 6 species, scarcity on sequence data has greatly impeded the studies in the superfamily Dermanyssoidea. Methods Echinolaelaps fukienensis were collected in 2019 from the body surface of Niviventer confucianus (Rodentia, Muridae) in Yunnan Province. The E. fukienensis mitogenome was determined and analyzed for the first time using the Illumina Novoseq 6000 platform. Phylogenetic analyses of the superfamily Dermanyssoidea were conducted based on the entire mitogenome sequences. Results The E. fukienensis mitogenome was 14,402 bp, which is known the smallest genome of the superfamily Dermanyssoidea, encoding a total of 37 genes, including 13 PCGs, 22 tRNAs, 2 rRNAs and 1 control region. Most protein-coding genes use ATN as the start codon and TAN as the stop codon. AT and GC skew of atp8 genes in E. fukienensis were both 0. The average length of 22 tRNA genes of E. fukienensis was 64 bp, and secondary structures of tRNAs showed base mismatches and missing D-arms in many places. Compared with gene arrangement pattern of the hypothetical ancestor of arthropods, the E. fukienensis mitogenome shows a novel arrangement pattern. Phylogenetic tree supported the monophyly of the superfamily Dermanyssoidea. Echinolaelaps fukienensis being the least genetic distant (0.2762) and most closely related to Varroa destructor. Conclusions This study analyzed comprehensive the structure and evolution of the E. fukienensis mitogenome for the first time, enriches molecular data of the genus Echinolaelaps, which will contribute to further understand phylogeny and rearrangement patterns of the superfamily Dermanyssoidea.

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Unitary structure of palindromes in DNA

Cited by 3 publications

References 46 publications

Palindromic Vectors, Symmetropy and Symmentropy as Symmetry Descriptors of Binary Data

Palindromic Vectors, Symmetropy and Symmentropy as Symmetry Descriptors of Binary Data

Mutation Mechanism In DNA: Non-Hermitian Approach

The complete mitochondrial genome of Echinolaelaps fukienensis provide insights into phylogeny and rearrangement in the superfamily Dermanyssoidea

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