Tertiary Motifs Revealed in Analyses of Higher-Order RNA Junctions

Christian Laing, Segun Jung, Abdul Iqbal, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

RNA junctions are secondary-structure elements formed when three or more helices come together. They are present in diverse RNA molecules with various fundamental functions in the cell. To better understand the intricate architecture of three-dimensional (3D) RNAs, we analyze currently solved 3D RNA junctions in terms of base-pair interactions and 3D configurations. First, we study base-pair interaction diagrams for solved RNA junctions with 5 to 10 helices and discuss common features. Second, we compare these higher-order junctions to those containing 3 or 4 helices and identify global motif patterns such as coaxial stacking and parallel and perpendicular helical configurations. These analyses show that higher-order junctions organize their helical components in parallel and helical configurations similar to lower-order junctions. Their sub-junctions also resemble local helical configurations found in three- and four-way junctions and are stabilized by similar long-range interaction preferences such as A-minor interactions. Furthermore, loop regions within junctions are high in adenine but low in cytosine, and in agreement with previous studies, we suggest that coaxial stacking between helices likely forms when the common single-stranded loop is small in size; however, other factors such as stacking interactions involving noncanonical base pairs and proteins can greatly determine or disrupt coaxial stacking. Finally, we introduce the ribo-base interactions: when combined with the along-groove packing motif, these ribo-base interactions form novel motifs involved in perpendicular helix-helix interactions. Overall, these analyses suggest recurrent tertiary motifs that stabilize junction architecture, pack helices, and help form helical configurations that occur as sub-elements of larger junction networks. The frequent occurrence of similar helical motifs suggest nature's finite and perhaps limited repertoire of RNA helical conformation preferences. More generally, studies of RNA junctions and tertiary building blocks can ultimately help in the difficult task of RNA 3D structure prediction.

Original languageEnglish (US)
Pages (from-to)67-82
Number of pages16
JournalJournal of Molecular Biology
Volume393
Issue number1
DOIs
StatePublished - Oct 16 2009

Fingerprint

RNA
Base Pairing
Nucleic Acid Conformation
Cytosine
Adenine
Proteins

Keywords

  • junction
  • non-Watson-Crick base pair
  • ribo-base interaction
  • RNA structure
  • tertiary motif

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Tertiary Motifs Revealed in Analyses of Higher-Order RNA Junctions. / Laing, Christian; Jung, Segun; Iqbal, Abdul; Schlick, Tamar.

In: Journal of Molecular Biology, Vol. 393, No. 1, 16.10.2009, p. 67-82.

Research output: Contribution to journalArticle

Laing, Christian ; Jung, Segun ; Iqbal, Abdul ; Schlick, Tamar. / Tertiary Motifs Revealed in Analyses of Higher-Order RNA Junctions. In: Journal of Molecular Biology. 2009 ; Vol. 393, No. 1. pp. 67-82.
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