Solving nucleic acid structures by molecular replacement: examples from group II intron studies

Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2174-85. doi: 10.1107/S0907444913013218. Epub 2013 Oct 12.


Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

Keywords: RCrane; RNA structure; de novo structure design; homology modeling; long noncoding RNA; nucleic acid sequence homology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Amino Acid Substitution / genetics*
  • Conserved Sequence / genetics
  • Crystallography, X-Ray / methods
  • Forecasting / methods
  • Introns*
  • Models, Molecular
  • RNA, Long Noncoding / chemistry*
  • RNA, Long Noncoding / genetics
  • Sequence Homology, Amino Acid
  • Sequence Homology, Nucleic Acid
  • Transcription, Genetic / genetics


  • RNA, Long Noncoding