Detailed DSSR results for the G-quadruplex: PDB entry 6up0
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- PDB id
- 6up0
- Class
- RNA
- Method
- X-ray (2.8 Å)
- Summary
- Structure of the mango-iii fluorescent aptamer bound to yo3-biotin
- Reference
- Jeng SCY, Trachman III RJ, Weissenboeck F, Truong L, Link KA, Jepsen MDE, Knutson JR, Andersen ES, Ferre-D'Amare AR, Unrau PJ (2021): "Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET." Rna, 27, 433-444. doi: 10.1261/rna.078220.120.
- Abstract
- To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor-acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.
- G4 notes
- 4 G-tetrads, 2 G4 helices, 2 G4 stems, 2(-P-P-Lw), hybrid-2R(3+1), UUUD
Base-block schematics in six views
List of 4 G-tetrads
1 glyco-bond=---s sugar=-33- groove=--wn planarity=0.492 type=other nts=4 GGGG C.G9,C.G13,C.G18,C.G25 2 glyco-bond=---s sugar=-3-3 groove=--wn planarity=0.274 type=other nts=4 GGGG C.G10,C.G14,C.G19,C.G23 3 glyco-bond=---s sugar=-33- groove=--wn planarity=0.521 type=other nts=4 GGGG D.G9,D.G13,D.G18,D.G25 4 glyco-bond=---s sugar=-3-3 groove=--wn planarity=0.280 type=other nts=4 GGGG D.G10,D.G14,D.G19,D.G23
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, 2 G-tetrad layers, INTRA-molecular, with 1 stem
 |
1 glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G25 2 glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG C.G10,C.G14,C.G19,C.G23 step#1 pm(>>,forward) area=11.01 rise=3.42 twist=29.6 strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG C.G9,C.G10 strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG C.G13,C.G14 strand#3 RNA glyco-bond=-- sugar=3- nts=2 GG C.G18,C.G19 strand#4 RNA glyco-bond=ss sugar=-3 nts=2 GG C.G25,C.G23 |
| 1 stacking diagram | |
 |
1 glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G25 |
Helix#2, 2 G-tetrad layers, INTRA-molecular, with 1 stem
 |
1 glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG D.G9,D.G13,D.G18,D.G25 2 glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG D.G10,D.G14,D.G19,D.G23 step#1 pm(>>,forward) area=10.20 rise=3.44 twist=29.2 strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG D.G9,D.G10 strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG D.G13,D.G14 strand#3 RNA glyco-bond=-- sugar=3- nts=2 GG D.G18,D.G19 strand#4 RNA glyco-bond=ss sugar=-3 nts=2 GG D.G25,D.G23 |
| 1 stacking diagram | |
 |
1 glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG D.G9,D.G13,D.G18,D.G25 |
List of 2 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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUD, hybrid-(mixed), 2(-P-P-Lw), hybrid-2R(3+1)
 |
1 glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G25 2 glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG C.G10,C.G14,C.G19,C.G23 step#1 pm(>>,forward) area=11.01 rise=3.42 twist=29.6 strand#1 U RNA glyco-bond=-- sugar=-- nts=2 GG C.G9,C.G10 strand#2 U RNA glyco-bond=-- sugar=33 nts=2 GG C.G13,C.G14 strand#3 U RNA glyco-bond=-- sugar=3- nts=2 GG C.G18,C.G19 strand#4* D RNA glyco-bond=ss sugar=-3 nts=2 GG C.G25,C.G23 bulged-nts=1 U C.U24 loop#1 type=propeller strands=[#1,#2] nts=2 AA C.A11,C.A12 loop#2 type=propeller strands=[#2,#3] nts=3 AUU C.A15,C.U16,C.U17 loop#3 type=lateral strands=[#3,#4] nts=3 UAU C.U20,C.A21,C.U22 |
Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUD, hybrid-(mixed), 2(-P-P-Lw), hybrid-2R(3+1)
 |
1 glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG D.G9,D.G13,D.G18,D.G25 2 glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG D.G10,D.G14,D.G19,D.G23 step#1 pm(>>,forward) area=10.20 rise=3.44 twist=29.2 strand#1 U RNA glyco-bond=-- sugar=-- nts=2 GG D.G9,D.G10 strand#2 U RNA glyco-bond=-- sugar=33 nts=2 GG D.G13,D.G14 strand#3 U RNA glyco-bond=-- sugar=3- nts=2 GG D.G18,D.G19 strand#4* D RNA glyco-bond=ss sugar=-3 nts=2 GG D.G25,D.G23 bulged-nts=1 U D.U24 loop#1 type=propeller strands=[#1,#2] nts=2 AA D.A11,D.A12 loop#2 type=propeller strands=[#2,#3] nts=3 AUU D.A15,D.U16,D.U17 loop#3 type=lateral strands=[#3,#4] nts=3 UAU D.U20,D.A21,D.U22 |