Classification of nucleic acid junctions
Classification of nucleic acid junctions
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DOI：
10.1006/jmbi.1996.0599
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发表时间：
1996-11-08
影响因子：
5.6
通讯作者：
Altona, C
中科院分区：
文献类型：
--
作者：
Altona, C
分支核酸物种，特别是三向和四向连接，构成了RNA和DNA的重要结构元素，要么作为结构的一部分(主要是RNA)，要么作为生物过程的潜在中间体(主要是DNA)。关于支链核酸的研究报告数量正在迅速增长。到目前为止，各小组报告的三级结构的比较仍然很困难，因为缺乏统一的描述和符号。因此，我们提出了一套简单的规则，允许根据分支点的碱基对对几乎任何连接进行唯一的分类和统一的描述。在其最简单的形式中，该方法描述和排列了n路(NH)结中的n个碱基对，但它很容易扩展，以便包括单链区、错配和倒数第二个碱基对。仅计算分支点的碱基对，就可以构建不同的膨胀型3HS(2)三向连接，分为八个不同的类别。由于对称性的原因，只有36个不同的固定4H连接可能，排列在6个类别中，只有24个紧密的~3H连接，在4个类别中。在一般的NHS(M)情况下，不同的结点数是4(N)，当计算中包括S-m个不成对的碱基时，乘以4(M)。(C)1996年学术出版社有限公司
Branched nucleic acid species, three-way and four-way junctions in particular, constitute important structural elements in RNA and DNA, either as part of the architecture (mainly RNA) or as potential intermediates in biological processes (mainly DNA). The number of research reports on branched nucleic acids is growing rapidly. Thus far, comparison of tertiary structures reported by various groups remains difficult as it is hampered through lack of uniform depiction and notation. We therefore propose a set of simple rules that allow a unique classification as well as a uniform depiction of virtually any junction in terms of the base-pairs at the branch point. In its simplest form the methodology describes and arranges the n base-pairs in an n-way (nH) junction but it is easily extended in order to include single-stranded regions, mismatches and penultimate base-pairs. Counting only base-pairs at the branch point, 64 different bulged 3HS(2) three-way junctions can be constructed, arranged into eight different classes. For reasons of symmetry, only 36 different immobilized 4H junctions are possible, arranged into six classes, and only 24 tight 3H junctions, in four classes. The number of different junctions in the general nHS(m) case is 4(n), multiplied by 4(m) when the S-m unpaired bases are included in the calculation. (C) 1996 Academic Press Limited