RNA 3D structure course

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RNA 3D Structure Course

RNA resources

Online Recorded Lectures and Slides by Professor Leontis on RNA from 2013

Databases for RNA Structure

Software for visualizing 3D Structures in PDB format

What is RNA?

RNA compared to DNA

The RNA Bases: Purines and Pyrimidines

Exercise 1: Get to know the RNA bases

RNA base hydrogen bonding potential

RNA base pairs

Exercise 2: Canonical Watson-Crick AU and GC base pairs

Non-Watson-Crick basepairs

Leontis-Westhof system for annotating RNA basepairs

Base edges

Basepair orientations cis and trans

Three-character annotation of RNA basepairs

Exercise 3: Canonical Watson-Crick basepairs

Exercise 4: Triangle representation of RNA basepairs

Exercise 5: Annotating RNA basepairs

Successive RNA basepairs

Exercise 6: Annotate successive RNA basepairs

Exercise 7: Form potential RNA basepairs from hydrogen bonding potential

Exercise 8: Annotate RNA basepairs

Symbolic representation of base pairing

Leontis-Westhof basepair symbols

Exercise 9: Using Leontis-Westhof symbols

RNA Basepair Catalog

RNA basepair annotations

RNA base stacking

Base faces

Base stacking annotation

Exercise 9: Identify 3’ and 5’ faces of bases

Exercise 10: Annotate base stacking

Exercise 11: Annotate base stacking

Symbols for base stacking from François Major’s group

Suggestions for making 2-dimensional RNA interaction diagrams

Exercise 13: Annotating an RNA motif

Base-phosphate interactions

Base-phosphate interaction locations

Base-phosphate interaction and the assignment of atoms to nucleotides

Base-phosphate interaction character annotation

Base-phosphate interaction symbolic annotation

Exercise 14: Annotate base-phosphate interactions

Exercise 15: Annotate base-phosphate interactions in a helix

Exercise 16: Annotate base-phosphate interactions in a motif

Exercise 17: Extended investigation of basepairs

Anti versus syn conformation of the glycosidic bond

Exercise 18: Anti and syn in RNA helices

Exercise 19: Annotate anti and syn conformation

Exercise 20: Annotate anti and syn in an RNA motif

Exercise 21: Annotate anti and syn in an RNA motif

Experimentally determined RNA 3D structures

Where can one get RNA 3D structures?

Tour of RNA 3D structures using Representative Sets

RNA 3D Motif Atlas

Sequence variability in structured RNA molecules

Nucleotide to nucleotide alignments of RNA 3D structures

Exercise 22 - needs to be rewritten

RNA Basepair isostericity

Choosing basepair exemplars from each basepairing family

RNA Basepair Catalog

Displaying basepair exemplars from each geometric basepairing family

Position of glycosidic bonds in RNA basepairs in the same geometric family

IsoDiscrepancy Index to measure the degree of isostericity between two basepairs

IsoDiscrepancy values within each geometric basepairing family

Exercise 23

RNA secondary structure

Exercise 24

Interactive RNA secondary structure

Exercise 25: Analysis of a tRNA structure

Exercise 26: The T-loop

Exercise 27:

Sequence variability in the Sarcin-Ricin motif

PDB entry for 1S72

RNA 3D Motif Atlas entry for instance IL_1S72_103 of the sarcin-ricin loop

RNA 3D Motif Atlas motif group IL_49493

Exercise 28:

Multiple sequence alignments of RNA sequences

Sequence variants of instance IL_3V2F_007 of the sarcin-ricin internal loop

Sequence variants of the sarcin-ricin motif across many instances

Inferring the geometry of RNA motifs with JAR3D

Searching RNA 3D structures with FR3D

Circular interaction diagrams

Multi-helix junctions

Crossing number

Other interactions on circular diagrams

Exercise: AG basepairs

Constructing FR3D searches

Symbolic search for two basepaired nucleotides

Exercise: Search for all GA basepairs in which G uses its Sugar edge

Motif diagrams

Exercise: Motif diagram for the core of the Sarcin-Ricin loop

Exercise

FR3D symbolic constraint summary

Nucleotides which border or delimit a single-stranded region

Exercise: Symbolic search for hairpin loops and a little bit of context

Exercise: Symbolic search for internal loops

FR3D geometric and mixed searches

GNRA hairpin loop geometric search

Geometric discrepancy

FR3D guaranteed results in geometric searches

3-way junctions

What determines the 3D structure of a 3-way junction?

Internal loop sequences with different geometry

Exercise

Rustbelt RNA 2018 workshop

Getting and using the Swiss PDB Viewer Program: Short Presentation

Instructions for PC

Instructions for Mac

Goals of the Rustbelt Workshop

Changes by

RNA 3D structure course