Detailed DSSR results for the G-quadruplex: PDB entry 6tc8
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
- 6tc8
- Class
- DNA
- Method
- NMR
- Summary
- 2'-f-arabinoguanosine and 2'-f-riboguanosine modified hybrid type g-quadruplex with v-loop
- Reference
- Haase L, Weisz K (2020): "Switching the type of V-loop in sugar-modified G-quadruplexes through altered fluorine interactions." Chem.Commun.(Camb.), 56, 4539-4542. doi: 10.1039/d0cc01285h.
- Abstract
- Mixed 2'-F-riboguanosine and 2'-F-arabinoguanosine disubstitutions of a hybrid-type G-quadruplex are found to induce a refolding into two alternative structures with different types of V-loops upon positional exchange of the two G analogs. While conformational preferences of the incorporated G surrogates fail to fully account for the observed rearrangements, additional hydrogen bonds with a fluorine acceptor are suggested to be critical determinants of the two distinct V-loop conformers imposing different tetrad polarities.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-LwX+P), UD3(1+3), UDDD
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=s--- sugar=---- groove=w--n planarity=0.474 type=other nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16 2 glyco-bond=-ss- sugar=---. groove=w-n- planarity=0.489 type=other nts=4 GGGg A.DG2,A.DG6,A.DG20,A.GF2/15 3 glyco-bond=-s-- sugar=-3-- groove=wn-- planarity=0.383 type=saddle nts=4 GgGG A.DG8,A.GFL14,A.DG17,A.DG22
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-tetrad layers, INTRA-molecular, with 1 stem
 |
1 glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.GF2/15 2 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16 3 glyco-bond=s--- sugar=3--- groove=w--n Major-->WC nts=4 gGGG A.GFL14,A.DG8,A.DG22,A.DG17 step#1 mm(<>,outward) area=12.86 rise=3.49 twist=19.9 step#2 pm(>>,forward) area=10.97 rise=3.48 twist=30.0 strand#1 DNA glyco-bond=-ss sugar=--3 nts=3 GGg A.DG2,A.DG1,A.GFL14 strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG6,A.DG7,A.DG8 strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22 strand#4 DNA glyco-bond=--- sugar=.-- nts=3 gGG A.GF2/15,A.DG16,A.DG17 |
| 2 stacking diagrams | |
 |
1 glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.GF2/15 |
 |
2 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16 |
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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDDD, hybrid-(mixed), 2(-LwX+P), UD3(1+3)
 |
1 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16 2 glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGg A.DG2,A.DG6,A.DG20,A.GF2/15 step#1 mm(<>,outward) area=12.86 rise=3.49 twist=19.9 strand#1 U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2 strand#2 D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG7,A.DG6 strand#3 D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG21,A.DG20 strand#4 D DNA glyco-bond=-- sugar=-. nts=2 Gg A.DG16,A.GF2/15 loop#1 type=lateral strands=[#1,#2] nts=3 GAT A.DG3,A.DA4,A.DT5 loop#2 type=diag-prop strands=[#2,#4] nts=7 GACACAg A.DG8,A.DA9,A.DC10,A.DA11,A.DC12,A.DA13,A.GFL14 loop#3 type=propeller strands=[#4,#3] nts=3 GAC A.DG17,A.DA18,A.DC19 |
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=lateral helix=#1 nts=7 GACACAg A.DG8,A.DA9,A.DC10,A.DA11,A.DC12,A.DA13,A.GFL14 2 type=V-shaped helix=#1 nts=4 ggGG A.GFL14,A.GF2/15,A.DG16,A.DG17