Classification of nucleic acid junctions

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 3HS2 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 nHSm case is 4n, multiplied by 4m when the Sm unpaired bases are included in the calculation.