DSSR-enabled G4 identification/annotation: PDB entry 8vy1
Summary information and primary citation
- PDB-id
- 8vy1
- Class
- RNA
- Method
- X-ray (3.1 Å)
- Summary
- Mango ii bound to 365a-088
- Reference
- Yang M, Prestwood PR, Passalacqua LFM, Balaratnam S, Fullenkamp CR, Arney JW, Weeks KM, Ferre-D'Amare A, Schneekloth Jr JS (2025): "Structure-informed design of an ultrabright RNA-activated fluorophore." Nat.Chem., 17, 1188-1195. doi: 10.1038/s41557-025-01832-w.
- Abstract
- RNA-based fluorogenic aptamers, such as Mango, are uniquely powerful tools for imaging RNA that activate the fluorescence of a weakly or non-fluorescent small molecule when bound. A central challenge has been to develop brighter, more specific and high-affinity aptamer-ligand systems for cellular imaging. Here we report an ultrabright fluorophore for the Mango II system discovered using a structure-informed, fragment-based small-molecule microarray approach. This dye-termed SALAD1 (structure-informed, array-enabled LigAnD 1)-exhibits subnanomolar aptamer affinity and 3.5-fold brighter fluorescence than Mango II-TO1-biotin pair, a widely used fluorogenic system. Performance was improved by modulating RNA-dye molecular recognition without altering the fluorophore's π-system. High-resolution X-ray structures reveal the binding mode for SALAD1, which exhibits improved pocket occupancy, a more defined binding pose and a unique bonding interaction with potassium. SALAD1 is cell-permeable and facilitates improved in-cell confocal RNA imaging. This work introduces an additional RNA-activated fluorophore demonstrating how fragment-based ligand discovery can be used to create high-performance ligands for RNA targets.
- G4 notes
- 9 G-tetrads, 2 G4 helices, 3 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, 3(-P-P-P), coaxial interfaces: 5'/5'
Cartoon-block schematics in six views (download the tarball)
List of 9 G-tetrads
1 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.255 type=other O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G26 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.139 type=planar O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 3 glyco-bond=---- sugar=---- groove=---- planarity=0.131 type=planar O- nts=4 GGGG 1:A.G13,1:A.G29,1:A.G24,1:A.G18 4 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.317 type=other O+ nts=4 GGGG 1:B.G10,1:B.G15,1:B.G20,1:B.G26 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.178 type=other O+ nts=4 GGGG 1:B.G11,1:B.G16,1:B.G21,1:B.G27 6 glyco-bond=---- sugar=---- groove=---- planarity=0.131 type=planar O- nts=4 GGGG 1:B.G13,1:B.G29,1:B.G24,1:B.G18 7 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.301 type=bowl-2 O+ nts=4 GGGG 1:C.G10,1:C.G15,1:C.G20,1:C.G26 8 glyco-bond=---- sugar=3333 groove=---- planarity=0.132 type=planar O+ nts=4 GGGG 1:C.G11,1:C.G16,1:C.G21,1:C.G27 9 glyco-bond=---- sugar=---- groove=---- planarity=0.203 type=other O- nts=4 GGGG 1:C.G13,1:C.G29,1:C.G24,1:C.G18
List of 2 G4-helices
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.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:A.G13,1:A.G18,1:A.G24,1:A.G29 step#1 pm(>>,forward) area=8.69 rise=3.30 twist=34.7 step#2 pp(><,inward) area=28.32 rise=3.30 twist=28.1 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.G24 strand#4 RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G26,1:A.G27,1:A.G29 |
| 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.G26 |
|
2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 |
Helix#2, 6 G-tetrads, inter-molecular, with 2 stems
