Hierarchy of codon usage frequencies from codon-anticodon interaction in the crystal basis model

Antonino Sciarrino, Paul Sorba
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Abstract

Analyzing the codon usage frequencies of a specimen of 20 plants, for which the codon-anticodon pattern is known, we have remarked that the hierarchy of the usage frequencies present an almost "universal" behavior. Searching to explain this behavior, we assume that the codon usage probability results from the sum of two contributions: the first dominant term is an almost "universal" one and it depends on the codon-anticodon interaction; the second term is a local one, i.e. depends on the biological species. The codon-anticodon interaction is written as a spin-spin plus a z-spin term in the formalism of the crystal basis model. From general considerations, in particular from the choice of the signs and some constraints on the parameters defining the interaction, we are able to explain most of the observed data.
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晶体基础模型中密码子与反密码子相互作用产生的密码子使用频率的层次结构
通过分析已知密码子-反密码子模式的 20 种植物标本的密码子使用频率,我们注意到使用频率的层次结构呈现出一种几乎 "普遍 "的行为。为了解释这种行为,我们假定密码子的使用概率来自两个贡献的总和:第一个主导项几乎是 "普遍 "的,它取决于密码子与反密码子之间的相互作用;第二个主导项是局部的,即取决于生物物种。在晶体基础模型的形式中,密码子与反密码子的相互作用被写成一个自旋-自旋项和一个 z-自旋项。根据一般考虑,特别是符号的选择和对定义相互作用的参数的一些限制,我们能够解释大部分观测数据。
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