title: Solving nucleic acid structures by molecular replacement: examples from group II intron studies.
abstract: 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.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.
authors.forename: Marco
authors.initials: M
authors.lastname: Marcia
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Humphris-Narayanan
authors.forename: Kevin S
authors.initials: KS
authors.lastname: Keating
authors.forename: Srinivas
authors.initials: S
authors.lastname: Somarowthu
authors.forename: Kanagalaghatta
authors.initials: K
authors.lastname: Rajashankar
authors.forename: Anna Marie
authors.initials: AM
authors.lastname: Pyle
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D018360:Crystallography, X-Ray / Q000379:methods; D005544:Forecasting / Q000379:methods; D007438:Introns; D008958:Models, Molecular; D062085:RNA, Long Noncoding / Q000737:chemistry* / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D062085:RNA, Long Noncoding
keywords: RCrane; RNA structure; de novo structure design; homology modeling; long noncoding RNA; nucleic acid sequence homology