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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° motifsSecondary structure--stems, bulges & loops
Coaxial stackingMetal ion binding
Tertiary motifs (Pseudoknots, A-A platform, tetraloop/tetraloop receptor,A-minor motif, ribose zipper)
Patterns and principles of RNA structure
RNA vs. DNAnucleoside
nucleotide
glycosidicbond
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RNA vs. DNA: who cares?
Base-catalyzed RNA cleavage!
-OH
Stablebackbone
Unstablebackbone
RNA transesterification mechanism
Base-catalyzed RNA cleavage!
transition state
++
-OH
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Different bases in RNA and DNA
RNAonly
DNAonly DNA and RNA
RNA chain is made single stranded!
Chain is directional. Convention: 5’ 3’.
Chemical schematic One-letter code
ssDNA cansignal DNAdamage andpromote celldeath
dsRNA canblock proteinsynthesis and signal viralinfections
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Six backbone dihedral angles (α−ζ)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 fromundamageddsDNA
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-OH, what a difference an O makes!
Different functions of DNA and RNA
Stores genetic info Stores genetic infossDNA signals cell death ssRNA OK
E.g. mRNA = gene copydsDNA OK dsRNA (“A” form) signals infection,
mediates editing, RNA interference,. . .
Double helical (B form) Forms complex structuresSupercoiled Enzymes (e.g. ribosome),
Binding sites & scaffoldsSignalsTemplates (e.g. telomeres)
gene1gene2
gene3 . . .
Examples of RNA structural motifsStem, bulge, loop4-helix junctionTetraloopPseudoknotSheared AA pairsPurine stacksMetal binding sitesA-A platformTetraloop receptorA-minor motifRibose zipper . . .
Secondary structures Tertiary structures
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Cloverleaf representation of yeast Phe tRNA
Coaxial stacking of adjacentstems forms an L-shaped fold
“Cloverleaf” conservedin all tRNAs
Schematic drawing of yeast Phe tRNA fold
Mg2+ (balls)
Spermine
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Non-WC base pairs and base triples in yeasttRNA Phe
LOTS OF BASE COMBOS!! Enable alternate backbone orientations:
A9 intercalates between adjacent G45 andm7G46 in yeast tRNA Phe
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Examples of RNA structural motifs
TetraloopPseudoknot4-helix junctionSheared AA pairsPurine stacksMetal binding sitesA-A platformTetraloop receptorA-minor motif . . .
UNCG tetraloop
Stabilizes attached stem
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HIV TAR RNA mediates Tat binding2° structure schematic
Nomenclature for secondarystructure: stem, loop & bulge
Coaxial stacking
Basetriple Arg binds
GC bp
HIV TAR RNA mediates Tat binding2° structure schematic
Nomenclature for secondarystructure: stem, loop & bulge
Coaxial stacking
Basetriple
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HIV TAR RNA mediates Tat binding2° structure schematic
Nomenclature for secondarystructure: stem, loop & bulge
Coaxial stacking
Basetriple Arg binds
G26/C39 bp
PseudoknotsHDV ribozyme formsa double pseudoknot
Bases in loop of stem 1form stem 2 (with
bases outside stem 1)
1
2
1
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Hepatitis Delta Virus (HDV) ribozyme doublepseudoknot
“Top” view
U1A protein cocrystals2° structureschematic
Hepatitis Delta Virus (HDV) ribozyme doublepseudoknot
“Top” view
U1A protein cocrystals2° structureschematic
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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.
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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 4-helix junction
Mg2+ ions (gold balls)Cd2+ ions (magenta)Hg2+ (rose)
RNA interactions ofthe central Cd2+ ion
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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.
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Tertiary interactions in the P4-P6 domain
Cross-strand purine stack.
Sheared AA Standard AU
Sheared AA bpsfill minor groove
Tertiary interactions in the P4-P6 domain
Side view
A-A platformAdjacent As pair side-by-side
Top view
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Tertiary interactions in the P4-P6 domain
Side view
A-A platformAdjacent As pair side-by-side
Top view
Tertiary interactions in the P4-P6 domain
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Tertiary interactions in the P4-P6 domain
Tertiary interactions in the P4-P6 domain
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Metal ion core in the P4-P6 domain
Divalent metal ions(Mg2+) are required forproper folding.
These ions bind tospecific sites andmediate the closeapproach of thephosphate backbones
At one position in themolecule the phosphatebackbone turns inward andcoordinates two metalions.
Adenosine-minor-groove base triples: the A-minor motif
A fills minorgroove & ribose2’ OH forms H-bonds
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Hydrogen bondsbetween adjacentbackboneatoms create a“ribose zipper”
Adjacent base-triples bring together RNA strands
Deoxynucleotidesdestabilize P4-P6
The A-minor motif is widespreadConserved As are abundant in unpaired regions of structured RNAs.
Group I intron
P4-P6
% of As in “single-stranded regions
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What happens in very large RNAs?
% of As in “single-stranded regions
A-minor motifs are the predominant tertiaryinteraction in the 50S ribosomal subunit
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Summary1. RNA structure can be specific, globular, stable and
complex. (As a result, RNA mediates specific recognitionand catalytic reactions.)
2. Secondary structures include stems, bulges, and loops.3. Tertiary motifs include base triples, pseudoknots, A-A
platforms, the tetraloop/tetraloop receptor,A-minor motifs, ribose zippers
4. Principles: stems and loops conserved,many non-WC base contacts,coaxial stacking,metal ion binding,H-bonding of ribose 2’ OH, andrepeated “motifs”.