Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia; University hospital centre Zagreb (ret.), Zagreb, Croatia.
Department of Physics, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia; Algebra University College, 10000 Zagreb, Croatia.
J Theor Biol. 2019 Dec 21;483:109985. doi: 10.1016/j.jtbi.2019.08.016. Epub 2019 Aug 27.
After explanation of the Chargaff´s first parity rule in terms of the Watson-Crick base-pairing between the two DNA strands, the Chargaff´s second parity rule for each strand of DNA (also named strand symmetry), which cannot be explained by Watson-Crick base-pairing only, is still a challenging issue already fifty years. We show that during evolution DNA preserves its identity in the form of quadruplet A+T and C+G rich matrices based on purine-pyrimidine mirror symmetries of trinucleotides. Identical symmetries are present in our classification of trinucleotides and the genetic code table. All eukaryotes and almost all prokaryotes (bacteria and archaea) have quadruplet mirror symmetries in structural form and frequencies following the principle of Chargaff's second parity rule and Natural symmetry law of DNA creation and conservation. Some rare symbionts have mirror symmetry only in their structural form within each DNA strand. Based on our matrix analysis of closely related species, humans and Neanderthals, we find that the circular cycle of inverse proportionality between trinucleotides preserves identical relative frequencies of trinucleotides in each quadruplet and in the whole genome. According to our calculations, a change in frequencies in quadruplet matrices could lead to the creation of new species. Violation of quadruplet symmetries is practically inconsistent with life. DNA symmetries provide a key for understanding the restriction of disorder (entropy) due to mutations in the evolution of DNA.
在解释查加夫第一碱基对规则（Chargaff's first parity rule）是基于两条 DNA 链之间的沃森-克里克碱基配对之后，查加夫第二碱基对规则（Chargaff's second parity rule）对于每条 DNA 链（也称为链对称性），仅通过沃森-克里克碱基配对无法解释，这仍然是一个具有挑战性的问题，已经有五十年了。我们表明，在进化过程中，DNA 以四联体 A+T 和 C+G 丰富矩阵的形式保存其身份，这些矩阵基于三核苷酸的嘌呤-嘧啶镜像对称性。在我们的三核苷酸分类和遗传密码表中存在相同的对称性。所有真核生物和几乎所有原核生物（细菌和古细菌）都具有结构形式和频率的四联体镜像对称性，遵循查加夫第二碱基对规则和 DNA 生成和保存的自然对称规律的原则。一些罕见的共生体在每条 DNA 链的结构形式中仅具有镜像对称性。基于我们对密切相关物种（人类和尼安德特人）的矩阵分析，我们发现三核苷酸的反比例循环保持了每个四联体和整个基因组中三核苷酸的相同相对频率。根据我们的计算，四联体矩阵中频率的变化可能导致新物种的产生。违反四联体对称性实际上与生命不一致。DNA 对称性为理解 DNA 进化中由于突变导致的无序（熵）限制提供了关键。
