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三核苷酸的四重对称性以及遵循查加夫第二对等规则的DNA生成自然对称法则。

Trinucleotide's quadruplet symmetries and natural symmetry law of DNA creation ensuing Chargaff's second parity rule.

作者信息

Rosandić Marija, Vlahović Ines, Glunčić Matko, Paar Vladimir

机构信息

a Croatian Academy of Sciences and Arts, HAZU, Bioinformatics and Biological Physics , Zrinski trg 11, 10000 Zagreb , Croatia.

b Faculty of Science , University of Zagreb , Bijenicka 32, 10000 Zagreb , Croatia.

出版信息

J Biomol Struct Dyn. 2016 Jul;34(7):1383-94. doi: 10.1080/07391102.2015.1080628. Epub 2016 May 4.

Abstract

For almost 50 years the conclusive explanation of Chargaff's second parity rule (CSPR), the equality of frequencies of nucleotides A=T and C=G or the equality of direct and reverse complement trinucleotides in the same DNA strand, has not been determined yet. Here, we relate CSPR to the interstrand mirror symmetry in 20 symbolic quadruplets of trinucleotides (direct, reverse complement, complement, and reverse) mapped to double-stranded genome. The symmetries of Q-box corresponding to quadruplets can be obtained as a consequence of Watson-Crick base pairing and CSPR together. Alternatively, assuming Natural symmetry law for DNA creation that each trinucleotide in one strand of DNA must simultaneously appear also in the opposite strand automatically leads to Q-box direct-reverse mirror symmetry which in conjunction with Watson-Crick base pairing generates CSPR. We demonstrate quadruplet's symmetries in chromosomes of wide range of organisms, from Escherichia coli to Neanderthal and human genomes, introducing novel quadruplet-frequency histograms and 3D-diagrams with combined interstrand frequencies. These "landscapes" are mutually similar in all mammals, including extinct Neanderthals, and somewhat different in most of older species. In human chromosomes 1-12, and X, Y the "landscapes" are almost identical and slightly different in the remaining smaller and telocentric chromosomes. Quadruplet frequencies could provide a new robust tool for characterization and classification of genomes and their evolutionary trajectories.

摘要

近50年来,Chargaff第二对等规则(CSPR),即核苷酸A=T、C=G频率相等,或同一DNA链中正向和反向互补三核苷酸频率相等,一直没有得到确凿的解释。在这里,我们将CSPR与映射到双链基因组的20个三核苷酸符号四联体(正向、反向互补、互补和反向)中的链间镜像对称性联系起来。对应于四联体的Q盒对称性可作为沃森-克里克碱基配对和CSPR共同作用的结果而获得。或者,假设DNA生成的自然对称法则,即DNA一条链中的每个三核苷酸必须同时也出现在相反的链中,这会自动导致Q盒正向-反向镜像对称性,该对称性与沃森-克里克碱基配对一起产生CSPR。我们展示了从大肠杆菌到尼安德特人和人类基因组等广泛生物的染色体中的四联体对称性,引入了新的四联体频率直方图和具有组合链间频率的三维图。这些“景观”在所有哺乳动物中相互相似,包括已灭绝的尼安德特人,而在大多数较古老的物种中则有所不同。在人类染色体1 - 12以及X、Y染色体中,“景观”几乎相同,而在其余较小的端着丝粒染色体中则略有不同。四联体频率可为基因组的表征和分类及其进化轨迹提供一种新的强大工具。

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