Unformatted text preview: Patterns and principles of RNA structure
RNA structure can be specific, stable and complex. (As a result, RNA mediates specific recognition and catalytic reactions.) Principles/ideas--RNAs contain characteristic 2 and 3 motifs Secondary structure--stems, bulges & loops Coaxial stacking Metal ion binding Tertiary motifs (Pseudoknots, A-A platform, tetraloop/tetraloop receptor, A-minor motif, ribose zipper) RNA vs. DNA
nucleoside glycosidic bond nucleotide 1 RNA vs. DNA: who cares? -OH Unstable backbone Stable backbone Base-catalyzed RNA cleavage! RNA transesterification mechanism transition state Base-catalyzed RNA cleavage!
+ -OH + 2 Different bases in RNA and DNA RNA only DNA only DNA and RNA RNA chain is made single stranded!
Chemical schematic One-letter code dsRNA can block protein synthesis and signal viral infections ssDNA can signal DNA damage and promote cell death Chain is directional. Convention: 5' 3'. 3 Six backbone dihedral angles (-) per nucleotide in RNA and DNA Is ssDNA floppy or rigid? Is RNA more or less flexible than ssDNA? Two orientations of the bases: Anti and syn DNA and RNA Absent from undamaged dsDNA 4 -OH, what a difference an O makes!
DNA Different functions of and RNA
gene1gene2 gene3 . . . Stores genetic info ssDNA signals cell death dsDNA OK Double helical (B form) Supercoiled Stores genetic info ssRNA OK E.g. mRNA = gene copy dsRNA ("A" form) signals infection, mediates editing, RNA interference, ... Forms complex structures Enzymes (e.g. ribosome), Binding sites & scaffolds Signals Templates (e.g. telomeres) Examples of RNA structural motifs
Secondary structures Stem, bulge, loop 4-helix junction Tetraloop Pseudoknot Sheared AA pairs Purine stacks Metal binding sites A-A platform Tetraloop receptor A-minor motif Ribose zipper
... Tertiary structures 5 Cloverleaf representation of yeast Phe tRNA "Cloverleaf" conserved in all tRNAs Coaxial stacking of adjacent stems forms an L-shaped fold Schematic drawing of yeast Phe tRNA fold Mg2+ (balls) Spermine 6 Non-WC base pairs and base triples in yeast tRNA Phe LOTS OF BASE COMBOS!! Enable alternate backbone orientations: A9 intercalates between adjacent G45 and m7G46 in yeast tRNA Phe 7 Examples of RNA structural motifs
Tetraloop Pseudoknot 4-helix junction Sheared AA pairs Purine stacks Metal binding sites A-A platform Tetraloop receptor A-minor motif
... UNCG tetraloop Stabilizes attached stem 8 HIV TAR RNA mediates Tat binding
2 structure schematic Coaxial stacking Nomenclature for secondary structure: stem, loop & bulge Base triple Arg binds GC bp HIV TAR RNA mediates Tat binding
2 structure schematic Coaxial stacking Nomenclature for secondary structure: stem, loop & bulge Base triple 9 HIV TAR RNA mediates Tat binding
2 structure schematic Coaxial stacking Nomenclature for secondary structure: stem, loop & bulge Base triple Arg binds G26/C39 bp Pseudoknots
HDV ribozyme forms a double pseudoknot
1 2 1 Bases in loop of stem 1 form stem 2 (with bases outside stem 1) 10 Hepatitis Delta Virus (HDV) ribozyme double pseudoknot
"Top" view 2 structure schematic U1A protein cocrystals Hepatitis Delta Virus (HDV) ribozyme double pseudoknot
"Top" view 2 structure schematic U1A protein cocrystals 11 Four-helix junction: L11 protein binding site in 23S RNA Four-helix junction: L11 protein binding site in 23S RNA Four helices emerge from a central wheel. The four double-helical stems form two coaxial stacks. The two stacks have irregular but complementary shapes. The helices knit together to form a compact globular domain. 12 Base triples in the L11 4-helix junction Bulge and loop mediate long-range tertiary interactions. The riboses of A1084-A1086 (all A's) form a "ribose zipper. A1086 adopts a syn conformation to facilitate tight sugar packing. Metal ions stabilize the L11 RNA 4helix junction Mg2+ ions (gold balls) Cd2+ ions (magenta) Hg2+ (rose) RNA interactions of the central Cd2+ ion 13 P4-P6 Domain of the Group I ribozyme P4-P6 Domain of the Group I ribozyme Two helical stacks are arranged parallel to each other. The structure is one helical radius thick. Two regions of 3 interactions between the two helical stacks. 1. Tetraloop/Tetraloop-receptor. 2. A-rich, single-stranded loop and the minor groove of the opposing helix. 14 Tertiary interactions in the P4-P6 domain
Sheared AA Standard AU Sheared AA bps fill minor groove Cross-strand purine stack. Tertiary interactions in the P4-P6 domain
Adjacent As pair side-by-side A-A platform Side view Top view 15 Tertiary interactions in the P4-P6 domain
Adjacent As pair side-by-side A-A platform Side view Top view Tertiary interactions in the P4-P6 domain 16 Tertiary interactions in the P4-P6 domain Tertiary interactions in the P4-P6 domain 17 Metal ion core in the P4-P6 domain Divalent metal ions (Mg2+) are required for proper folding. These ions bind to specific sites and mediate the close approach of the phosphate backbones At one position in the molecule the phosphate backbone turns inward and coordinates two metal ions. Adenosine-minor-groove base triples: the A-minor motif A fills minor groove & ribose 2' OH forms Hbonds 18 Adjacent base-triples bring together RNA strands Hydrogen bonds between adjacent backbone atoms create a "ribose zipper" Deoxynucleotides destabilize P4-P6 The A-minor motif is widespread
Conserved As are abundant in unpaired regions of structured RNAs. Group I intron P4-P6 % of As in "single-stranded regions 19 What happens in very large RNAs? % of As in "single-stranded regions A-minor motifs are the predominant tertiary interaction in the 50S ribosomal subunit 20 Summary
1. 2. 3. 4. RNA structure can be specific, globular, stable and complex. (As a result, RNA mediates specific recognition and catalytic reactions.) Secondary structures include stems, bulges, and loops. Tertiary motifs include base triples, pseudoknots, A-A platforms, the tetraloop/tetraloop receptor, A-minor motifs, ribose zippers Principles: stems and loops conserved, many non-WC base contacts, coaxial stacking, metal ion binding, H-bonding of ribose 2' OH, and repeated "motifs". 21 ...
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This note was uploaded on 07/08/2009 for the course LIFESCI LS 3 taught by Professor Paulolague during the Fall '09 term at UCLA.
- Fall '09