Identification of structural motifs using networks of hydrogen-bonded base interactions in RNA crystallographic structures

Hazrina Yusof Hamdani, Mohd Firdaus-Raih

Research output: Contribution to journalArticle

Abstract

RNA structural motifs can be identified using methods that analyze base–base interactions and the conformation of a structure’s backbone; however, these approaches do not necessarily take into consideration the hydrogen bonds that connect the bases or the networks of inter-connected hydrogen-bonded bases that are found in RNA structures. Large clusters of RNA bases that are tightly inter-connected by a network of hydrogen bonds are expected to be stable and relatively rigid substructures. Such base arrangements could therefore be present as structural motifs in RNA structures, especially when there is a requirement for a highly stable support platform or substructure to ensure the correct folding and spatial maintenance of functional sites that partake in catalysis or binding interactions. In order to test this hypothesis, we conducted a search in available RNA crystallographic structures in the Protein Data Bank database using queries that searched for profiles of bases inter-connected by hydrogen bonds. This method of searching does not require to have prior knowledge of the arrangement being searched. Our search results identified two clusters of six bases that are inter-connected by a network of hydrogen bonds. These arrangements of base sextuples have never been previously reported, thus making this the first report that proposes them as novel RNA tertiary motifs.

Original languageEnglish
Article number550
JournalCrystals
Volume9
Issue number11
DOIs
Publication statusPublished - Nov 2019

Fingerprint

RNA
Hydrogen
hydrogen bonds
Hydrogen bonds
hydrogen
substructures
interactions
folding
maintenance
catalysis
platforms
proteins
requirements
Catalysis
Conformations
profiles
Proteins

Keywords

  • Base-base interactions
  • Classification of base arrangement
  • RNA crystallographic structures
  • RNA structural motifs

ASJC Scopus subject areas

  • Chemical Engineering(all)
  • Materials Science(all)
  • Condensed Matter Physics
  • Inorganic Chemistry

Cite this

Identification of structural motifs using networks of hydrogen-bonded base interactions in RNA crystallographic structures. / Hamdani, Hazrina Yusof; Firdaus-Raih, Mohd.

In: Crystals, Vol. 9, No. 11, 550, 11.2019.

Research output: Contribution to journalArticle

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