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442703 VO Principles of RNA 3D Structure I (2013W)
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Anmeldungen zur Veranstaltung bitte an: craig.zirbel@univie.ac.at
Details
Language: English
Examination dates
Lecturers
Classes
Currently no class schedule is known.
Information
Aims, contents and method of the course
Assessment and permitted materials
Minimum requirements and assessment criteria
The goal of the course is to open up the world of RNA 3D structure to students and researchers who work with RNA but are not already familiar with 3D structure. A more complete description and some interesting links are available at http://tinyurl.com/RNA3DWien
Examination topics
There will be short lectures interspersed with individual work on various RNA tools available online or for download.
Reading list
Association in the course directory
Last modified: We 19.08.2020 08:11
RNA helices, AU, GC basepairs, 3D structure of these basepairs, GU pairs and other cis Watson-Crick/Watson-Crick basepairs.
Sequence alignments and covariation analysis to identify RNA helices.
Secondary structures of ribosomal RNAs, to get familiar with all of the features of RNA structures.
RNA 3D structures. Crystallography. Electron density. Fitting to electron density. Cryo EM. NMR.
RNA basepairs of all 12 types. Isostericity among base combinations within families.
Nucleotide to nucleotide alignments of ribosomal RNAs. Strong conservation of basepairs and families.
RNA motifs. Specific RNA motifs. Recurrent motifs. RNA hairpins. Specific types. RNA internal loops. RNA 3D motif atlas.
Identification of internal loop motifs from sequence.
RNA junctions.
Tertiary interactions, kissing hairpins, pseudoknots, loop-receptor interactions, A-minor motifs. Ribose zippers, etc.
RNA sequence variability, basepair isostericity, limitations on sequence variability RNA-protein interactions.
RNA phylogeny together with secondary structure prediction.
Molecular dynamics simulations of RNA 3D structure.