Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
6r9k
Class
DNA
Method
NMR
Summary
A quadruplex hybrid structure with lpp loop orientation and 3 syn residues
Reference
Karg, B., Mohr, S., Weisz, K.: (2019) "Duplex-Guided Refolding into Novel G-Quadruplex (3+1) Hybrid Conformations." Angew.Chem.Int.Ed.Engl., 58, 11068-11071.
Abstract
The oligomer d(GCGTG3 TCAG3 TG3 TG3 ACGC) with short complementary flanking sequences at the 5'- and 3'-ends was shown to fold into three different DNA G-quadruplex species. In contrast, a corresponding oligomer that lacks base complementarity between the two overhang sequences folds into a single parallel G-quadruplex. The three coexisting quadruplex structures were unambiguously identified and structurally characterized through detailed spectral comparisons with well-defined G-quadruplexes formed upon the deliberate incorporation of syn-favoring 8-bromoguanosine analogues into specific positions of the G-core. Two (3+1) hybrid structures coexist with the parallel fold and feature a novel lateral-propeller-propeller loop architecture that has not yet been confirmed experimentally. Both hybrid quadruplexes adopt the same topology and only differ in their pattern of anti‚Üísyn transitions and tetrad stackings.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(+Ln+P+P), hybrid-1R(1+3), UDDD

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s--- groove=w--n planarity=0.108 type=planar nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13
 2 glyco-bond=s--- groove=w--n planarity=0.139 type=planar nts=4 gGGG A.BGM6,A.DG20,A.DG16,A.DG12
 3 glyco-bond=s--- groove=w--n planarity=0.284 type=other  nts=4 gGGG A.BGM7,A.DG19,A.DG15,A.DG11

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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=s--- groove=w--n Major-->WC nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13
 2  glyco-bond=s--- groove=w--n Major-->WC nts=4 gGGG A.BGM6,A.DG20,A.DG16,A.DG12
 3  glyco-bond=s--- groove=w--n Major-->WC nts=4 gGGG A.BGM7,A.DG19,A.DG15,A.DG11
  step#1  mp(<<,backward) area=13.79 rise=3.40 twist=27.9
  step#2  mp(<<,backward) area=18.55 rise=3.43 twist=23.5
  strand#1 DNA glyco-bond=sss nts=3 Ggg A.DG5,A.BGM6,A.BGM7
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG21,A.DG20,A.DG19
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG17,A.DG16,A.DG15
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG13,A.DG12,A.DG11

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2 stacking diagrams
 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13
2 glyco-bond=s--- groove=w--n Major-->WC nts=4 gGGG A.BGM6,A.DG20,A.DG16,A.DG12
step#1 mp(<<,backward) area=13.79 rise=3.40 twist=27.9

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 2  glyco-bond=s--- groove=w--n Major-->WC nts=4 gGGG A.BGM6,A.DG20,A.DG16,A.DG12
3 glyco-bond=s--- groove=w--n Major-->WC nts=4 gGGG A.BGM7,A.DG19,A.DG15,A.DG11
step#2 mp(<<,backward) area=18.55 rise=3.43 twist=23.5

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List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

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-tetrad layers, 3 loops, INTRA-molecular, UDDD, hybrid-(mixed), 3(+Ln+P+P), hybrid-1R(1+3)

 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13
 2  glyco-bond=s--- groove=w--n Major-->WC nts=4 gGGG A.BGM6,A.DG20,A.DG16,A.DG12
 3  glyco-bond=s--- groove=w--n Major-->WC nts=4 gGGG A.BGM7,A.DG19,A.DG15,A.DG11
  step#1  mp(<<,backward) area=13.79 rise=3.40 twist=27.9
  step#2  mp(<<,backward) area=18.55 rise=3.43 twist=23.5
  strand#1  U DNA glyco-bond=sss nts=3 Ggg A.DG5,A.BGM6,A.BGM7
  strand#2  D DNA glyco-bond=--- nts=3 GGG A.DG21,A.DG20,A.DG19
  strand#3  D DNA glyco-bond=--- nts=3 GGG A.DG17,A.DG16,A.DG15
  strand#4  D DNA glyco-bond=--- nts=3 GGG A.DG13,A.DG12,A.DG11
  loop#1 type=lateral   strands=[#1,#4] nts=3 TCA A.DT8,A.DC9,A.DA10
  loop#2 type=propeller strands=[#4,#3] nts=1 T A.DT14
  loop#3 type=propeller strands=[#3,#2] nts=1 T A.DT18

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)