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O- nts=4 GGGG 1:B.G13,1:B.G29,1:B.G24,1:B.G18 2 glyco-bond=---- sugar=3333 groove=---- Major-->WC O+ nts=4 GGGG 1:B.G11,1:B.G27,1:B.G21,1:B.G16 3* glyco-bond=---- sugar=-3-3 groove=---- Major-->WC O+ nts=4 GGGG 1:B.G10,1:B.G26,1:B.G20,1:B.G15 4 glyco-bond=---- sugar=3-3- groove=---- WC-->Major O+ nts=4 GGGG 1:C.G15,1:C.G20,1:C.G26,1:C.G10 5 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:C.G16,1:C.G21,1:C.G27,1:C.G11 6 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:C.G18,1:C.G24,1:C.G29,1:C.G13 step#1 pp(><,inward) area=29.41 rise=3.32 twist=27.7 step#2 mp(<<,backward) area=8.29 rise=3.30 twist=34.7 step#3 mm(<>,outward) area=17.99 rise=3.61 twist=10.0 step#4 pm(>>,forward) area=7.53 rise=3.30 twist=34.6 step#5 pp(><,inward) area=29.50 rise=3.35 twist=27.8 strand#1 RNA glyco-bond=------ sugar=-3-33- nts=6 GGGGGG 1:B.G13,1:B.G11,1:B.G10,1:C.G15,1:C.G16,1:C.G18 strand#2 RNA glyco-bond=------ sugar=-33-3- nts=6 GGGGGG 1:B.G29,1:B.G27,1:B.G26,1:C.G20,1:C.G21,1:C.G24 strand#3 RNA glyco-bond=------ sugar=-3-33- nts=6 GGGGGG 1:B.G24,1:B.G21,1:B.G20,1:C.G26,1:C.G27,1:C.G29 strand#4 RNA glyco-bond=------ sugar=-33-3- nts=6 GGGGGG 1:B.G18,1:B.G16,1:B.G15,1:C.G10,1:C.G11,1:C.G13 |
| 5 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O- nts=4 GGGG 1:B.G13,1:B.G29,1:B.G24,1:B.G18 |
|
2 glyco-bond=---- sugar=3333 groove=---- Major-->WC O+ nts=4 GGGG 1:B.G11,1:B.G27,1:B.G21,1:B.G16 |
|
3* glyco-bond=---- sugar=-3-3 groove=---- Major-->WC O+ nts=4 GGGG 1:B.G10,1:B.G26,1:B.G20,1:B.G15 |
|
4 glyco-bond=---- sugar=3-3- groove=---- WC-->Major O+ nts=4 GGGG 1:C.G15,1:C.G20,1:C.G26,1:C.G10 |
|
5 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:C.G16,1:C.G21,1:C.G27,1:C.G11 |
List of 3 G4-stems
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.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:A.G13,1:A.G18,1:A.G24,1:A.G29 step#1 pm(>>,forward) area=8.69 rise=3.30 twist=34.7 step#2 pp(><,inward) area=28.32 rise=3.30 twist=28.1 strand#1* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:A.G10,1:A.G11,1:A.G13 bulged-nts=1 A 1:A.A12 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.G24 bulged-nts=2 AA 1:A.A22,1:A.A23 strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G26,1:A.G27,1:A.G29 bulged-nts=1 A 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.A25 |
Stem#2, 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:B.G10,1:B.G15,1:B.G20,1:B.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:B.G11,1:B.G16,1:B.G21,1:B.G27 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:B.G13,1:B.G18,1:B.G24,1:B.G29 step#1 pm(>>,forward) area=8.29 rise=3.30 twist=34.7 step#2 pp(><,inward) area=29.41 rise=3.32 twist=27.7 strand#1* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:B.G10,1:B.G11,1:B.G13 bulged-nts=1 A 1:B.A12 strand#2* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:B.G15,1:B.G16,1:B.G18 bulged-nts=1 A 1:B.A17 strand#3* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:B.G20,1:B.G21,1:B.G24 bulged-nts=2 AA 1:B.A22,1:B.A23 strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:B.G26,1:B.G27,1:B.G29 bulged-nts=1 A 1:B.A28 loop#1 type=propeller strands=[#1,#2] nts=1 A 1:B.A14 loop#2 type=propeller strands=[#2,#3] nts=1 A 1:B.A19 loop#3 type=propeller strands=[#3,#4] nts=1 A 1:B.A25 |
Stem#3, 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:C.G10,1:C.G15,1:C.G20,1:C.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:C.G11,1:C.G16,1:C.G21,1:C.G27 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:C.G13,1:C.G18,1:C.G24,1:C.G29 step#1 pm(>>,forward) area=7.53 rise=3.30 twist=34.6 step#2 pp(><,inward) area=29.50 rise=3.35 twist=27.8 strand#1* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:C.G10,1:C.G11,1:C.G13 bulged-nts=1 A 1:C.A12 strand#2* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:C.G15,1:C.G16,1:C.G18 bulged-nts=1 A 1:C.A17 strand#3* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:C.G20,1:C.G21,1:C.G24 bulged-nts=2 AA 1:C.A22,1:C.A23 strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:C.G26,1:C.G27,1:C.G29 bulged-nts=1 A 1:C.A28 loop#1 type=propeller strands=[#1,#2] nts=1 A 1:C.A14 loop#2 type=propeller strands=[#2,#3] nts=1 A 1:C.A19 loop#3 type=propeller strands=[#3,#4] nts=1 A 1:C.A25 |
List of 1 G4 coaxial stack
1 G4 helix#2 contains 2 G4 stems: [#2,#3] [5'/5']