rna structure 1.rna = dna 2.elements & motifs : rna :: helices : dna 3. sequence dependence...
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![Page 1: RNA Structure 1.RNA = DNA 2.Elements & Motifs : RNA :: Helices : DNA 3. Sequence Dependence ElementNo MotifYes](https://reader033.vdocuments.net/reader033/viewer/2022061605/56649f565503460f94c7a64e/html5/thumbnails/1.jpg)
RNA Structure
1. RNA = DNA
2. Elements & Motifs : RNA ::
Helices : DNA
3. Sequence Dependence
Element No
Motif Yes
/
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RNA: Methods & HistoryMethods
•X-ray diffraction
•Fiber
•Crystal
•NMR
•Chemical probing
•Mutation
•Modeling (constraints)
History
• A-helix
• Ricin-Sarcin loop
• tRNA
• Self-splicing intron
• ribosomes
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RNA: Constraints
•Electron density
•NMR nuclear interactions
•Chemical reactivities
•Evolutionary covariation
•Stability prediction
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RNA Constraints: Covariation
ACGTAATTGCGTAACAGCGTAACAACGTAATCACGTAATGGCGTAGCGGCGTAGCA
ACGTAATTGCGTAACAGCGTAACAACGTAATCACGTAATGGCGTAGCGGCGTAGCA
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RNA Constraints: RNA folding
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Jossinet, F. et al. Bioinformatics 2005 21:3320-3321; doi:10.1093/bioinformatics/bti504
An S2S screenshot displaying the S2SViewer core tool (on the left), Rnalign (middle low), Rna3DViewer using PyMOL (middle up) and Rna2DViewer (on the right)
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RNA ElementsRNA Elements
• are recognized, commonly occurring features of RNA 3-D structure that are not dictated by the sequence.
• are principally assembled by Watson-Crick base pairing and stacking.
• A-helix
• Stems
• Coaxially stacked helices
• Cross-strand helices
• Pseudoknots
• Kissing loops
• Backbone zippers
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RNA Element: A-Helix
Figure 4.01a: A-DNA
Protein Data Bank ID: 213D. Ramakrishnan, B., and Sundaralingam, M., Biophys. J. 69 (1995): 553-558 (top).
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RNA Element: Stem
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RNA Element: Coaxially Stacked Helices
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RNA Element: Cross-strand Helices
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RNA Element: Pseudoknot
Image from Staple et al.
Hepatitis Delta Virus (Image from Ke et al.).
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RNA Element: Kissing Loops
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RNA Element: Backbone Zipper
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RNA MotifsRNA Motifs
• are recognized, commonly occurring features of RNA 3-D structure that depend, in part, on the nucleotide sequence.
• often involve non-Watson-Crick pairings and higher order base interactions.
• Tetraloops
• Turns
• Interstrand structures
• Distant interactions
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RNA Motifs: Tetraloops
• UNCG
• GNRA
• CUYG
• U-turn (YUNR)
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RNA Motif: UNCG Tetraloop
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RNA Motif: GNRA Tetraloop
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RNA Motif: CUYG Tetraloop
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U-turn
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RNA Motifs: Turns
• K-turn
• Bulge-helix-bulge
• S-turn
• Hook turn
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RNA Motif: K-turn
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RNA Motif: K-turn
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TERRY A. GOODY et al. RNA 2004; 10: 254-264
FIGURE 2. Anomalous electrophoretic migration of K-turn RNA is dependent on the presence of magnesium ions
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RNA Motif: Bulge-helix-bulge
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RNA Motif: S-turn
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SZILVIA SZEP et al. RNA 2003; 9: 44-51
RNA Motif: Hook Turn
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SZILVIA SZEP et al. RNA 2003; 9: 44-51
FIGURE 5. Stereodiagrams of some
hook-turns found in rRNAs
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RNA Motifs: Cross-strand Structures
• A-platforms
• bulged G
• T-loop
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RNA Motif: A Platform
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RNA Motif: Bulged G motif
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RNA Motif: T-loop
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RNA Motifs: Distant Interactions
• A-minor
• Receptor--GNRA Tetraloop
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RNA Motif: A minor motif
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RNA Motif: GNRA Tetraloop & Receptor
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RNA Structure: Classification
Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A. and Leontis, N.B., 2008. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. Journal of mathematical biology 56, 215-52.
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RNA Structure
1. RNA = DNA
2. Elements & Motifs : RNA ::
Helices : DNA
3. Sequence Dependence
Element No
Motif Yes
/
FUNCTION: next