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NC-IUBMB nomenclature for the classification of nucleic acid junctions:

In order to make RNAJunction more useful and easier to use, we have applied a naming convention to each structure. This nomenclature is based on the 1994 Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC_IUBMB) entitled "A nomenclature of junctions and branchpoints in nucleic acids1."

The convention:

  • H -> helical stem: region where two strands have three or more adjacent base-pair interactions
  • S -> strand: refers to the unpaired strand (i.e. loop region) connecting helical stems. The number that follows is equal to the number of unpaired bases on the strand.
  • Numbers which precede an H indicate repetition (e.g. 2HS3 denotes 2 helices, each connected by strands with loop-length=3)

Example:

  • 2HS2HS12HS14HS5HS10
  • 2 helices with strands, loop-length= 2
  • 1 helix with strand, loop-length=12
  • 1 ..... .... ......, ...........=14
  • 1 ..... .... ......, ...........= 5
  • 1 ..... .... ......, ...........=10
  • 7-way junction with total loop-length=43

1Lilley DM, Clegg RM, et al. (1995)."Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). A nomenclature of junctions and branchpoints in nucleic acids. Recommendations 1994." Eur J Biochem.230(1):1-2.