Summary information and primary citation

PDB-id
8u5r
Class
RNA
Method
X-ray (2.6 Å)
Summary
Structure of mango ii variant aptamer bound to t01-6a
Reference
Lu X, Passalacqua LFM, Nodwell M, Kong KYS, Caballero-Garcia G, Dolgosheina EV, Ferre-D'Amare AR, Britton R, Unrau PJ (2024): "Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD." Nucleic Acids Res., 52, 8039-8051. doi: 10.1093/nar/gkae493.
Abstract
Artificial RNA tags that tightly bind fluorogenic ligands have many RNA imaging and RNA-protein biomolecular purification applications. Here, we report and structurally characterize a very small (20-nt) biologically compatible G-quadruplex based aptamer that can be inserted into commonly found GNRA tetraloops. This aptamer binds its fluorogenic ligand with an unprecedented picomolar binding affinity and is very stable against thermal and chemical insults. As the ligand can be modified to include biotin, this RNA tag can also be bound to streptavidin magnetic beads. After washing, tagged RNA can be cleanly eluted by exposing the beads to intense green light, which photobleaches the bound fluorogenic ligand, triggering the release of the bound RNA complex.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)

Cartoon-block schematics in six views (download the tarball)

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.325 type=bowl-2 O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G25
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.213 type=other  O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G26
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.171 type=other  O- nts=4 GGGG 1:A.G13,1:A.G29,1:A.G23,1:A.G18

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 3 G-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G25
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G26
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:A.G13,1:A.G18,1:A.G23,1:A.G29
  step#1  pm(>>,forward)  area=8.89  rise=3.30 twist=34.1
  step#2  pp(><,inward)   area=25.84 rise=3.34 twist=28.0
  strand#1 RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:A.G10,1:A.G11,1:A.G13
  strand#2 RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G15,1:A.G16,1:A.G18
  strand#3 RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:A.G20,1:A.G21,1:A.G23
  strand#4 RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G25,1:A.G26,1:A.G29

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2 stacking diagrams 
 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G25
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G26
  step#1  pm(>>,forward)  area=8.89  rise=3.30 twist=34.1

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 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G26
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:A.G13,1:A.G18,1:A.G23,1:A.G29
  step#2  pp(><,inward)   area=25.84 rise=3.34 twist=28.0

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List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 3 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)
 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G25
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G26
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:A.G13,1:A.G18,1:A.G23,1:A.G29
  step#1  pm(>>,forward)  area=8.89  rise=3.30 twist=34.1
  step#2  pp(><,inward)   area=25.84 rise=3.34 twist=28.0
  strand#1* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:A.G10,1:A.G11,1:A.G13 bulged-nts=1 U 1:A.U12
  strand#2* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G15,1:A.G16,1:A.G18 bulged-nts=1 A 1:A.A17
  strand#3* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:A.G20,1:A.G21,1:A.G23 bulged-nts=1 C 1:A.C22
  strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G25,1:A.G26,1:A.G29 bulged-nts=2 AA 1:A.A27,1:A.A28
  loop#1 type=propeller strands=[#1,#2] nts=1 A 1:A.A14
  loop#2 type=propeller strands=[#2,#3] nts=1 A 1:A.A19
  loop#3 type=propeller strands=[#3,#4] nts=1 A 1:A.A24

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